|
1
|
Feng T, Li J, Mao X, Jin X, Cheng L, Xie H, Ma Y. A comparative analysis of the rhizosphere microbial communities among three species of the Salix genus. PeerJ 2025; 13:e19182. [PMID: 40166043 PMCID: PMC11956769 DOI: 10.7717/peerj.19182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Accepted: 02/25/2025] [Indexed: 04/02/2025] Open
Abstract
Rhizosphere microorganisms exert a significant influence in counteracting diverse external stresses and facilitating plant nutrient uptake. While certain rhizosphere microorganisms associated with Salix species have been investigated, numerous rhizosphere microorganisms from various Salix species remain underexplored. In this study, we employed high-throughput sequencing to examine the rhizosphere bacterial and fungal communities composition and diversity of three Salix species: Salix zangica (SZ), Salix myrtilllacea (SM), and Salix cheilophila (SC). Furthermore, the BugBase and FUNGuild were utilized to predict the functional roles of bacterial and fungal microorganisms. The findings revealed notable variations in the alpha and beta diversities of bacterial and fungal communities among the three Salix species exhibited significant differences (p < 0.05). The relative abundance of Flavobacterium was highest in the SZ samples, while Microvirga exhibited significant enrichment in the SM samples. Microvirga and Vishniacozyma demonstrate the highest number of nodes within their respective bacterial and fungal community network structures. The functions of bacterial microorganisms, including Gram-positive, potentially pathogenic, Gram-negative, and stress-tolerant types, exhibited significant variation among the three Salix species (p < 0.05). Furthermore, for the function of fungal microbe, the ectomycorrhizal guild had the highest abundance of symbiotic modes. This results demonstrated the critical role of ectomycorrhizal fungi in enhancing nutrient absorption and metabolism during the growth of Salix plants. Additionally, this findings also suggested that S. zangica plant was better well-suited for cultivation in stressful environments. These findings guide future questions about plant-microbe interactions, greatly enhancing our understanding of microbial communities for the healthy development of Salix plants.
Collapse
Affiliation(s)
- Tianqing Feng
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai-Tibetan Plateau in Qinghai Province, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| | - Juan Li
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Xiaoning Mao
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai-Tibetan Plateau in Qinghai Province, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| | - Xionglian Jin
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai-Tibetan Plateau in Qinghai Province, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| | - Liang Cheng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Huichun Xie
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai-Tibetan Plateau in Qinghai Province, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| | - Yonggui Ma
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai-Tibetan Plateau in Qinghai Province, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| |
Collapse
|
|
2
|
Chen J, Zhang X, Zhao J, Ding W, Zhang X, Pan L, Xu H. Study of the Correlation Between Endophyte Abundances and Metabolite Levels in Different Parts of the Tissue of Cultivated and Wild Arnebia euchroma (Royle) Johnst. Based on Microbiome Analysis and Metabolomics. Molecules 2025; 30:734. [PMID: 39942836 PMCID: PMC11820562 DOI: 10.3390/molecules30030734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 02/03/2025] [Accepted: 02/04/2025] [Indexed: 02/16/2025] Open
Abstract
Arnebia euchroma (Royle) Johnst. has high medicinal and economic value, but in recent years, wild resources of this species have been depleted and the quality of artificially cultivated A. euchroma has been poor. The endophyte community of medicinal plants is rich, serving as an internal resource that promotes the growth of medicinal plants and the accumulation of secondary metabolites, and has important potential application value in improving the quality of medicinal materials. A. euchroma cultivars and wild varieties contain abundant endophyte communities and metabolites in different tissues. However, the relationships between A. euchroma endophytes and metabolites with different growth patterns and different tissue sites remain unclear. In this study, microbiome analysis and metabolomics were used to analyze the diversity of endophytes in the root and leaf tissues of cultivated and wild A. euchroma and their correlations with metabolites. The results revealed that the diversity of endophytes in A. euchroma was different from that in wild A. euchroma and that there was tissue specificity among different tissues. A species composition analysis revealed that the dominant endophytic fungi belonged to Ascomycota and Basidiomycota, and the dominant endophytic bacteria belonged to Proteobacteria and Cyanobacteria. A total of 248 metabolites, including quinones, flavonoids, alkaloids, organic acids, sugars, amino acids, coumarins, sterols, terpenoids, polyphenols, fatty ketones, and their derivatives, were identified in positive ion mode via LC-MS/MS. According to their different growth patterns and associated tissue parts, 9 differentially abundant metabolites were screened between AEZ-L (cultivated leaf tissue of A. euchroma) and AEY-L (wild leaf tissue of A. euchroma), 6 differentially abundant metabolites were screened between AEZ-R (cultivated root tissue of A. euchroma) and AEY-R (wild root tissue of A. euchroma), and 104 differentially abundant metabolites were screened between AEZ-R and AEZ-L. Eighty-two differentially abundant metabolites were screened between AEY-R and AEY-L. The contents of eight naphthoquinones in AEZ-R and AEY-R were determined via HPLC. The contents of β,β'-dimethylacrylylakanin in wild A. euchroma were greater than those in cultivated A. euchroma. A correlation analysis revealed that the dominant endophytes in the four groups were significantly correlated with a variety of metabolites, and the eight naphthoquinones in the root tissue were also significantly correlated with the dominant endophytes. The diversity of the A. euchroma endophyte community differed across different growth patterns and different tissue parts. There were significant differences in the relative contents of A. euchroma metabolites in different tissues. A correlation analysis verified the correlation between A. euchroma endophytes and metabolites.
Collapse
Affiliation(s)
- Jingjing Chen
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
| | - Xiaoqing Zhang
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
| | - Jinrong Zhao
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
| | - Wenhuan Ding
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
- Central Laboratory, Xinjiang Medical University, Urumqi 830054, China
| | - Xuejia Zhang
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
- Xinjiang Key Laboratory of Planting Standards for Authentic and Superior Chinese Medicinal Materials, Xinjiang Medical University, Urumqi 830017, China
| | - Lan Pan
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
- Xinjiang Key Laboratory of Planting Standards for Authentic and Superior Chinese Medicinal Materials, Xinjiang Medical University, Urumqi 830017, China
| | - Haiyan Xu
- College of Traditional Chinese Medicine, Xinjiang Medical University, Urumqi 830017, China; (J.C.); (X.Z.); (J.Z.); (W.D.); (X.Z.); (L.P.)
- Xinjiang Key Laboratory of Planting Standards for Authentic and Superior Chinese Medicinal Materials, Xinjiang Medical University, Urumqi 830017, China
| |
Collapse
|
|
3
|
Li N, Mao Y, Huang Y, Zhang L, Hou L, Liu X, Du Y, Chen D, Sun K. Seasonal succession of endophyte and the association with active ingredients in Rheum palmatum. Microbiol Spectr 2024; 12:e0118424. [PMID: 39315856 PMCID: PMC11537013 DOI: 10.1128/spectrum.01184-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/06/2024] [Indexed: 09/25/2024] Open
Abstract
The endophyte is closely related to medicinal plant growth and development, stress resistance, and active ingredients' accumulation. However, a seasonal succession of endophytes and the association with active ingredients is still unclear. In this study, we used high-throughput sequencing methods to compare the endophyte diversity of Rheum palmatum under different seasons and analyze the association between endophytes and five active ingredients. The results show that the diversity of endophytic fungi increased and then decreased, while bacterial diversity increased with the change of season. Community composition showed that the dominant genera of endophytic fungi were different under the different seasons, while the dominant genera of endophytic bacteria were Delftia. Analysis of co-occurrence network maps showed that the connectivity and complexity of endophytic fungi and bacterial networks decreased with the change of season. Spearman analysis indicated that the active ingredients of R. palmatum were significantly positive correlation with genera of endophytic fungi (Chalara). FUNGuild and PICRUSt predictive analysis indicated that the function of endophytic fungi and bacteria, respectively, were symbiotroph and metabolism, and relative abundances were different under the different seasons. Our results help elucidate the mechanism of medicinal plant-endophyte interaction. IMPORTANCE Through the investigation of the seasonal succession of endophytes and the association with active ingredients in Rheum palmatum, we found that the diversity and composition of endophytes in R. palmatum exhibited seasonal dynamics, and the active ingredients of R. palmatum showed a significantly positive correlation with the genus of endophytic fungi (Chalara). Our results may lay a foundation for understanding the interaction mechanism of endophyte and medicinal plant, and can also provide a theoretical basis for sustainable production of medicinal plants.
Collapse
Affiliation(s)
- Ni Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - YiFan Mao
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - YaLi Huang
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - LingXuan Zhang
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - Lu Hou
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - XiaoJun Liu
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - YaRong Du
- Key Laboratory of Space Radiobiology of Gansu Province & CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - DaWei Chen
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| | - Kun Sun
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, Gansu, China
| |
Collapse
|
|
4
|
Zhong J, Pan W, Jiang S, Hu Y, Yang G, Zhang K, Xia Z, Chen B. Flue-cured tobacco intercropping with insectary floral plants improves rhizosphere soil microbial communities and chemical properties of flue-cured tobacco. BMC Microbiol 2024; 24:446. [PMID: 39497066 PMCID: PMC11533348 DOI: 10.1186/s12866-024-03597-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 10/22/2024] [Indexed: 11/06/2024] Open
Abstract
BACKGROUND Continuous cropping of the same crop leads to land degradation. This is also called the continuous-cropping obstacle. Currently, intercropping tobacco with other crops can serve as an effective strategy to alleviate continuous cropping obstacles. RESULTS In this study, tobacco K326 and insectary floral plants were used as materials, and seven treatments of tobacco monoculture (CK), tobacco intercropped with Tagetes erecta, Vicia villosa, Fagopyrum esculentum, Lobularia maritima, Trifolium repens, and Argyranthemum frutescens respectively, were set up to study their effects on rhizosphere soil chemical properties and composition and structure of rhizosphere soil microbial community of tobacco. The 16 S rRNA gene and ITS amplicons were sequenced using Illumina high-throughput sequencing. tobacco/insectary floral plants intercropping can influence rhizosphere soil chemical properties, which also change rhizosphere microbial communities. The CK and treatment groups tobacco rhizosphere soil microorganisms had significantly different genera, such as tobacco intercropping with T. repens and A. frutescens significantly increased the number of Fusarium and intercropping T. erecta, V. villosa, L. maritima, T. repens, and A. frutescens significantly increased the number of Sphingomonas and unknown Gemmatimonadaceae. Additionally, intercropping T. erecta, V. villosa and L. maritima changed the rhizosphere fungal and bacteria community and composition of tobacco and the positive correlation between tobacco rhizosphere the genera of fungi and bacterial were greater than CK. The pathway of the carbohydrate metabolism, amino acid metabolism, and energy metabolism in rhizosphere bacteria were significantly decreased after continuous cropping. Fungal symbiotic trophic and saprophytic trophic were significantly increased after intercropping V. villosa, L. maritima and plant pathogen and animal pathogen were increased after intercropping T. repens and A. frutescens. Additionally, bacterial and fungal communities significantly correlated with soil chemical properties, respectively. CONCLUSION This study reveals that intercropping tobacco with insectary floral plants, particularly T. erecta, V. villosa, L. maritima and A. frutescens significantly affects soil chemical properties and alters rhizosphere microbial communities, increasing the abundance of certain microbial genera. Additionally, intercropping enhances pathways related to carbohydrate, amino acid, and energy metabolism in rhizosphere bacteria. These findings suggest that intercropping could provide a promising strategy to overcome challenges associated with continuous tobacco cropping by regulating the rhizosphere environment.
Collapse
Affiliation(s)
- Jin Zhong
- State Key Laboratory of Yunnan Biological Resources Protection and Utilization, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Wenze Pan
- State Key Laboratory of Yunnan Biological Resources Protection and Utilization, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Shenglan Jiang
- State Key Laboratory of Yunnan Biological Resources Protection and Utilization, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Yanxia Hu
- Yunnan Provincial Tobacco Company Dali State Branch, Dali, China
| | - Guangyuan Yang
- State Key Laboratory of Yunnan Biological Resources Protection and Utilization, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Ke Zhang
- State Key Laboratory of Yunnan Biological Resources Protection and Utilization, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Zhenyuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China.
| | - Bin Chen
- State Key Laboratory of Yunnan Biological Resources Protection and Utilization, College of Plant Protection, Yunnan Agricultural University, Kunming, China.
| |
Collapse
|
|
5
|
Ren Y, Ciwang R, Mehmood K, Li K. Effects of forages on the microbiota of crossed sheep on cold Plateau. Anim Biotechnol 2024; 35:2362639. [PMID: 38856695 DOI: 10.1080/10495398.2024.2362639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Diet is an important component to influence microbiota, there are less data available about the microbiome of Suffolk cross with Tibetan (SCT) animals with different fodders. The current study was conducted for comparing the fungi microbiota in SCT sheep fed with different forages. Sequencing of ileum samples from sheep groups of AH (alfalfa and oat grass), BH (mixture of grass and concentrated feeds), CH (concentrated feed I), DH (concentrated feed II) and EH (concentrated feed III) achieved 3,171,271 raw and 2,719,649 filtered sequences. Concentrated feeds changed fungi microbiota in SCT sheep with three phyla and 47 genera significantly different among the groups. Genera include positive genus of Scytalidium and negative fungi of Sarocladium, Kazachstania, Gibberella, Scytalidium, Candida, Wickerhamomyces. The findings of our study will contribute to efficient feeding of SCT sheep at cold plateau areas.
Collapse
Affiliation(s)
- Yue Ren
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, PR China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, PR China
| | - Renzeng Ciwang
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, PR China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, PR China
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
| |
Collapse
|
|
6
|
Mao Y, Li N, Huang Y, Chen D, Sun K. Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats. Microbiol Spectr 2024; 12:e0167024. [PMID: 39258920 PMCID: PMC11448439 DOI: 10.1128/spectrum.01670-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 08/14/2024] [Indexed: 09/12/2024] Open
Abstract
Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.
Collapse
Affiliation(s)
- YiFan Mao
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - Ni Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - YaLi Huang
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - DaWei Chen
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - Kun Sun
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| |
Collapse
|
|
7
|
Chen J, Cai Y, Wang Z, Wang S, Li J, Song C, Zhuang W, Liu D, Wang S, Song A, Xu J, Ying H. Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas Production via Anaerobic Digestion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9446-9455. [PMID: 38748977 DOI: 10.1021/acs.est.4c02789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Biological pretreatment is a viable method for enhancing biogas production from straw crops, with the improvement in lignocellulose degradation efficiency being a crucial factor in this process. Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, and forest soil. Subsequently, synthetic microbial communities were constructed for fermentation-enzyme production. The crude enzyme solution obtained was used to pretreat WS and was compared with two commercial enzymes. The synthetic microbial community enzyme-producing pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme solution, followed by anaerobic digestion achieved satisfactory results. SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS, which was 38.79% higher than that observed for WS, 22.15% higher than that of solid-state commercial enzyme pretreatment and 25.41% higher than that of liquid commercial enzyme pretreatment. These results indicate that enzyme-pretreated WS can significantly enhance biogas production. This study represents a solution to the environmental burden and energy use of crop residues.
Collapse
Affiliation(s)
- Jinmeng Chen
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Yafan Cai
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
- Luzhou LaoJiao Co., Ltd, Luzhou 646000, China
| | - Zhi Wang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | | | - Jia Li
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Chuan Song
- Luzhou LaoJiao Co., Ltd, Luzhou 646000, China
| | - Wei Zhuang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Dong Liu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Andong Song
- College of Life Science, Henan Agricultural University, 218 Ping An Avenue, Zhengdong New District, Zhengzhou 450002, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Hanjie Ying
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| |
Collapse
|
|
8
|
Chen ZJ, Li ML, Gao SS, Sun YB, Han H, Li BL, Li YY. Plant Growth-Promoting Bacteria Influence Microbial Community Composition and Metabolic Function to Enhance the Efficiency of Hybrid pennisetum Remediation in Cadmium-Contaminated Soil. Microorganisms 2024; 12:870. [PMID: 38792702 PMCID: PMC11124114 DOI: 10.3390/microorganisms12050870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The green and efficient remediation of soil cadmium (Cd) is an urgent task, and plant-microbial joint remediation has become a research hotspot due to its advantages. High-throughput sequencing and metabolomics have technical advantages in analyzing the microbiological mechanism of plant growth-promoting bacteria in improving phytoremediation of soil heavy metal pollution. In this experiment, a pot trial was conducted to investigate the effects of inoculating the plant growth-promoting bacterium Enterobacter sp. VY on the growth and Cd remediation efficiency of the energy plant Hybrid pennisetum. The test strain VY-1 was analyzed using high-throughput sequencing and metabolomics to assess its effects on microbial community composition and metabolic function. The results demonstrated that Enterobacter sp. VY-1 effectively mitigated Cd stress on Hybrid pennisetum, resulting in increased plant biomass, Cd accumulation, and translocation factor, thereby enhancing phytoremediation efficiency. Analysis of soil physical-chemical properties revealed that strain VY-1 could increase soil total nitrogen, total phosphorus, available phosphorus, and available potassium content. Principal coordinate analysis (PCoA) indicated that strain VY-1 significantly influenced bacterial community composition, with Proteobacteria, Firmicutes, Chloroflexi, among others, being the main differential taxa. Redundancy analysis (RDA) revealed that available phosphorus, available potassium, and pH were the primary factors affecting bacterial communities. Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated that strain VY-1 modulated the metabolite profile of Hybrid pennisetum rhizosphere soil, with 27 differential metabolites showing significant differences, including 19 up-regulated and eight down-regulated expressions. These differentially expressed metabolites were primarily involved in metabolism and environmental information processing, encompassing pathways such as glutamine and glutamate metabolism, α-linolenic acid metabolism, pyrimidine metabolism, and purine metabolism. This study utilized 16S rRNA high-throughput sequencing and metabolomics technology to investigate the impact of the plant growth-promoting bacterium Enterobacter sp. VY-1 on the growth and Cd enrichment of Hybrid pennisetum, providing insights into the regulatory role of plant growth-promoting bacteria in microbial community structure and metabolic function, thereby improving the microbiological mechanisms of phytoremediation.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yu-Ying Li
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, College of Water Resource and Environment Engineering, Nanyang Normal University, Nanyang 473061, China; (Z.-J.C.)
| |
Collapse
|
|
9
|
Zhao S, Li Y, Liu F, Song Z, Yang W, Lei Y, Tian P, Zhao M. Dynamic changes in fungal communities and functions in different air-curing stages of cigar tobacco leaves. Front Microbiol 2024; 15:1361649. [PMID: 38567079 PMCID: PMC10985334 DOI: 10.3389/fmicb.2024.1361649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Air curing (AC) plays a crucial role in cigar tobacco leaf production. The AC environment is relatively mild, contributing to a diverse microbiome. Fungi are important components of the tobacco and environmental microbiota. However, our understanding of the composition and function of fungal communities in AC remains limited. Methods In this study, changes in the chemical constituents and fungal community composition of cigar tobacco leaves during AC were evaluated using flow analysis and high-throughput sequencing. Results The moisture, water-soluble sugar, starch, total nitrogen, and protein contents of tobacco leaves exhibited decreasing trends, whereas nicotine showed an initial increase, followed by a decline. As determined by high-throughput sequencing, fungal taxa differed among all stages of AC. Functional prediction showed that saprophytic fungi were the most prevalent type during the AC process and that the chemical composition of tobacco leaves is significantly correlated with saprophytic fungi. Conclusion This study provides a deeper understanding of the dynamic changes in fungal communities during the AC process in cigar tobacco leaves and offers theoretical guidance for the application of microorganisms during the AC process.
Collapse
Affiliation(s)
- Songchao Zhao
- College of Tobacco Science, Flavors and Fragrance Engineering and Technology Research Center of Henan Province, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuanyuan Li
- College of Tobacco Science, Flavors and Fragrance Engineering and Technology Research Center of Henan Province, Henan Agricultural University, Zhengzhou, Henan, China
| | - Fang Liu
- College of Tobacco Science, Flavors and Fragrance Engineering and Technology Research Center of Henan Province, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhaopeng Song
- College of Tobacco Science, Flavors and Fragrance Engineering and Technology Research Center of Henan Province, Henan Agricultural University, Zhengzhou, Henan, China
| | - Weili Yang
- Dazhou City Branch of Sichuan Province Tobacco Company, Dazhou, Sichuan, China
| | - Yunkang Lei
- Deyang City Branch of Sichuan Province Tobacco Company, Deyang, Sichaun, China
| | - Pei Tian
- China Tobacco Jiangshu Industry Co., Ltd., Xuzhou Cigarette Factory, Xuzhou, Jiangsu, China
| | - Mingqin Zhao
- College of Tobacco Science, Flavors and Fragrance Engineering and Technology Research Center of Henan Province, Henan Agricultural University, Zhengzhou, Henan, China
| |
Collapse
|
|
10
|
Li J, Hou L, Zhang G, Cheng L, Liu Y. Comparative Analysis of Rhizosphere and Endosphere Fungal Communities in Healthy and Diseased Faba Bean Plants. J Fungi (Basel) 2024; 10:84. [PMID: 38276030 PMCID: PMC10817651 DOI: 10.3390/jof10010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89-99.56%) and Basidiomycota (0.33-25.78%). In healthy endosphere samples, Glomeromycota (0.08-1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04-1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47-35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48-91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.
Collapse
Affiliation(s)
- Juan Li
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Gui Zhang
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Liang Cheng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yujiao Liu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| |
Collapse
|
|
11
|
Guo Q, Gong L. Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas. Microbiol Spectr 2024; 12:e0264223. [PMID: 38095470 PMCID: PMC10783054 DOI: 10.1128/spectrum.02642-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.
Collapse
Affiliation(s)
- Qian Guo
- College of Ecology and Environment, Xinjiang University, Urumqi, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| | - Lu Gong
- College of Ecology and Environment, Xinjiang University, Urumqi, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| |
Collapse
|
|
12
|
Chen J, Cai Y, Wang Z, Xu Z, Li J, Ma X, Zhuang W, Liu D, Wang S, Song A, Xu J, Ying H. Construction of a synthetic microbial community based on multiomics linkage technology and analysis of the mechanism of lignocellulose degradation. BIORESOURCE TECHNOLOGY 2023; 389:129799. [PMID: 37774801 DOI: 10.1016/j.biortech.2023.129799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
The efficient degradation of lignocellulose is a bottleneck for its integrated utilization. This research performed species analysis and made functional predictions in various ecosystems using multiomics coupling to construct a core synthetic microbial community with efficient lignocellulose degradation function. The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. The degradation mechanisms were resolved using proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% nitrogen source ratio and a fermentation time of 23 d. Under these conditions, the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, 45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin 1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to lignocellulose degradation. The metabolic pathways involved in lignocellulose degradation and the functional roles of eight strains were obtained. The synthesis of a microbial community via multiomics linkage technology can effectively decompose lignocellulose, which is useful for their further utilization.
Collapse
Affiliation(s)
- Jinmeng Chen
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Yafan Cai
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Zhi Wang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Zhengzhong Xu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Jia Li
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Xiaotian Ma
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Wei Zhuang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China; National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Dong Liu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China; National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China.
| | - Andong Song
- College of Life Science, Henan Agricultural University, 218 Ping An Avenue, Zhengdong New District, Zhengzhou 450002, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Hanjie Ying
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China; National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| |
Collapse
|
|
13
|
Wu X, Hu Y, Wang Q, Liu J, Fang S, Huang D, Pang X, Cao J, Gao Y, Ning Y. Study on the correlation between the dominant microflora and the main flavor substances in the fermentation process of cigar tobacco leaves. Front Microbiol 2023; 14:1267447. [PMID: 38075898 PMCID: PMC10699171 DOI: 10.3389/fmicb.2023.1267447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/23/2023] [Indexed: 09/28/2024] Open
Abstract
The flavor of cigar tobacco leaf determines the quality of finished cigar tobacco, and the enhancement of flavor generally relies on microbial fermentation. In this paper, the correlation between the dominant microorganisms and the main flavor substances of cigar tobacco leaves during fermentation and the correlation between the two were investigated to reveal the correlation between microorganisms and flavor and the metabolic pathways of microorganisms affecting the flavor substances. During the fermentation process, the main flavors of cigar tobacco leaves were sweet, light and grassy, with hexanal, 2,6-dimethylpyridine, nonanal, phenylacetaldehyde, naphthalene, and methyl benzoate as the main constituents, and the key microorganisms Haloferax mediterranei, Haloterrigena limicola, Candidatus Thorarchaeota archaeon SMTZ-45, the genera Methyloversatilis, Sphingomonas, Thauera, Pseudomonas, Penicillium, and Aspergillus. Correlation analysis revealed that fungi were negatively correlated with the main aroma and inhibited the main flavor substances, while bacteria were positively correlated with Benzoic acid, methyl ester in the main flavor substances, which was conducive to the accumulation of green aroma. Functional analysis revealed that the dominant bacterial population was producing aroma by metabolizing glycoside hydrolases and glycosyltransferases, performing amino acid metabolism, carbohydrate metabolism and film transport metabolism. The present study showed that the bacterial and fungal dominant microorganisms during the fermentation of cigar tobacco were influencing the production and degradation of the main flavor substances through the enzyme metabolism by the occurrence of the Merad reaction.
Collapse
Affiliation(s)
- Xue Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanqi Hu
- Shandong China Tobacco Industry Limited Company, Jinan, China
| | - Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jian Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Song Fang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dewen Huang
- Hunan Tobacco Company Chenzhou Company, Chenzhou, China
| | - Xueli Pang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jianmin Cao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yumeng Gao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Ning
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| |
Collapse
|
|
14
|
Yu E, Liu Q, Gao Y, Li Y, Zang P, Zhao Y, He Z. An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification, and evaluation of Mycena. Front Microbiol 2023; 14:1220670. [PMID: 37928654 PMCID: PMC10620705 DOI: 10.3389/fmicb.2023.1220670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Gastrodia elata Bl. f. glauca is an important traditional Chinese medicinal plant. The yield and quality of Gastrodia elata Bl. have significantly decreased due to multigenerational asexual reproduction. Therefore, it is necessary to have sexual reproduction of Gastrodia elata Bl. to supplement the market supply. Seeds of G. elata Bl. have no endosperm, and their sexual reproduction depends on the nutrients provided by the embryo cells infected by Mycena fungi to complete seed germination. However, Mycena fungi are small and have many species, and not all Mycena fungi can promote the germination of G. elata Bl. seeds. Therefore, it is of great significance to isolate and identify suitable germination fungi and explore the mechanism for improving the production performance and yield, and quality of G. elata Bl. Six closely related Mycena isolates, JFGL-01, JFGL-02, JFGL-03, JFGL-04, JFGL-05, and JFGL-06, were isolated from the leaves and protocorms of G. elata Bl. f. glauca and were identified as Mycena purpureofusca. The mycelial state and number of germinating protocorms were used as indicators to preferentially select Mycena fungi, and it was concluded that JFGL-06 had the best mycelial state and ability to germinate G. elata Bl. seeds. Finally, a mechanism to increase the yield of G. elata Bl. was explored by comparing the changes in nutrient elements and microbial diversity in the soil around G. elata Bl. with different strains. JFGL-06 proved to be an excellent Mycena fungal strain suitable for G. elata Bl. f. glauca. Compared with the commercial strain, JFGL-06 significantly increased the C, N, Na, Mg, S, Cl, K, Ca, and Fe contents of the soil surrounding the protocorms of G. elata Bl. f. glauca. JFGL-06 improved the composition, diversity, and metabolic function of the surrounding soil microbial community of G. elata Bl. f. glauca protocorms at the phylum, class, and genus levels, significantly increased the relative abundance of bacteria such as Acidobacteria and fungi such as Trichoderma among the dominant groups, and increased the abundance of functional genes in metabolic pathways such as nucleotide metabolism and energy metabolism. There was a significant reduction in the relative abundance of bacteria, such as Actinomycetes, and fungi, such as Fusarium, in the dominant flora, and a reduced abundance of functional genes, such as amino acid metabolism and xenobiotic biodegradation and metabolism. This is the main reason why the JFGL-06 strain promoted high-quality and high-yield G. elata Bl. f. glauca in Changbai Mountain.
Collapse
Affiliation(s)
- En Yu
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Qun Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing, China
| | - Yugang Gao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yaqi Li
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Pu Zang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Zhongmei He
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| |
Collapse
|
|
15
|
Zhou L, Wu S, Ma M. First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemonemexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China. Biodivers Data J 2023; 11:e101950. [PMID: 38327346 PMCID: PMC10848652 DOI: 10.3897/bdj.11.e101950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/26/2023] [Indexed: 02/09/2024] Open
Abstract
The water-level fluctuation zone (WLFZ) of Wudongde reservoir of the upper Yangtze river is a completely new aquatic-terrestrial transitional zone, and its plant degenerate issue is attracting global concerns. Uncovering the unknown rhizosphere microbiome of dominant plants of this zone is helpful in understanding the plant-microbe interactions and their growth under the largely varying environment. Here, a first exploration of the rhizosphere bacterial and fungal communities of wilted (JB) and unwilted (JA) Argemonemexicana L. individuals from the WLFZ of Wudongde reservoir was carried out using high-throughput sequencing and MetaCyc metabolic pathway analyses. The results showed that rhizosphere of wilted A.mexicana L individuals exhibited a higher microbial richness and diversity than the unwilted ones, irrespective of the bacterial and fungal communities. It was noted that 837 common bacterial amplicon sequence variants (ASV) and 92 common fungal ASV were presented in both JA and JB with 3108 bacteria and 212 fungi unique to JA, and 3569 bacteria and 693 fungi unique to JB. Linear discriminant analysis effect Size (LEfSe) analyses indicated that the taxa that had the most contribution to observed differences between both JA and JB was Proteobacteria, Actinobacteria and Ascomycota for JA, and Bacteroidetes, Firmicutes, Verrucomicrobia, Basidiomycota and Ascomycota for JB. Organic compound conversion pathway (degradation/reduction/oxidation) was consistently highly represented in the rhizosphere microbiomes of both JA and JB. Overall, this study provides insights into the rhizosphere microbiome composition, diversity and metabolic pathways of both wilted and unwilted A.mexicana L. individuals in the WLFZ of Wudongde reservoir, and the results give valuable clues for manipulating microbes to support plant growth in such a recently-formed WLFZ under a dry-hot valley environment.
Collapse
Affiliation(s)
- Lanfang Zhou
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, ChinaSchool of River and Ocean Engineering, Chongqing Jiaotong UniversityChongqingChina
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, ChinaKey Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of SciencesChongqingChina
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, ChinaChongqing School, University of Chinese Academy of SciencesChongqingChina
| | - Shengjun Wu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, ChinaKey Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of SciencesChongqingChina
| | - Maohua Ma
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, ChinaKey Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of SciencesChongqingChina
| |
Collapse
|
|
16
|
Muratova A, Golubev S, Romanova V, Sungurtseva I, Nurzhanova A. Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil. Microorganisms 2023; 11:1516. [PMID: 37375018 DOI: 10.3390/microorganisms11061516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.
Collapse
Affiliation(s)
- Anna Muratova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Sergey Golubev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Valeria Romanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420021 Kazan, Russia
| | - Irina Sungurtseva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Asil Nurzhanova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| |
Collapse
|
|
17
|
Gao P, Qi K, Han Y, Ma L, Zhang B, Zhang Y, Guan X, Qi J. Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot. Front Microbiol 2023; 14:1204688. [PMID: 37333630 PMCID: PMC10272447 DOI: 10.3389/fmicb.2023.1204688] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.
Collapse
Affiliation(s)
- Peixin Gao
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Kai Qi
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yujuan Han
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liguo Ma
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Bo Zhang
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yueli Zhang
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiumin Guan
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Junshan Qi
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| |
Collapse
|
|
18
|
Zhao W, Wang P, Dong L, Li S, Lu X, Zhang X, Su Z, Guo Q, Ma P. Effect of incorporation of broccoli residues into soil on occurrence of verticillium wilt of spring-sowing-cotton and on rhizosphere microbial communities structure and function. Front Bioeng Biotechnol 2023; 11:1115656. [PMID: 36761302 PMCID: PMC9902944 DOI: 10.3389/fbioe.2023.1115656] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
Cotton verticillium wilt (CVW) represented a typical plant soil-borne disease and resulted in widespread economic losses in cotton production. However, the effect of broccoli residues (BR) on verticillium wilt of spring-sowing-cotton was not clear. We investigated the effects of BR on CVW, microbial communities structure and function in rhizosphere of two cotton cultivars with different CVW resistance using amplicon sequencing methods. Results showed that control effects of BR on CVW of susceptible cultivar (cv. EJ-1) and resistant cultivar (cv. J863) were 58.49% and 85.96%, and the populations of V. dahliae decreased by 14.31% and 34.19%, respectively. The bacterial diversity indices significantly increased in BR treatment, while fungal diversity indices significantly decreased. In terms of microbial community composition, the abilities to recruit bacteria and fungi were enhanced in BR treatment, including RB41, Gemmatimonas, Pontibacter, Streptomyces, Blastococcus, Massilia, Bacillus, and Gibberella, Plectosphaerella, Neocosmospora, Aspergillus and Preussia. However, the relative abundances of Sphingomonas, Nocardioides, Haliangium, Lysobacter, Penicillium, Mortierella and Chaetomidium were opposite tendency between cultivars in BR treatment. According to PICRUSt analysis, functional profiles prediction showed that significant shifts in metabolic functions impacting KEGG pathways of BR treatment were related to metabolism and biosynthesis. FUNGuild analysis indicated that BR treatment altered the relative abundances of fungal trophic modes. The results of this study demonstrated that BR treatment decreased the populations of V. dahliae in soil, increased bacterial diversity, decreased fungal diversity, changed the microbial community structure and function, and increased the abundances of beneficial microorganisms.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Ping Ma
- *Correspondence: Qinggang Guo, ; Ping Ma,
| |
Collapse
|
|
19
|
Yu E, Gao Y, Li Y, Zang P, Zhao Y, He Z. An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria. BMC PLANT BIOLOGY 2022; 22:621. [PMID: 36581798 PMCID: PMC9801631 DOI: 10.1186/s12870-022-04007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Gastrodia elata Bl. f. glauca, a perennial herb of G.elata Bl. in Orchidaceae, is one of the most valuable traditional Chinese medicines. G. elata Bl. is a chlorophyll-free myco-heterotrophic plant, which must rely on the symbiotic growth of Armillaria, but not all Armillaria strains can play the symbiotic role. Additionally, Armillaria is easy to degenerate after multiple generations, and the compatibility between the strains from other areas and G. elata Bl. f. glauca in Changbai Mountain is unstable. Therefore, it is incredibly significant to isolate, identify and screen the symbiotic Armillaria suitable for the growth of G. elata Bl. f. glauca in Changbai Mountain, and to explore the mechanism by which Armillaria improves the production performance of G. elata Bl. f. glauca. RESULTS Firstly, G. elata Bl. f. glauca tubers, and rhizomorphs and fruiting bodies of Armillaria were used for the isolation and identification of Armillaria. Five Armillaria isolates were obtained in our laboratory and named: JMG, JMA, JMB, JMC and JMD. Secondly, Armillaria was selected based on the yield and the effective component content of G. elata Bl. f. glauca. It was concluded that the yield and quality of G. elata Bl. f. glauca co-planted with JMG is the highest. Finally, the mechanism of its high quality and yield was explored by investigating the effects of different Armillaria strains on the soil, its nutrition element contents and the soil microbial diversity around G. elata Bl. f. glauca in Changbai Mountain. CONCLUSIONS Compared with commercial strains, JMG significantly increased the content of Na, Al, Si, Mn, Fe, Zn, Rb and the absorption of C, Na, Mg, Ca, Cr, Cu, Zn and Rb in G. elata Bl. f. glauca; it improved the composition, diversity and metabolic functions of soil microbial communities around G. elata Bl. f. glauca at phylum, class and genus levels; it markedly increased the relative abundance of bacteria such as Chthoniobacter and Armillaria in the dominant populations, and enhanced such functions as Cell motility, amino acid metabolism and Lipid metabolism; it dramatically decreased the relative abundance of Bryobacter and other fungi in the dominant populations, and reduced such functions as microbial energy metabolism, translation and carbohydrate metabolism. This is the main reason why excellent Armillaria strains promote the high quality and yield of G. elata Bl. f. glauca in Changbai Mountain.
Collapse
Affiliation(s)
- En Yu
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Yugang Gao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China.
| | - Yaqi Li
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Pu Zang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Zhongmei He
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| |
Collapse
|
|
20
|
Li XQ, Liu YQ, Li YJ, Han H, Zhang H, Ji MF, Chen ZJ. Enhancing Mechanisms of the Plant Growth-Promoting Bacterial Strain Brevibacillus sp. SR-9 on Cadmium Enrichment in Sweet Sorghum by Metagenomic and Transcriptomic Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16309. [PMID: 36498382 PMCID: PMC9737414 DOI: 10.3390/ijerph192316309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
To explore the mechanism by which the plant growth-promoting bacterium Brevibacillus sp. SR-9 improves sweet sorghum tolerance and enriches soil cadmium (Cd) under pot conditions, the effect of strain SR-9 inoculation on the microbial community of sorghum rhizosphere soil was analyzed by metagenomics. Gene expression in sweet sorghum roots was analyzed using transcriptomics. The results showed that strain SR-9 promoted the growth of sweet sorghum and improved the absorption and enrichment of Cd in the plants. Compared with the uninoculated treatment, the aboveground part and root dry weight in strain SR-9 inoculated with sorghum increased by 21.09% and 17.37%, respectively, and the accumulation of Cd increased by 135% and 53.41%, respectively. High-throughput sequencing showed that strain SR-9 inoculation altered the rhizosphere bacterial community, significantly increasing the relative abundance of Actinobacteria and Firmicutes. Metagenomic analysis showed that after inoculation with strain SR-9, the abundance of genes involved in amino acid transport metabolism, energy generation and conversion, and carbohydrate transport metabolism increased. KEGG functional classification showed that inoculation with strain SR-9 increased the abundance of genes involved in soil microbial metabolic pathways in the rhizosphere soil of sweet sorghum and the activity of soil bacteria. Transcriptome analysis identified 198 upregulated differentially expressed genes in sweet sorghum inoculated with strain SR-9, including those involved in genetic information processing, biological system, metabolism, environmental information processing, cellular process, and human disease. Most of the annotated differentially expressed genes were enriched in the metabolic category and were related to pathways such as signal transduction, carbohydrate metabolism, amino acid metabolism, and biosynthesis of other secondary metabolites. This study showed that plant growth-promoting bacteria can alter the rhizosphere bacterial community composition, increasing the activity of soil bacteria and upregulating gene expression in sweet sorghum roots. The findings enhance our understanding of the microbiological and botanical mechanisms by which plant growth-promoting bacterial inoculation improves the remediation of heavy metals by sorghum.
Collapse
|
|
21
|
Analysis of endophyte diversity of Rheum palmatum among different tissues and ages. Arch Microbiol 2022; 205:14. [PMID: 36469126 DOI: 10.1007/s00203-022-03349-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/19/2022] [Indexed: 12/07/2022]
Abstract
Rheum palmatum, a well-known Traditional Chinese Medicines (TCM), has been used for medical purposes for thousand years in China. However, endophyte diversity of R. palmatum among different tissues and ages is still not revealed. In this study, we used 16S and ITS amplicon sequencing and combined with PICRUSt and FUNGuild to compare endophyte diversity and ecological function among different tissues and ages of R. palmatum. The results showed that the diversity and OTUs (Operational taxonomic units) abundance of endophytic fungi and bacteria of R. palmatum differed among different tissues and ages. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year samples, while saprotroph was dominant trophic mode of endophytic fungi in different year samples. The dominant trophic modes of endophytic fungi were saprotroph, pathotroph-symbiotroph and symbiotroph, and relative abundances differed in the different tissue samples. Our results elucidated the comprehensive diversity and composition profiles of endophytes in different tissues and year of R. palmatum. Our data offered pivotal information to clarify the role of endophytes in the production of R. palmatum and its important metabolites.
Collapse
|
|
22
|
Liu W, Qiu K, Xie Y, Wang R, Li H, Meng W, Yang Y, Huang Y, Li Y, He Y. Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N. PeerJ 2022; 10:e14271. [PMID: 36340191 PMCID: PMC9635361 DOI: 10.7717/peerj.14271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.
Collapse
Affiliation(s)
- Wangsuo Liu
- School of Agriculture, Ningxia University, Yinchuan, China,Department of Desertification Prevention, Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Ruixia Wang
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Haichao Li
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Wenfen Meng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yayuan Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi He
- School of Agriculture, Ningxia University, Yinchuan, China
| |
Collapse
|
|
23
|
Li G, Cai M, Zheng X, Xie X, Zhu Y, Long Y. Impact of disinfectants on the intestinal bacterial symbionts and immunity of silkworm (Bombyx mori L.). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:79545-79554. [PMID: 35713834 DOI: 10.1007/s11356-022-21442-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
The insect egg surface can serve as a vehicle for vertical symbiont transmission from the maternal parent to its offspring. Hypochlorite and formaldehyde are two common disinfectants used for insect egg surface sterilization. Here, we explored the intestinal microecology and immune response profile of the silkworm Bombyx mori strain Dazao after disinfectant exposure by using high-throughput sequencing technology and real-time PCR analysis. After egg surface sterilization, no significant difference (P > 0.05) in overall body weight was observed among the control, sodium hypochlorite, and formaldehyde groups. 16S rRNA metagenomic sequencing revealed that the main abundant intestinal bacteria were Enterococcus, Burkholderia, Phenylobacterium, Ralstonia, Chitinophaga, Bradyrhizobium, Herbaspirillum, and two unclassified Bacteroidetes species. Egg surface sterilization evidently altered the composition and abundance of intestinal microbiota but did not significantly change its alpha diversity. The dysbiosis of intestinal microbiota resulted in the perturbation of the immune response profile of the silkworm intestine. Our findings reveal that hypochlorite has a blocking effect on the symbiont transmission compared with formaldehyde. More importantly, egg surface sterilization exerts substantial effects on the ecophysiological traits of insects. The present study contributes to the scientific and reasonable application of disinfectants for insect egg surface sterilization during industrial silk production and laboratory-scale insect rearing.
Collapse
Affiliation(s)
- Guannan Li
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400716, China
| | - Miao Cai
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400716, China
- Foshan Nanshanhu Experimental High School, Foshan, 528200, China
| | - Xi Zheng
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400716, China
| | - Xiaofan Xie
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400716, China
| | - Yong Zhu
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400716, China
| | - Yaohang Long
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
- Engineering Research Center of Medical Biotechnology, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| |
Collapse
|
|
24
|
Hou Q, Chen D, Wang YP, Ehmet N, Ma J, Sun K. Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites. PeerJ 2022; 10:e13949. [PMID: 36061750 PMCID: PMC9438771 DOI: 10.7717/peerj.13949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 08/04/2022] [Indexed: 01/19/2023] Open
Abstract
Background The difference of metabolites in medicinal plants has always been concerned to be influenced by external environmental factors. However, the relationship between endophytes and host metabolites remains unclear. Methods In this study, we used 16S and ITS amplicon sequencing to compare endophyte diversity among different tissue types and ages of Gentiana officinalis. Endophyte diversity and abundance was also analyzed in relation to the abundance of four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The diversity and richness of G. officinalis endophyte differed as a function of tissue types and ages. Four metabolites of G. officinalis were significantly correlated with the abundance of dominant endophyte genera. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year root samples, while saprotroph was dominant trophic modes of endophytic fungi in the different year root samples. The dominant trophic modes of endophytic fungi was saprotroph and pathotroph, and relative abundances differed in the different tissue samples. The results of this study will help to elucidate the plant-microbial interactions and provide key information on the role of endophytes in the production of G.officinalis and its important metabolites.
Collapse
Affiliation(s)
| | - DaWei Chen
- The Northwest Normal University, Lanzhou, China
| | - Yu-pei Wang
- Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | | | - Jing Ma
- The Northwest Normal University, Lanzhou, China
| | - Kun Sun
- The Northwest Normal University, Lanzhou, China
| |
Collapse
|
|
25
|
Zhu P, Yang S, Wu Y, Ru Y, Yu X, Wang L, Guo W. Shifts in Soil Microbial Community Composition, Function, and Co-occurrence Network of Phragmites australis in the Yellow River Delta. Front Microbiol 2022; 13:858125. [PMID: 35928147 PMCID: PMC9344067 DOI: 10.3389/fmicb.2022.858125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
Soil microorganisms play vital roles in regulating biogeochemical processes. The composition and function of soil microbial community have been well studied, but little is known about the responses of bacterial and fungal communities to different habitats of the same plant, especially the inter-kingdom co-occurrence pattern including bacteria and fungi. Herein, we used high-throughput sequencing to investigate the bacterial and fungal communities of five Phragmites australis habitats in the Yellow River Delta and constructed their inter-kingdom interaction network by network analysis. The results showed that richness did not differ significantly among habitats for either the bacterial or fungal communities. The distribution of soil bacterial community was significantly affected by soil physicochemical properties, whereas that of the fungal community was not. The main functions of the bacterial and fungal communities were to participate in the degradation of organic matter and element cycling, both of which were significantly affected by soil physicochemical properties. Network analysis revealed that bacteria and fungi participated in the formation of networks through positive interactions; the role of intra-kingdom interactions were more important than inter-kingdom interactions. In addition, rare species acted as keystones played a critical role in maintaining the network structure, while NO3−−N likely played an important role in maintaining the network topological properties. Our findings provided insights into the inter-kingdom microbial co-occurrence network and response of the soil microbial community composition and function to different P. australis habitats in coastal wetlands, which will deepen our insights into microbial community assembly in coastal wetlands.
Collapse
Affiliation(s)
- Pengcheng Zhu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Shuren Yang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuxin Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuning Ru
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Xiaona Yu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Lushan Wang,
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
- *Correspondence: Weihua Guo, whguo@
| |
Collapse
|
|
26
|
Wang J, Gao J, Zhang H, Tang M. Changes in Rhizosphere Soil Fungal Communities of Pinus tabuliformis Plantations at Different Development Stages on the Loess Plateau. Int J Mol Sci 2022; 23:ijms23126753. [PMID: 35743198 PMCID: PMC9223801 DOI: 10.3390/ijms23126753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
The soil fungal community is an important factor in the forest ecosystems, and a better understanding of its composition and dynamic changes will contribute to the maintenance, preservation, and sustainable development of the forest ecosystems. Pinus tabuliformis has been widely planted for local ecological restoration on the Loess Plateau in China in recent decades. However, these plantations have been degraded to different degrees with increasing stand age. Hence, we tried to find the possible causes for the plantation degradation by analyzing soil environmental changes and soil fungal community composition at different stand ages. We collected rhizosphere soil samples from young (10-year-old), middle-aged (20-year-old), and near-mature (30-year-old) P. tabuliformis plantations in this region and characterized their soil properties and soil fungal community diversity and composition. Our results showed that with increasing stand age, the contents of organic carbon, ammonium nitrogen (AN) and nitrate nitrogen (NN) in the soil increased significantly, while the content of available phosphorus (AP) decreased significantly. The main factors affecting the composition of the soil fungal community were the contents of AP, AN, and NN in the soil. In addition, the genus Suillus was the dominant ectomycorrhizal (ECM) fungus in all periods of P. tabuliformis plantations in this region. The results of structural equation modeling showed that the community composition of ECM fungi was significantly correlated with stand age, soil NN, and AP contents, and that of pathogenic (PAG) fungi was significantly correlated with soil AN and AP contents. The decrease in the relative abundance of ECM fungi and the increase in the relative abundance of PAG fungi would exacerbate the degradation of P. tabulaeformis plantation. Our results illustrated that the content of soil AP is not only an important factor limiting the development of plantations, but it also significantly affects the community composition of soil fungi in the rhizosphere of the P. tabuliformis plantation. This study provides a novel insight into the degradation of P. tabuliformis plantations and builds a solid foundation for their subsequent management, restoration, and sustainable development on the Loess Plateau of China.
Collapse
Affiliation(s)
- Jiaxing Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China;
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.G.); (H.Z.)
| | - Jing Gao
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.G.); (H.Z.)
| | - Haoqiang Zhang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.G.); (H.Z.)
| | - Ming Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China;
- Correspondence:
| |
Collapse
|
|
27
|
Ivashkin VT, Medvedev OS, Poluektova EA, Kudryavtseva AV, Bakhtogarimov IR, Karchevskaya AE. Direct and Indirect Methods for Studying Human Gut Microbiota. RUSSIAN JOURNAL OF GASTROENTEROLOGY, HEPATOLOGY, COLOPROCTOLOGY 2022; 32:19-34. [DOI: 10.22416/1382-4376-2022-32-2-19-34] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Aim: To review the main methods of intestinal microbiota studying.Key points. Currently, molecular genetic methods are used mainly for basic research and do not have a unified protocol for data analysis, which makes it difficult to implement them in clinical practice. Measurement of short chain fatty acids (SCFA) concentrations in plasma provides the data, which can serve as an indirect biomarker of the colonic microbiota composition. However, currently available evidence is insufficient to relate the obtained values (SCFA levels and ratio) to a particular disease with a high degree of certainty. Trimethylamine N-oxide (TMAO) levels in the blood plasma and urine can also reflect the presence of specific bacterial clusters containing genes Cut, CntA/CntB and YeaW/YeaX. Therefore, further studies are required to reveal possible correlations between certain disorders and such parameters as the composition of gut microbiota, dietary patterns and TMAO concentration. Gas biomarkers, i.e. hydrogen, methane and hydrogen sulphide, have been studied in more detail and are better understood as compared to other biomarkers of the gut microbiome composition and functionality. The main advantage of gas biomarkers is that they can be measured multiple times using non-invasive techniques. These measurements provide information on the relative proportion of hydrogenic (i.e. hydrogen producing) and hydrogenotrophic (i.e. methanogenic and sulfate-reducing) microorganisms. In its turn, this opens up the possibility of developing new approaches to correction of individual microbiota components.Conclusions. Integration of the data obtained by gut microbiota studies at the genome, transcriptome and metabolome levels would allow a comprehensive analysis of microbial community function and its interaction with the human organism. This approach may increase our understanding of the pathogenesis of various diseases as well open up new opportunities for prevention and treatment.
Collapse
Affiliation(s)
- V. T. Ivashkin
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - O. S. Medvedev
- M.V. Lomonosov Moscow State University; National Medical Research Center of Cardiology
| | - E. A. Poluektova
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | | | | | - A. E. Karchevskaya
- I.M. Sechenov First Moscow State Medical University (Sechenov University); N.N. Burdenko National Medical Research Center of Neurosurgery; Institute of Higher Nervous Activity and Neurophysiology
| |
Collapse
|
|
28
|
Hou QZ, Chen DW, Wang YP, Ehmet N, Ma J, Sun K. Analysis of endophyte diversity of two Gentiana plants species and the association with secondary metabolite. BMC Microbiol 2022; 22:90. [PMID: 35392806 PMCID: PMC8988345 DOI: 10.1186/s12866-022-02510-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
Background The influence of external environmental factors on secondary metabolites of medicinal plants has always been studied. However, little is known about the relationships between endophytes and host metabolites, especially the relationship differences between different plant species. Thus, we used high-throughput sequencing methods to compare endophyte diversity from roots of two closely related species, Gentiana officinalis and G. siphonantha, from the same production area, and analyze the association with four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The fungal and bacteria communities’ richness and diversity of G. siphonantha was higher than G. officinalis. Ascomycota and Proteobacteria were dominant fungal and bacterial phylum of the two closely related species. At the genus level, Tetracladium and Cadophora were dominant fungal genus in G. officinalis and G. siphonantha samples, respectively. While Pseudomonas was dominant bacterial genus in two closely related species, with relative abundances were 8.29 and 8.05%, respectively. Spearman analysis showed that the content of loganic acid was significantly positively correlated with endophytic fungi, the content of gentiopicroside, swertiamarine and sweroside were significantly positively correlated with endophytic bacteria in the two related species. PICRUSt and FUNGuild predictive analysis indicated that metabolism and saprotroph was primary function of endophytic bacteria and fungi in the two related species. Conclusion Our results will expand the knowledge on relationships of plant-microbe interactions and offer pivotal information to reveal the role of endophytes in the production of Gentiana plant and its important secondary metabolite. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02510-4.
Collapse
Affiliation(s)
- Qin Zheng Hou
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Da Wei Chen
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Yu Pei Wang
- Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, 730000, Gansu, China
| | - Nurbiye Ehmet
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Jing Ma
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Kun Sun
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, Gansu, China.
| |
Collapse
|
|
29
|
Wu X, Hu H, Li S, Zhao J, Li J, Zhang G, Li G, Xiu W. Chemical fertilizer reduction with organic material amendments alters co-occurrence network patterns of bacterium-fungus-nematode communities under the wheat–maize rotation regime. PLANT AND SOIL 2022; 473:605-623. [DOI: 10.1007/s11104-022-05314-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/20/2022] [Indexed: 01/22/2025]
|
|
30
|
Liu X, Shi Y, Kong L, Tong L, Cao H, Zhou H, Lv Y. Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network. Microorganisms 2022; 10:microorganisms10020462. [PMID: 35208916 PMCID: PMC8878586 DOI: 10.3390/microorganisms10020462] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.
Collapse
Affiliation(s)
- Xiayan Liu
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China;
| | - Lingyu Kong
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Lihong Tong
- State Key Laboratory of Hydroscience and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China;
| | - Haoxuan Cao
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Hu Zhou
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
| | - Yizhong Lv
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
| |
Collapse
|
|
31
|
Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils. SOIL SYSTEMS 2022. [DOI: 10.3390/soilsystems6010010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.
Collapse
|
|
32
|
Wang T. Analysis on the Structure and Function of the Bacterial Community in the Replanting Soil of Basswood Ganoderma lingzhi (Agaricomycetes). Int J Med Mushrooms 2022; 24:45-59. [DOI: 10.1615/intjmedmushrooms.2022044898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
|
33
|
Deng Q, Su C, Chen Z, Gong T, Lu X, Chen Z, Lin X. Effect of hydraulic retention time on the denitrification performance and metabolic mechanism of a multi-chambered bio-electrochemical system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113575. [PMID: 34474253 DOI: 10.1016/j.jenvman.2021.113575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The effects of hydraulic retention time (HRT) on the denitrification performance of the multi-chambered bio-electrochemistry system and the metabolic mechanism of the microbial community were investigated. Results indicated that the NO3--N and NO2--N removal efficiency was up to 99.5% and 99.9%, respectively. The electricity generation performance of the system was optimum at 24 h HRT, with the maximum power density and output voltage of the fourth chamber to be 471.2 mW/m3 and 602.4 mV, respectively. With the decrease of HRT from 24 h to 8 h, the protein-like substance in extracellular polymeric substance (EPS) of granular sludge was reduced and the fluorescence intensities were weakened. Besides, the abundance of metabolism pathway was the highest at 50.0% and 49.9%, respectively, and the methane metabolism (1.8% and 2.0%, respectively) and the nitrogen metabolism (0.8% and 0.9%, respectively) in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway played important roles in providing guaranteed stability and efficient removal of organic matter and nitrogen from the system.
Collapse
Affiliation(s)
- Qiujin Deng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| | - Chengyuan Su
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China; Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology for Science and Education Combined with Science and Technology Innovation Base, 12 Jiangan Road, Guilin, 541004, PR China; University Key Laboratory of Karst Ecology and Environmental Change of Guangxi Province (Guangxi Normal University), 15 Yucai Road, Guilin, 541004, PR China.
| | - Zhengpeng Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| | - Tong Gong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| | - Xinya Lu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| | - Zhuxin Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| | - Xiangfeng Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| |
Collapse
|
|
34
|
Yin F, Zhang F, Wang H. Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas. PLoS One 2021; 16:e0259515. [PMID: 34762689 PMCID: PMC8584676 DOI: 10.1371/journal.pone.0259515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.
Collapse
Affiliation(s)
- Fating Yin
- Agricultural College, Shihezi University, Shihezi City, China
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
| | - Fenghua Zhang
- Agricultural College, Shihezi University, Shihezi City, China
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
| | - Haoran Wang
- Agricultural College, Shihezi University, Shihezi City, China
| |
Collapse
|
|
35
|
Barq MG, Mubashar Hassan M, Yasmin H, shahzad A, Malik NH, Lorenz N, Abdullah Alsahli A, Dick RP, Ali N. Variation in archaeal and bacterial community profiles and their functional metabolic predictions under the influence of pure and mixed fertilizers in paddy soil. Saudi J Biol Sci 2021; 28:6077-6085. [PMID: 34764741 PMCID: PMC8568845 DOI: 10.1016/j.sjbs.2021.08.091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 11/23/2022] Open
Abstract
Impact of environmental perturbations i.e., nitrogen (N), phosphorus (P), potassium (K), and rice straw (Rs) on the dynamics of soil bacterial and archaeal communities are multifactor dependent and seeks a contemporary approach to study underlying mechanisms. The current study investigates the effect of pure and mixed fertilizers on soil physicochemical properties, the microbial community structure, and their functional metabolic predictions. It involved amendments with distinct combinations of N as C(H2N)2O, P and K as KH2PO4, K as KCl, and Rs in paddy soil microcosms with concentrations common in rice fields agriculture. Soil pH, electrical conductivity (EC), total carbon (TC), total nitrogen (TN), organic matter (OM), available K (AK), and total extractable P (TEP) were evaluated. To comprehend community variation and functional predictions, 16S rRNA-based high throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. Our findings showed enhanced community richness and diversity in all amendments compared to control. Proteobacteria, Actinobacteria, and Firmicutes were dominant bacterial phyla. Regarding relative abundance, Chloroflexi, Bacteroidetes, and Verrucomicrobia showed positive while Actinobacteria, Acidobacteria, and Gemmatimonadetes showed negative trends compared to controls. Thaumarchaeota and Euryarchaeota were dominant archaeal phyla and exhibited increasing and decreasing trends, respectively. The PICRUSt analysis indicated functional prediction more towards amino acid, carbohydrate, energy, and lipid metabolism while less towards others. Concerning energy metabolism, most and least responsive treatments were KP and controls, respectively. These outcomes enhanced our understanding regarding soil quality, fertilizer composition and application, and functional metabolomics of archaea and bacteria.
Collapse
Affiliation(s)
- Mohsin Gulzar Barq
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | | | - Humaira Yasmin
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Asim shahzad
- Department of Botany, Mohi-Ud-Din Islamic University, AJ&K, Pakistan
- College of Geography and Environment, Henan University, Jinming Ave, Kaifeng, China
| | | | - Nicola Lorenz
- School of Environment and Natural Resources, 2021 Coffey Road, The Ohio State University, Columbus, OH 43210-1085, USA
| | - Abdulaziz Abdullah Alsahli
- Department Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Richard P. Dick
- School of Environment and Natural Resources, 2021 Coffey Road, The Ohio State University, Columbus, OH 43210-1085, USA
| | - Naeem Ali
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
|
36
|
Chen ZJ, Tian W, Li YJ, Sun LN, Chen Y, Zhang H, Li YY, Han H. Responses of rhizosphere bacterial communities, their functions and their network interactions to Cd stress under phytostabilization by Miscanthus spp. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117663. [PMID: 34435565 DOI: 10.1016/j.envpol.2021.117663] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 06/13/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Miscanthus has good tolerance to heavy metals (HMs) and has received increasing attention in studies of HM-contaminated soil remediation. In this study, four Miscanthus cultivars (M. lutarioriparius Xiangnadi NO4, M. sinensis Xiangmang NO1, M. lutarioriparius × M. sinensis hybrid Xiangzamang NO1, and M. floridulus Wujiemang NO1) that grow in China were studied. Their tolerance and enrichment abilities in soils containing 50 mg kg-1 cadmium (Cd) and the structure and function of their rhizosphere bacterial communities during the remediation process were analyzed. The results exhibiting a tolerance index (TI) higher than 75 in roots and the aboveground parts (TI > 60, indicating highly tolerant plants) indicated that all four Miscanthus cultivars were tolerant to high Cd concentrations. Moreover, Cd was mainly enriched in roots, the translocation ability from roots to aboveground parts was weak, and the four cultivars exhibited phytostabilization ability in Cd-contaminated soils. High-throughput sequencing (HTS) analysis showed that the Miscanthus rhizosphere bacterial community comprised 33 phyla and 446 genera, including plant growth-promoting rhizobacteria (PGPRs), such as Bacillus, Sphingomonas, and Mesorhizobium. The addition of Cd affected the Miscanthus rhizosphere bacterial community and reduced community diversity. Phylogenetic molecular ecological networks (pMENs) indicated that Cd addition reduced interactions between Miscanthus rhizosphere bacteria and thereby led to a simpler network structure, increased the number of negative-correlation links, enhanced the competition between rhizosphere bacterial species, reduced the number of key bacteria, and changed the composition of those bacteria. PICRUSt functional predictive analysis indicated that Cd stress reduced soil bacterial functions in the Miscanthus rhizosphere. The results of this study provide a basis for the remediation of Cd-contaminated soils by Miscanthus and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by PGPRs or key bacteria.
Collapse
Affiliation(s)
- Zhao-Jin Chen
- Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Ying-Jun Li
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Le-Ni Sun
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Chen
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Hao Zhang
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Yu-Ying Li
- Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Hui Han
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China.
| |
Collapse
|
|
37
|
Nebeská D, Trögl J, Ševců A, Špánek R, Marková K, Davis L, Burdová H, Pidlisnyuk V. Miscanthus x giganteus role in phytodegradation and changes in bacterial community of soil contaminated by petroleum industry. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112630. [PMID: 34392149 DOI: 10.1016/j.ecoenv.2021.112630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/05/2021] [Accepted: 08/10/2021] [Indexed: 05/27/2023]
Abstract
The second generation energy crop Miscanthus x giganteus (Mxg) was cultivated in pots with mixtures of clean and petroleum industry contaminated soil affected by petroleum, Pb, Zn contamination and high salinity. The survival rate reached 100%, nevertheless the biomass parameters were negatively affected even in the lowest proportion of contaminated soil. In the lowest contamination, where the plant grew still quite successfully, C10-C40 degradation was significantly enhanced compared to the unplanted control with degradation of 58 ± 14%. The plant contribution to aliphatics degradation was significantly correlated with biomass, thus it was negligible in higher contamination. A similar pattern was documented in development of the soil bacterial community. The shift in community structure after Mxg cultivation was observed mainly in the soil with the lowest contaminant proportion, though an increase of bacterial diversity in the miscanthus rhizosphere was observed in all cases. Relative abundance of Actinobacteria was reduced on behalf of several less abundant phyla (Verrucomicrobia, Bacterioides, Acidobacteria). The majority of genera identified as potential petroleum degraders (Pseudomonas, Shinella, Altererythrobacter, Azospirillum, Mesorhizobium, Dyella) were more abundant in contaminated soil with miscanthus, suggesting that Mxg could be a promising crop for phytomanagement of petroleum contaminated soils but salt phytotoxicity needs to be mitigated first.
Collapse
Affiliation(s)
- Diana Nebeská
- Faculty of Environment, Jan Evangelista Purkyně University in Ústí nad Labem, Pasteurova 3632/15, 40096 Ústí nad Labem, Czech Republic.
| | - Josef Trögl
- Faculty of Environment, Jan Evangelista Purkyně University in Ústí nad Labem, Pasteurova 3632/15, 40096 Ústí nad Labem, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 46117 Liberec, Czech Republic
| | - Roman Špánek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 46117 Liberec, Czech Republic
| | - Kristýna Marková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 46117 Liberec, Czech Republic
| | - Lawrence Davis
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Charmers Hall, Manhattan, KS 66506, USA
| | - Hana Burdová
- Faculty of Environment, Jan Evangelista Purkyně University in Ústí nad Labem, Pasteurova 3632/15, 40096 Ústí nad Labem, Czech Republic
| | - Valentina Pidlisnyuk
- Faculty of Environment, Jan Evangelista Purkyně University in Ústí nad Labem, Pasteurova 3632/15, 40096 Ústí nad Labem, Czech Republic
| |
Collapse
|
|
38
|
Chen D, Jia L, Hou Q, Zhao X, Sun K. Analysis of Endophyte Diversity of Rheum palmatum from Different Production Areas in Gansu Province of China and the Association with Secondary Metabolite. Microorganisms 2021; 9:978. [PMID: 33946518 PMCID: PMC8147242 DOI: 10.3390/microorganisms9050978] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
Investigations of the differences in the metabolites of medicinal plants have typically focused on the effects of external environmental factors. However, little is known about the relationship between endophytes diversity and host metabolites. We used high-throughput sequencing methods to compare the endophyte diversity of Rheum palmatum from eight different production areas in Gansu Province of China and to analyze the association between those areas and five secondary metabolites (aloe-emodin, rhein, emodin, chrysophanol, and physcion). The results show that the diversity and OTUs (Operational taxonomic units) abundance of endophytic fungi and bacteria of R. palmatum differed according to production area. Spearman analysis showed that the five secondary metabolites of R. palmatum were positively correlated with the diversity and abundance of endophytic fungi. Comparing both space and environmental differences to determine influences on community structure, VPA analysis revealed that geographic factors explained more difference in community composition of fungal and bacterial endophytes than climate factors. PICRUSt and FUNGuild predictive analysis indicated that metabolites were the primary components of endophytic bacteria in all samples, while the function of endophytic fungi was composed of dominant trophic modes (saprotroph and pathotroph), and relative abundances were different. Our results help elucidate the correlation of plant-microbe interactions and offer pivotal information to reveal the role of endophytes in the production of R. palmatum and its important secondary metabolite.
Collapse
Affiliation(s)
| | | | | | | | - Kun Sun
- College of Life Sciences, Northwest Normal University, Lanzhou 730070, China; (D.C.); (L.J.); (Q.H.); (X.Z.)
| |
Collapse
|
|
39
|
Liu F, Wu Z, Zhang X, Xi G, Zhao Z, Lai M, Zhao M. Microbial community and metabolic function analysis of cigar tobacco leaves during fermentation. Microbiologyopen 2021; 10:e1171. [PMID: 33970539 PMCID: PMC8483401 DOI: 10.1002/mbo3.1171] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 11/19/2022] Open
Abstract
Cigar tobacco leaves (CTLs) contain abundant bacteria and fungi that are vital to leaf quality during fermentation. In this study, artificial fermentation was used for the fermentation of CTLs since it was more controllable and efficient than natural aging. The bacterial and fungal community structure and composition in unfermented and fermented CTLs were determined to understand the effects of microbes on the characteristics of CTLs during artificial fermentation. The relationship between the chemical contents and alterations in the microbial composition was evaluated, and the functions of bacteria and fungi in fermented CTLs were predicted to determine the possible metabolic pathways. After artificial fermentation, the bacterial and fungal community structure significantly changed in CTLs. The total nitrate and nicotine contents were most readily affected by the bacterial and fungal communities, respectively. FAPROTAX software predictions of the bacterial community revealed increases in functions related to compound transformation after fermentation. FUNGuild predictions of the fungal community revealed an increase in the content of saprotrophic fungi after fermentation. These data provide information regarding the artificial fermentation mechanism of CTLs and will inform safety and quality improvements.
Collapse
Affiliation(s)
- Fang Liu
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Zhiyong Wu
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Xiaoping Zhang
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Gaolei Xi
- China Tobacco Henan Ind Co Ltd, Ctr TechnolZhengzhouChina
| | - Zhe Zhao
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Miao Lai
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Mingqin Zhao
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| |
Collapse
|