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Zhang MZ, Li WT, Liu WJ, Zheng YL. Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata. BMC Microbiol 2024; 24:294. [PMID: 39107680 PMCID: PMC11302206 DOI: 10.1186/s12866-024-03450-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.
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Affiliation(s)
- Ming-Zhu Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Wei-Tao Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
| | - Wen-Jun Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Yu-Long Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Jia X, Lin S, Zhang Q, Wang Y, Hong L, Li M, Zhang S, Wang T, Jia M, Luo Y, Ye J, Wang H. The Ability of Different Tea Tree Germplasm Resources in South China to Aggregate Rhizosphere Soil Characteristic Fungi Affects Tea Quality. PLANTS (BASEL, SWITZERLAND) 2024; 13:2029. [PMID: 39124147 PMCID: PMC11314174 DOI: 10.3390/plants13152029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/11/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024]
Abstract
It is generally recognized that the quality differences in plant germplasm resources are genetically determined, and that only a good "pedigree" can have good quality. Ecological memory of plants and rhizosphere soil fungi provides a new perspective to understand this phenomenon. Here, we selected 45 tea tree germplasm resources and analyzed the rhizosphere soil fungi, nutrient content and tea quality. We found that the ecological memory of tea trees for soil fungi led to the recruitment and aggregation of dominant fungal populations that were similar across tea tree varieties, differing only in the number of fungi. We performed continuous simulation and validation to identify four characteristic fungal genera that determined the quality differences. Further analysis showed that the greater the recruitment and aggregation of Saitozyma and Archaeorhizomyces by tea trees, the greater the rejection of Chaetomium and Trechispora, the higher the available nutrient content in the soil and the better the tea quality. In summary, our study presents a new perspective, showing that ecological memory between tea trees and rhizosphere soil fungi leads to differences in plants' ability to recruit and aggregate characteristic fungi, which is one of the most important determinants of tea quality. The artificial inoculation of rhizosphere fungi may reconstruct the ecological memory of tea trees and substantially improve their quality.
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Affiliation(s)
- Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Hong
- College of Life Science, Longyan University, Longyan 364012, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan 364012, China
| | - Shuqi Zhang
- College of Life Science, Longyan University, Longyan 364012, China
| | - Tingting Wang
- College of Life Science, Longyan University, Longyan 364012, China
| | - Miao Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Yangxin Luo
- College of Life Science, Longyan University, Longyan 364012, China
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
- College of Life Science, Longyan University, Longyan 364012, China
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3
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Duan X, Li J, He W, Huang J, Xiong W, Chi S, Luo S, Liu J, Zhang X, Li J. Microbial diversity and their extracellular enzyme activities among different soil particle sizes in mossy biocrust under N limitation in the southeastern Tengger Desert, China. Front Microbiol 2024; 15:1328641. [PMID: 38357343 PMCID: PMC10866007 DOI: 10.3389/fmicb.2024.1328641] [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: 10/27/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Mossy biocrust represents a stable stage in the succession of biological soil crust in arid and semi-arid areas, providing a microhabitat that maintains microbial diversity. However, the impact of mossy biocrust rhizoid soil and different particle sizes within the mossy biocrust layer and sublayer on microbial diversity and soil enzyme activities remains unclear. Methods This study utilized Illumina MiSeq sequencing and high-throughput fluorometric technique to assess the differences in microbial diversity and soil extracellular enzymes between mossy biocrust rhizoid soil and different particle sizes within the mossy biocrust sifting and sublayer soil. Results The results revealed that the total organic carbon (TOC), total nitrogen (TN), ammonium (NH4+) and nitrate (NO3-) in mossy biocrust rhizoid soil were the highest, with significantly higher TOC, TN, and total phosphorus (TP) in mossy biocrust sifting soil than those in mossy biocrust sublayer soil. Extracellular enzyme activities (EAAs) exhibited different responses to various soil particle sizes in mossy biocrust. Biocrust rhizoid soil (BRS) showed higher C-degrading enzyme activity and lower P-degrading enzyme activity, leading to a significant increase in enzyme C: P and N: P ratios. Mossy biocrust soils were all limited by microbial relative nitrogen while pronounced relative nitrogen limitation and microbial maximum relative carbon limitation in BRS. The diversity and richness of the bacterial community in the 0.2 mm mossy biocrust soil (BSS0.2) were notably lower than those in mossy biocrust sublayer, whereas the diversity and richness of the fungal community in the rhizoid soil were significantly higher than those in mossy biocrust sublayer. The predominant bacterial phyla in mossy biocrust were Actinobacteriota, Protebacteria, Chloroflexi, and Acidobacteriota, whereas in BSS0.2, the predominant bacterial phyla were Actinobacteriota, Protebacteria, and Cyanobacteria. Ascomycota and Basidiomycota were dominant phyla in mossy biocrust. The bacterial and fungal community species composition exhibited significant differences. The mean proportions of Actinobacteriota, Protebacteria, Chloroflexi, Acidobacteriota, Acidobacteria, Cyanobacteria, and Bacteroidota varied significantly between mossy biocrust rhizoid and different particle sizes of mossy biocrust sifting and sublayer soil (p < 0.05). Similarly, significant differences (p < 0.05) were observed in the mean proportions of Ascomycota, Basidiomycota, and Glomeromycota between mossy biocrust rhizoid and different particle sizes within the mossy biocrust sifting and sublayer soil. The complexity and connectivity of bacterial and fungal networks were higher in mossy biocrust rhizoid soil compared with different particle sizes within the mossy biocrust sifting and sublayer soil. Discussion These results offer valuable insights to enhance our understanding of the involvement of mossy biocrust in the biogeochemical cycle of desert ecosystems.
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Affiliation(s)
- Xiaomin Duan
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
| | - Jiajia Li
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
| | - Wangping He
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Jingjing Huang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Wanxiang Xiong
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Shijia Chi
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Siyuan Luo
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Jianli Liu
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
| | - Xiu Zhang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
| | - Jingyu Li
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
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Dhaka V, Singh S, Ramamurthy PC, Samuel J, Swamy Sunil Kumar Naik T, Khasnabis S, Prasad R, Singh J. Biological degradation of polyethylene terephthalate by rhizobacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:116488-116497. [PMID: 35460002 DOI: 10.1007/s11356-022-20324-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
In view of the growing demand for plastic products, an enormous proportion of plastic waste causing the biological issue is produced. Plants in collaboration with their rhizobacteria partners are also exposed to these contaminants. The study aims to determine the rhizobacterial ability to biodegrade PET plastic. We isolated the rhizobacteria capable of degrading the PET plastic in minimal salt media using it as a sole carbon source. The three rhizospheric isolates, namely Priestia aryabhattai VT 3.12 (GenBank accession No. OK135732.1), Bacillus pseudomycoides VT 3.15 (GenBank accession No. OK135733.1), and Bacillus pumilus VT 3.16 (GenBank accession No. OK1357324.1), showed the highest degradation percentage for PET sheet and powder. The biodegradation end products post 28 days for PET sheet and 18 days of PET powder were studied by Fourier transform infrared spectroscopy (FTIR), high-performance liquid chromatography (HPLC), and scanning electron microscopy (SEM). Our results showed significant biodegradation of PET plastic, and the rate of degradation could account for over 65%. The present study proves soil rhizobacteria's potential and capabilities for efficient degradation of PET plastic occurring at the waste sites. It also implies that rhizobacteria could be beneficial in the remediation of PET waste in future applications.
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Affiliation(s)
- Vaishali Dhaka
- Department of Microbiology, Lovely Professional University, Phagwara, 144411, Punjab, India
| | - Simranjeet Singh
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Science, 56001, Bangalore, India
| | - Praveen C Ramamurthy
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Science, 56001, Bangalore, India
| | - Jastin Samuel
- Department of Microbiology, Lovely Professional University, Phagwara, 144411, Punjab, India
- Waste Valorization Research Lab, Lovely Professional University, Phagwara, 144411, Punjab, India
| | | | - Sutripto Khasnabis
- Department of Materials Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, 845401, Bihar, India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, 144411, Punjab, India.
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Fu X, Fu Q, Zhu X, Yang X, Chen H, Li S. Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields. FRONTIERS IN PLANT SCIENCE 2023; 14:1266218. [PMID: 37905168 PMCID: PMC10613529 DOI: 10.3389/fpls.2023.1266218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023]
Abstract
Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.
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Affiliation(s)
- Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiaozheng Zhu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
| | - Xian Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
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Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Characteristics of rhizosphere and bulk soil microbial community of Chinese cabbage ( Brassica campestris) grown in Karst area. Front Microbiol 2023; 14:1241436. [PMID: 37789857 PMCID: PMC10542900 DOI: 10.3389/fmicb.2023.1241436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023] Open
Abstract
Understanding the rhizosphere soil microbial community and its relationship with the bulk soil microbial community is critical for maintaining soil health and fertility and improving crop yields in Karst regions. The microbial communities in the rhizosphere and bulk soils of a Chinese cabbage (Brassica campestris) plantation in a Karst region, as well as their relationships with soil nutrients, were examined in this study using high-throughput sequencing technologies of 16S and ITS amplicons. The aim was to provide theoretical insights into the healthy cultivation of Chinese cabbage in a Karst area. The findings revealed that the rhizosphere soil showed higher contents of organic matter (OM), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), total potassium (TK), total nitrogen (TN), catalase (CA), urease (UR), sucrase (SU), and phosphatase (PHO), in comparison with bulk soil, while the pH value showed the opposite trend. The diversity of bacterial and fungal communities in the bulk soil was higher than that in the rhizosphere soil, and their compositions differed between the two types of soil. In the rhizosphere soil, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla, while Olpidiomycota, Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungal phyla. In contrast, the bulk soil was characterized by bacterial dominance of Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota and fungal dominance of Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota. The fungal network was simpler than the bacterial network, and both networks exhibited less complexity in the rhizosphere soil compared with the bulk soil. Moreover, the rhizosphere soil harbored a higher proportion of beneficial Rhizobiales. The rhizosphere soil network was less complicated than the network in bulk soil by building a bacterial-fungal co-occurrence network. Furthermore, a network of relationships between soil properties and network keystone taxa revealed that the rhizosphere soil keystone taxa were more strongly correlated with soil properties than those in the bulk soil; despite its lower complexity, the rhizosphere soil contains a higher abundance of bacteria which are beneficial for cabbage growth compared with the bulk soil.
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Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tianling Fu
- Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Institute of New Rural Development, Guizhou University, Guiyang, China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, China
- Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Institute of New Rural Development, Guizhou University, Guiyang, China
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7
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Guo W, Zhang J, Li MH, Qi L. Soil fungal community characteristics vary with bamboo varieties and soil compartments. Front Microbiol 2023; 14:1120679. [PMID: 36814565 PMCID: PMC9939831 DOI: 10.3389/fmicb.2023.1120679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities.
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Affiliation(s)
- Wen Guo
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China,Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jian Zhang
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China
| | - Mai-He Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland,Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China,School of Life Science, Hebei University, Baoding, China,*Correspondence: Mai-He Li,
| | - Lianghua Qi
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China,Sanya Research Base, International Centre for Bamboo and Rattan, Sanya, China,Lianghua Qi,
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8
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Chen Y, Yang X, Fu W, Chen B, Hu H, Feng K, Geisen S. Conversion of natural grassland to cropland alters microbial community assembly across northern China. Environ Microbiol 2022; 24:5630-5642. [PMID: 35880696 DOI: 10.1111/1462-2920.16127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/12/2023]
Abstract
To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the diversity and community compositions of bacteria, archaea, fungi and protists, using a paired sampling of grassland and cropland soils across the agro-pastoral ecotone of northern China. Land-use conversion decreased α diversity of bacteria, fungi and protists, and altered the structures of the entire soil microbial community (archaea, bacteria, fungi and protists). The community assembly of archaea and bacteria was dominated by stochastic processes, and that of protists dominated by deterministic processes in both land-use types. By contrast, the fungal community was governed more strongly by stochastic processes in grassland soil, than by deterministic processes in cropland soil. Our findings support the 'size-plasticity' hypothesis that smaller body-sized microorganisms (archaea and bacteria) are more structured by stochastic processes, and larger one (protist) is more influenced by deterministic processes. Our study demonstrates that distinct ecological processes govern microbial community assembly, and land-use change regulates the balance between determinism and stochasticity.
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Affiliation(s)
- Yongliang Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Xue Yang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Kai Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
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Yang T, Tedersoo L, Soltis PS, Soltis DE, Sun M, Ma Y, Ni Y, Liu X, Fu X, Shi Y, Lin HY, Zhao YP, Fu C, Dai CC, Gilbert JA, Chu H. Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China. SCIENCE CHINA LIFE SCIENCES 2022; 66:1134-1150. [PMID: 36462107 DOI: 10.1007/s11427-022-2174-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022]
Abstract
Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, 50409, Estonia
- College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Miao Sun
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Han-Yang Lin
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Peng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210003, China
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Zhang J, Lu J, Zhu Y, Huang Q, Qin L, Zhu B. Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2022; 13:1045147. [PMID: 36483959 PMCID: PMC9722746 DOI: 10.3389/fpls.2022.1045147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production. METHODS In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum. RESULTS The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively. DISCUSSION This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.
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Affiliation(s)
| | | | | | | | | | - Bo Zhu
- *Correspondence: Luping Qin, ; Bo Zhu,
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11
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Microbial degradation of polyethylene terephthalate: a systematic review. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-05143-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
AbstractPlastic pollution levels have increased rapidly in recent years, due to the accumulation of plastic waste, including polyethylene terephthalate (PET). Both high production and the lack of efficient methods for disposal and recycling affect diverse aquatic and terrestrial ecosystems owing to the high accumulation rates of plastics. Traditional chemical and physical degradation techniques have caused adverse effects on the environment; hence, the use of microorganisms for plastic degradation has gained importance recently. This systematic review was conducted for evaluating the reported findings about PET degradation by wild and genetically modified microorganisms to make them available for future work and to contribute to the eventual implementation of an alternative, an effective, and environmentally friendly method for the management of plastic waste such as PET. Both wild and genetically modified microorganisms with the metabolic potential to degrade this polymer were identified, in addition to the enzymes and genes used for genetic modification. The most prevalent wild-type PET-degrading microorganisms were bacteria (56.3%, 36 genera), followed by fungi (32.4%, 30 genera), microalgae (1.4%; 1 genus, namely Spirulina sp.), and invertebrate associated microbiota (2.8%). Among fungi and bacteria, the most prevalent genera were Aspergillus sp. and Bacillus sp., respectively. About genetically modified microorganisms, 50 strains of Escherichia coli, most of them expressing PETase enzyme, have been used. We emphasize the pressing need for implementing biological techniques for PET waste management on a commercial scale, using consortia of microorganisms. We present this work in five sections: an Introduction that highlights the importance of PET biodegradation as an effective and sustainable alternative, a section on Materials and methods that summarizes how the search for articles and manuscripts in different databases was done, and another Results section where we present the works found on the subject, a final part of Discussion and analysis of the literature found and finally we present a Conclusion and prospects.
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12
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Mataranyika PN, Chimwamurombe PM, Venturi V, Uzabakiriho JD. Bacterial bioinoculants adapted for sustainable plant health and soil fertility enhancement in Namibia. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1002797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The increase in dryland agriculture elicits the need to develop sustainable practices that improve crop yield and protect soil fertility. The use of biofertilisers adapted to nutrient deficient soils and arid climates would help achieve this. In this review, the use of plant growth-promoting bacteria is explored as a possible solution to the current state of dryland agriculture and climate change threats to agriculture. Plant microbe interactions form the basis of this review as evidence has shown that these interactions often exist to improve the health of plants. This is achieved by the production of important biochemicals and enzymes like indole acetic acid and amino cyclopropane-1-carboxylate deaminase while also actively protecting plants from pathogens including fungal pathogens. Research, therefore, has shown that these plant-growth promoting bacteria may be exploited and developed into biofertilisers. These biofertilisers are both economically and environmentally sustainable while improving soil quality and crop yield. The literature presented in this review is in context of the Namibian climate and soil profiles.
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13
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Jing L, Jia-min A, Xiao-dong L, Ying-ying J, Chao-chao Z, Rui-hua Z, Zhen-shan D. Environmental filtering drives the establishment of the distinctive rhizosphere, bulk, and root nodule bacterial communities of Sophora davidii in hilly and gully regions of the Loess Plateau of China. Front Microbiol 2022; 13:945127. [PMID: 35935225 PMCID: PMC9355530 DOI: 10.3389/fmicb.2022.945127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
In addition to the rhizobia, other non-rhizobial endophytes (NREs) have been simultaneously isolated from the root nodules. The existence of NREs in leguminous root nodules is a universal phenomenon, and they have the potential to enhance legume survival, especially under conditions of environmental stress. However, the diversity and biogeographic patterns of microbial communities inhabiting root nodules are not well studied or understood. Here, we explored and characterized the diversity of NRE bacteria by using 16S rRNA gene high-throughput amplicon sequencing. Additionally, we compared the biogeography and co-occurrence patterns in review of the bacterial microbiota inhabiting the rhizosphere, the bulk soil and the root nodule bacterial communities associated with Sophora davidii, a native N-fixing wild leguminous shrub in hilly and gully regions of the Loess Plateau of China. The results showed the presence of a large diversity of bacteria belonging to 81 phyla, 154 classes, 333 orders, 463 families, and 732 genera inside the nodules. Proteobacteria were dominant in the nodule and rhizosphere soil samples, and Actinomycetes were dominant in the bulk soil samples. Mesorhizobium was the dominant genus in the nodules, accounting for between 60.15 and 83.74% of the bacteria. The microbial community composition of the NRE in the root nodules differed from that in the rhizosphere soil and the bulk soil of S. davidii. Moreover, we found that the biogeographic patterns and assembly process of the rhizobia and non-rhizobia communities differed in the root nodule, the rhizosphere soil and the bulk soil. Furthermore, the correlation analysis between the soil’s physical and chemical properties and the bacteria showed that available phosphorus was the predominant factor affecting the bacterial diversity within the rhizosphere soil. Finally, our results revealed that the microbial network diagram of co-occurrence patterns showed more complexes in the soil than in the root nodules. This indicates that only specific microorganisms could colonize and thrive in the rhizosphere through the selection and filtering effects of roots. In conclusion, there are significant differences in bacterial community composition in the nodules, rhizosphere and bulk soil in the hilly and gully region of the Loess Plateau, which is the result of environmental filtration. Our study improves the understanding of the biogeographic patterns and diversity of bacterial microbiota inhabiting root nodules and can help quantify and define the root nodule assemblage process of S. davidii.
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Geographic Dispersal Limitation Dominated Assembly Processes of Bacterial Communities on Microplastics Compared to Water and Sediment. Appl Environ Microbiol 2022; 88:e0048222. [PMID: 35695570 PMCID: PMC9275213 DOI: 10.1128/aem.00482-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Microplastics provide new microbial niches in aquatic environments. Nevertheless, information on the assembly processes and potential ecological mechanisms of bacterial communities on microplastics from reservoirs is lacking. Here, we investigated the assembly processes and potential ecological mechanisms of bacterial communities on microplastics through full-length 16S rRNA sequencing in the Three Gorges Reservoir area of the Yangtze River, compared to water and sediment. The results showed that the Burkholderiaceae were the dominant composition of bacterial communities in microplastics (9.95%), water (25.14%), and sediment (7.22%). The niche width of the bacterial community on microplastics was lower than those in water and sediment. For the microplastics and sediment, distance-decay relationship results showed that the bacterial community similarity was significantly decreased with increasing geographical distance. In addition, the spatial turnover rate of the bacterial community on microplastics along the ~662-km reaches of the Yangtze River in the Three Gorges Reservoir area was higher than that in sediment. Null model analysis showed that the assembly processes of the bacterial community on microplastics were also different from those in water and sediments. Dispersal limitation (52.4%) was the primary assembly process of the bacterial community on microplastics, but variable selection was the most critical assembly process of the bacterial communities in water (47.6%) and sediment (66.7%). Thus, geographic dispersal limitation dominated the assembly processes of bacterial communities on microplastics. This study can enhance our understanding of the assembly mechanism of bacterial communities caused by the selection preference for microplastics from the surrounding environment. IMPORTANCE In river systems, microplastics create new microbial niches that significantly differ from those of the surrounding environment. However, the potential relationships between the biogeographic distribution and assembly processes of microbial communities on microplastics were still not well understood. This study could help us address the lack of knowledge about the assembly processes of bacterial communities on microplastics caused by selection from the surrounding environment. In this study, strong geographic dispersal limitation dominated assembly processes of bacterial communities on microplastics, compared to water and sediment, which may be responsible for the microplastic bacterial richness, and the niche distance was lower than those in water and sediment. In addition, sediment may be the main potential source of bacterial communities on microplastics in the Three Gorges Reservoir area, which makes higher community similarity between microplastics and sediment than between microplastics and water.
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15
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Van Syoc E, Albeke SE, Scasta JD, van Diepen LT. Quantifying the immediate response of the soil microbial community to different grazing intensities on irrigated pastures. AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2022; 326:107805. [PMID: 35068628 PMCID: PMC8782393 DOI: 10.1016/j.agee.2021.107805] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Grazing is known to affect soil microbial communities, nutrient cycling, and forage quantity and quality over time. However, a paucity of information exists for the immediate changes in the soil physicochemical and microbial environment in response to different grazing strategies. Soil microbes drive nutrient cycling and are involved in plant-soil-microbe relationships, making them potentially vulnerable to plant-driven changes in the soil environment caused by grazing. To test the hypothesis that variable grazing intensities modulate immediate effects on the soil microbial community, we conducted a grazing trial of three management approaches; high-intensity, short-duration grazing (HDG), low-intensity, medium-duration grazing (LDG), and no grazing (NG). Soil and vegetation samples were collected before grazing and 24 hours, 1 week, and 4 weeks after HDG grazing ended. Soil labile carbon (C) and nitrogen (N) pools, vegetation biomass, and soil microbial diversity and functional traits were determined, including extracellular enzymatic assays and high-throughput sequencing of the bacterial 16S rRNA and fungal ITS2 regions. We found that labile soil C and inorganic N increased following the LDG grazing while C-cycling extracellular enzymatic activities increased in response to HDG grazing but both total extracellular enzymatic activity profiles and soil abiotic profiles were mostly affected by temporal fluxes. The soil fungal community composition was strongly affected by the interaction of sampling time and grazing treatment, while the soil bacterial community composition was largely affected by sampling time with a lesser impact from grazing treatment. We identified several key fungal taxa that may influence immediate responses to grazing and modulate plant-soil-microbe interactions. There was strong evidence of temporal influences on soil biogeochemical variables and the soil microbiome, even within our narrow sampling scheme. Our results indicate that the soil ecosystem is dynamic and responsive to different grazing strategies within very short time scales, showing the need for further research to understand plant-soil-microbe interactions and how these feedback mechanisms can inform sustainable land management.
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Affiliation(s)
- Emily Van Syoc
- Department of Ecosystem Science and Management, University of Wyoming, Wyoming, USA
- Integrative & Biomedical Physiology and Clinical & Translational Sciences Dual-Title Ph.D. Program, The Pennsylvania State University, Pennsylvania, USA
| | - Shannon E. Albeke
- Wyoming Geographic Information Science Center, University of Wyoming, Wyoming, USA
| | - John Derek Scasta
- Department of Ecosystem Science and Management, University of Wyoming, Wyoming, USA
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16
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Zhang X, Liu S, Jiang Z, Wu Y, Huang X. Gradient of microbial communities around seagrass roots was mediated by sediment grain size. Ecosphere 2022. [DOI: 10.1002/ecs2.3942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province Sanya Institute of Oceanology, SCSIO Sanya China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
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17
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Berrios L. The genus Caulobacter and its role in plant microbiomes. World J Microbiol Biotechnol 2022; 38:43. [PMID: 35064419 DOI: 10.1007/s11274-022-03237-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 11/27/2022]
Abstract
Recent omics approaches have revealed the prevalent microbial taxa that constitute the microbiome of various plant species. Across global scales and environmental conditions, strains belonging to the bacterial genus Caulobacter have consistently been found in association with various plant species. Aligned with agroecological relevance and biotechnological advances, many scientific communications have demonstrated that several Caulobacter strains (spanning several Caulobacter species) harbor the potential to enhance plant biomass for various plant species ranging from Arabidopsis to Citrullus and Zea mays. In the past several years, co-occurrence data have driven mechanistically resolved communications about select Caulobacter-plant interactions. Given the long-standing history of Caulobacter as a model organism for cell cycle regulation, genetic studies, and the prevalence of Caulobacter species in various plant microbiomes, the genus Caulobacter offers researchers a unique opportunity to leverage for investigating plant-microbe interactions and realizing targeted biotechnological applications. In this review, recent developments regarding Caulobacter-plant interactions are presented in terms of model utility for future biotechnological investigations.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, USA.
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18
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Cook K, Sharma J, Taylor AD, Herriott IC, Taylor DL. Epiphytic fungal communities vary by substrate type and at sub-meter spatial scales. Mol Ecol 2022; 31:1879-1891. [PMID: 35060231 DOI: 10.1111/mec.16358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/17/2021] [Accepted: 01/07/2022] [Indexed: 11/30/2022]
Abstract
Fungal species have numerous important environmental functions. Where these functions occur will depend on how fungi are spatially distributed, but spatial structures of fungal communities are largely unknown, especially in understudied hyperdiverse tropical tree canopy systems. We explore fungal communities in a Costa Rican tropical rainforest canopy, with a focus on local-scale spatial structure and substrate specificity of fungi. Samples of ~1 cm3 were collected from 135 points along 5 adjacent tree branches, with inter-sample distances from 1 to 800 cm, and dissected into four substrates: outer host tree bark, inner bark, dead bryophytes, and living bryophytes. We sequenced the ITS2 region to characterize total fungal communities. Fungal community composition and diversity varied among substrate types, even when multiple substrates were in direct contact. Fungi were most diverse in living bryophytes, with 39% of all OTUs found exclusively in this substrate, and the least diverse in inner bark. Fungal communities had significant positive spatial autocorrelation and distance decay of similarity only at distances less than one meter. Similarity among samples declines by half in less than ten cm, and even at these short distances, similarities are low with few OTUs shared among samples. These results indicate that community turnover is high and occurs at very small spatial scales, with any two locations sharing very few fungi in common. High heterogeneity of fungal communities in space and among substrates may have implications for the distributions, population dynamics, and diversity of other tree canopy organisms, including epiphytic plants.
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Affiliation(s)
- Kel Cook
- Department of Biology, University of New Mexico, Castetter Hall 1480, MSC03-2020, 219 Yale Blvd NE, Albuquerque, NM, 87131-0001, USA
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Bayer Plant Science Building, Room 219, 2911 15th Street, Mail Stop 2122, Lubbock, TX, 79409-2122, USA
| | - Andrew D Taylor
- Department of Biology, University of Hawai'i at Manoa, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI, 96822, USA
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska, 311 Irving I Building, Fairbanks, AK, 99775, USA
| | - D Lee Taylor
- Department of Biology, University of New Mexico, Castetter Hall 1480, MSC03-2020, 219 Yale Blvd NE, Albuquerque, NM, 87131-0001, USA
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Wang J, Liao L, Wang G, Liu H, Wu Y, Liu G, Zhang C. N-induced root exudates mediate the rhizosphere fungal assembly and affect species coexistence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150148. [PMID: 34520919 DOI: 10.1016/j.scitotenv.2021.150148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Root exudates play essential roles in shaping root-associated microbial communities in plant-soil systems. However, knowledge regarding the influence of root exudates on soil communities, particularly concerning their assembly processes and species coexistence patterns, remains limited. In this study, we performed a 20-month pot experiment using a nitrogen (N) addition gradient (0, 2.5, 5, 7.5, 10, and 15 g N m-2 yr-1), amplicon sequencing, and metabolomics to investigate the effect of short-term N addition on the assembly process and species coexistence of fungal communities, as well as their association with root exudates in the rhizosphere and bulk soils around Bothriochloa ischaemum. The results demonstrated that short-term N addition led to distinct differences in the diversity, composition, assembly process, and co-occurrence networks of fungal communities in the rhizosphere and bulk soils. The diversity of fungal communities in the rhizosphere soil increased with the rate of N input and peaked at N10 treatment; this could be correlated with the increased abundance in long-chain organic acids (LCOAs). However, above the threshold N rate of 10 g N m-2 yr-1, diversity decreased probably because of the high N-induced inhibitory effect on root exudates (i.e., LCOAs). N addition increased the relative abundance of Sordariomycetes in the rhizosphere and decreased the relative abundance of Mortierellomycetes in the bulk soil, while enhancing the abundance of pathotrophs in both bulk and rhizosphere soils. The rhizosphere fungal community was dominated by a stochastic process at a low N input (N0 and N2.5) and by deterministic processes at a high N input (N10 and N15), which is opposite to the trends in the bulk soil. These fungal assembly processes determine the coexistence of fungal species; deterministic processes lead to less interconnected networks in rhizosphere soils that harbor a more complex network than the bulk soil. Associations between the assembly process and species coexistence in the rhizosphere of B. ischaemum were closely related to the changes in root exudates, such as amino acids, short-chain organic acids, and phenols, which were stimulated by N addition. Collectively, our study emphasizes the key roles of root exudates in the establishment of fungal communities in the plant-soil system and furthers our understanding of plant-microbe interactions.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China
| | - Lirong Liao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, PR China
| | - Guoliang Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China
| | - Hongfei Liu
- College of Forestry, Northwest A&F University, Yangling 712100, PR China; Department of Agroecology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Yang Wu
- College of Forestry, Northwest A&F University, Yangling 712100, PR China
| | - Guobin Liu
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, PR China
| | - Chao Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China.
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Liu Y, Wang H, Peng Z, Li D, Chen W, Jiao S, Wei G. Regulation of root secondary metabolites by partial root-associated microbiotas under the shaping of licorice ecotypic differentiation in northwest China. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:2093-2109. [PMID: 34655272 DOI: 10.1111/jipb.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Interactions between plant hosts and their microbiotas are becoming increasingly evident, while the effects of plant communities on microbial communities in different geographic environments are poorly understood. Here, the differentiation of licorice plant ecotypes and the distribution of root-associated microbiotas were investigated across five sampling sites in northwest China. The interactions between the environment, plant and microbial communities, and their effects on licorice root secondary metabolites, were elucidated. The plant community was clearly differentiated into distinct ecotypes based on genotyping-by-sequencing and was primarily driven by geographic distance and available soil nitrogen. The bulk soil and root-associated microbiotas (rhizosphere soil and root endosphere) partially correlated with plant community, but all were significantly discriminated by plant clade. Moreover, these microbiotas were explained to different extents by distinct combinations of environment, geography, and plant community. Similarly, three structural equation models showed that licorice root secondary metabolites were complicatedly modulated by multiple abiotic and biotic factors, and were mostly explained by these factors in the rhizosphere model. Collectively, the results provide novel insights into the role of environment-plant-microbiota interactions in regulating root secondary metabolites. That should be accounted for when selecting appropriate licorice planting sites and management measures.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Da Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
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He R, Zeng J, Zhao D, Wang S, Wu QL. Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle-Lower Yangtze plain. Mol Ecol 2021; 31:1180-1195. [PMID: 34846091 DOI: 10.1111/mec.16298] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/31/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022]
Abstract
Comparison of the spatial distribution and assembly processes between bulk and rhizosphere bacterial communities at multiple spatial scales is vital for understanding the generation and maintenance of microbial diversity under the influence of plants. However, biogeographical patterns and the underlying mechanisms of microbial communities in bulk and rhizosphere sediments of aquatic ecosystems remain unclear. Here, we collected 140 bulk and rhizosphere sediment samples of Phragmites australis from 14 lakeshore zones across a 510-km transect in the Middle-Lower Yangtze plain. We performed high-throughput sequencing to investigate the bacterial diversity, composition, spatial distribution and assembly processes of these samples. Bacterial communities in the rhizosphere sediment exhibited higher alpha diversity but lower beta diversity than those in the bulk sediment. Both bulk and rhizosphere sediment bacterial communities had significant distance-decay relationships, but spatial turnover of the rhizosphere sediment bacterial community was strikingly lower than that of bulk sediment. Despite variable selection dominating the assembly processes of bacterial communities in bulk sediment, the rhizosphere of P. australis enhanced the role of dispersal limitation in governing bacterial communities. The relative importance of different ecological processes in determining bacterial assembly presented distinct patterns of increasing or decreasing linearly with an increase of scale. This investigation highlights the convergent selection of the aquatic plant rhizosphere for surrounding bacterial communities and emphasizes the importance of different ecological processes on bacterial community assembly in sediment environments over different scales. Furthermore, we provide a preliminary framework for exploring the scale dependence of microbial community assembly in aquatic ecosystems.
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Affiliation(s)
- Rujia He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Shuren Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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22
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Sun X, Pei J, Zhao L, Ahmad B, Huang LF. Fighting climate change: soil bacteria communities and topography play a role in plant colonization of desert areas. Environ Microbiol 2021; 23:6876-6894. [PMID: 34693620 DOI: 10.1111/1462-2920.15799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022]
Abstract
Global warming has exacerbated desertification in arid regions. Exploring the environmental variables and microbial communities that drive the dynamics of geographic patterns of desert crops is important for large-scale standardization of crops that can control desertification. Here, predictions based on future climate data from CMIP6 show that a steady expand in the suitable production areas for three desert plants (Cistanche deserticola, Cynomorium songaricum and Cistanche salsa) under global warming, demonstrating their high adaptability to future climate change. We examined the biogeography of three desert plant soil bacteria communities and assessed the environmental factors affecting the community assembly process. The α-diversity significantly decreased along elevated latitudes, indicating that the soil bacterial communities of the three species have latitude diversity patterns. The neutral community model evaluated 66.6% of the explained variance of the bacterial community in the soil of desert plants and Modified Stochasticity Ratio <0.5, suggesting that deterministic processes dominate the assembly of bacterial communities in three desert plants. Moreover, topography (longitude, elevation) and precipitation as well as key OTUs (OTU4911: Streptomyces eurythermus and OTU4672: Streptomyces flaveus) drive the colonization of three desert plants. This research offers a promising solution for desert management in arid areas under global warming.
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Affiliation(s)
- Xiao Sun
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, 611137, China.,Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Lei Zhao
- Central Medical District of Chinese PLA General Hospital, Beijing, 100193, China
| | - Bashir Ahmad
- Center for Biotechnology & Microbiology, University of Peshawar, Peshawar, 25000, Pakistan
| | - Lin-Fang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
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Zhang J, Xing P, Niu M, Wei G, Shi P. Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China. Front Microbiol 2021; 12:738129. [PMID: 34603268 PMCID: PMC8485050 DOI: 10.3389/fmicb.2021.738129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R 2 = 0.37-0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R 2 = 0.08-0.09) or cultivar type (R 2 = 0.02-0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.
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Affiliation(s)
| | | | | | | | - Peng Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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24
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Petrolli R, Augusto Vieira C, Jakalski M, Bocayuva MF, Vallé C, Cruz EDS, Selosse MA, Martos F, Kasuya MCM. A fine-scale spatial analysis of fungal communities on tropical tree bark unveils the epiphytic rhizosphere in orchids. THE NEW PHYTOLOGIST 2021; 231:2002-2014. [PMID: 33983644 DOI: 10.1111/nph.17459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Approximately 10% of vascular plants are epiphytes and, even though this has long been ignored in past research, are able to interact with a variety of fungi, including mycorrhizal taxa. However, the structure of fungal communities on bark, as well as their relationship with epiphytic plants, is largely unknown. To fill this gap, we conducted environmental metabarcoding of the ITS-2 region to understand the spatial structure of fungal communities of the bark of tropical trees, with a focus on epiphytic orchid mycorrhizal fungi, and tested the influence of root proximity. For all guilds, including orchid mycorrhizal fungi, fungal communities were more similar when spatially close on bark (i.e. they displayed positive spatial autocorrelation). They also showed distance decay of similarity with respect to epiphytic roots, meaning that their composition on bark increasingly differed, compared to roots, with distance from roots. We first showed that all of the investigated fungal guilds exhibited spatial structure at very small scales. This spatial structure was influenced by the roots of epiphytic plants, suggesting the existence of an epiphytic rhizosphere. Finally, we showed that orchid mycorrhizal fungi were aggregated around them, possibly as a result of reciprocal influence between the mycorrhizal partners.
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Affiliation(s)
- Rémi Petrolli
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Conrado Augusto Vieira
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
| | - Marcin Jakalski
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
| | - Melissa F Bocayuva
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
| | - Clément Vallé
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Everaldo Da Silva Cruz
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Maria Catarina M Kasuya
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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Huang M, Chai L, Jiang D, Zhang M, Jia W, Huang Y. Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions. MICROBIAL ECOLOGY 2021; 82:202-214. [PMID: 32322922 DOI: 10.1007/s00248-020-01509-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.
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Affiliation(s)
- Muke Huang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Liwei Chai
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Dalin Jiang
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Weiqian Jia
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Yi Huang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China.
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26
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Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Wang W, Wang X, Yu L, Zhao Q. Spartina alterniflora invasions reduce soil fungal diversity and simplify co-occurrence networks in a salt marsh ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143667. [PMID: 33248759 DOI: 10.1016/j.scitotenv.2020.143667] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/30/2020] [Accepted: 11/08/2020] [Indexed: 05/14/2023]
Abstract
Soil fungal communities drive diverse ecological processes and are critical in maintaining ecosystems' stability, but the effects of plant invasion on soil fungal diversity, community composition, and functional groups are not well understood. Here, we investigated soil fungal communities in a salt marsh ecosystem with both native (Suaeda salsa) and exotic (Spartina alterniflora) species in the Yellow River Delta. We characterized fungal diversity based on the PCR-amplified Internal Transcribed Spacer 2 (ITS2) DNA sequences from soil extracted total DNA. The plant invasion evidently decreased fungal richness and phylogenetic diversity and significantly altered the taxonomic community composition (indicated by the permutation test, P < 0.001). Co-occurrence networks between fungal species showed fewer network links but were more assembled because of the high modularity after the invasion. As indicated by the fungal Bray-Curtis and weighted UniFrac distances, the fungal community became homogenized with the invasion. FUNGuild database analyses revealed that the invaded sites had a higher proportion of saprophytic fungi, suggesting higher organic matter decomposition potential with the invasion. The plant invasion dramatically inhibited the growth of pathogenic fungi, which may facilitate the expansion of invasive plants in the intertidal habitats. Soil pH and salinity were identified as the most important edaphic factors in shaping the fungal community structures in the context of Spartina alterniflora invasion. Overall, this study elucidates the linkage between plant invasion and soil fungal communities and poses potential consequences for fungal contribution to ecosystem function, including the decomposition of soil organic substrates.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, Braunschweig 38116, Germany
| | - Laibin Huang
- Department of Land, Air, and Water Resources, University of California-Davis, CA 95616, USA
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Lu Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, PR China; Ecology Institute of Shandong Academy of Sciences, Ji'nan 250103, PR China
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27
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The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1546-1559. [PMID: 33439456 DOI: 10.1007/s11427-020-1843-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
Urban soils harbor billions of bacterial cells and millions of species. However, the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils. It is also unknown if we can use the bacteria to track soil sources to certain cities and districts. Here, Illumina MiSeq sequencing was used to survey soil bacterial communities from 529 random plots spanning 61 districts and 10 major cities in China. Over a 3,000 km range, community similarity declined with increasing geographic distance (Mantel r=0.62), and community composition was clustered by city (R2=0.50). Within cities (<100 km), the aforementioned biogeographic patterns were weakened. Process analysis showed that homogenizing dispersal and dispersal limitation dominated soil bacterial assembly at small and large spatial scales, respectively. Accordingly, the probabilities of accurately tracking random soil sources to certain cities and districts were 90.0% and 66.7%, respectively. When the tested samples originated from cities that were more than 1,265 km apart, the soil sources could be identified with nearly 100% accuracy. Overall, this study demonstrates the strong distance-decay relationship and the clear geographic zoning of urban soil bacterial communities among cities. The varied importance of different community assembly processes at multiple spatial scales strongly affects the accuracy of microbial source tracking.
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Liu Y, Li D, Qi J, Peng Z, Chen W, Wei G, Jiao S. Stochastic processes shape the biogeographic variations in core bacterial communities between aerial and belowground compartments of common bean. Environ Microbiol 2020; 23:949-964. [PMID: 32893947 DOI: 10.1111/1462-2920.15227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Although studies of biogeography in soil bacterial communities have attracted considerable attention, the generality of these patterns along with assembly processes and underlying drivers is poorly understood in the inner tissues of plants. Plant tissues provide unique ecological habitats for microorganisms, which play an essential role in plant performance. Here, we compared core bacterial communities among five soil-plant associated compartments of common bean across five sampling sites in China. Neutral and null modelling consistently suggested that stochastic processes dominated the core community assembly processes and escalated from the belowground compartments to the inner tissues of aerial plant parts. The multiple distance-decay relationships also varied and had flattened patterns in the stem endosphere, which were shaped by distinct environmental factors in each compartment. Coexistence patterns also varied in topological features, in addition with the sparsest networks in the stem endosphere resulted from the interaction with the stochastic processes. This study considerably expanded our understanding of various biogeographic patterns, assembly processes, and the underlying mechanisms of core bacterial communities between aerial and belowground compartments of common bean. That will provide a scientific basis for the reasonable regulation of core bacterial consortia to get better plant performance.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Da Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiejun Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Hou J, Wu L, Liu W, Ge Y, Mu T, Zhou T, Li Z, Zhou J, Sun X, Luo Y, Christie P. Biogeography and diversity patterns of abundant and rare bacterial communities in rice paddy soils across China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 730:139116. [PMID: 32402971 DOI: 10.1016/j.scitotenv.2020.139116] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Bacteria are critical ecosystem drivers in both aquatic and terrestrial ecosystems. However, our understanding of the mechanisms generating and maintaining biodiversity on large spatial scales remains limited, especially mechanisms involving rare taxa in soil ecosystems. In the present study we took paddy soils in China as model ecosystems and studied the ecological diversity and assembly mechanisms of both the rare and abundant bacterial subcommunities. We collected 339 paddy soil samples from 113 sites across 19 Chinese provinces that span distances of up to 3869 km. The bacterial community was characterized by high-throughput sequencing of the 16S rRNA gene. The α-diversity of rare and abundant subcommunities showed opposite quadratic correlations with the key environmental factor soil pH. Rare taxa exhibited a stronger distance-decay relationship than the abundant subcommunity. Moreover, deterministic selection processes dominated in the assembly of the abundant subcommunity while stochastic processes dominated in that of the rare subcommunity based on both variation partitioning analysis and the phylogenetic null model. Soil pH was also the main deterministic factor driving the geographical distributions of both the rare and abundant subcommunity. Besides, mean annul temperature and soil texture were also found to be important factors affecting the biogeography and diversity patterns of abundant and rare subcommunities. These results indicate that the mechanisms generating and maintaining the diversity of the abundant and rare subcommunities were totally different in paddy soils, suggesting that these two subcommunities may respond differently to future environmental change.
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Affiliation(s)
- Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Yanyan Ge
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Tingting Mu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhu Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiawen Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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30
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Zhang M, Chai L, Huang M, Jia W, Guo J, Huang Y. Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau. BMC Microbiol 2020; 20:235. [PMID: 32738877 PMCID: PMC7395985 DOI: 10.1186/s12866-020-01913-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/19/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear. RESULTS High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. CONCLUSIONS Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.
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Affiliation(s)
- Mengjun Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Liwei Chai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Muke Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Jiabao Guo
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087.
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Chen W, Wang J, Meng Z, Xu R, Chen J, Zhang Y, Hu T. Fertility-related interplay between fungal guilds underlies plant richness-productivity relationships in natural grasslands. THE NEW PHYTOLOGIST 2020; 226:1129-1143. [PMID: 31863600 DOI: 10.1111/nph.16390] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
The plant richness-productivity relationship is a central subject in ecology, yet the mechanisms behind this pattern remain debated. Soil fungi are closely associated with the dynamics of plant communities, however empirical evidence on how fungal communities integrate into the richness-productivity relationships of natural environments is lacking. We used Illumina high-throughput sequencing to identify rhizosphere fungal communities across a natural plant richness gradient at two sites with different fertility conditions, and related the subsequent information to plant richness and productivity to elucidate the role of fungal guilds in integrating the linkages of both plant components. Saprotrophs, mycorrhizal fungi and potential plant pathogens interacted differently between the sites, with saprotrophic and mycorrhizal fungal abundances being positively correlated at the high-nutrient site and abundances of mycorrhizal fungi and potential plant pathogens being negatively correlated at the low-nutrient site. The synergistic associations between these fungal guilds with plant richness and productivity operated in concert to promote positive richness-productivity relationships. Our findings provide empirical evidence for the importance of soil fungal guilds in integrating the linkages of plant richness and productivity, and suggest that future work incorporating soil fungal communities into richness-productivity relationships would advance our mechanistic understanding of their linkages.
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Affiliation(s)
- Wenqing Chen
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jianyu Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zexin Meng
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ran Xu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun Chen
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yingjun Zhang
- Department of Grassland Science, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
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32
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Jamil A, Yang JY, Su DF, Tong JY, Chen SY, Luo ZW, Shen XM, Wei SJ, Cui XL. Rhizospheric soil fungal community patterns of Duchesnea indica in response to altitude gradient in Yunnan, southwest China. Can J Microbiol 2020; 66:359-367. [PMID: 32053399 DOI: 10.1139/cjm-2019-0589] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The magnitude of the impact of altitude gradient on microbial community and diversity has been studied in recent decades. Whereas bacteria have been the focus of most studies, fungi have been given relatively less attention. As a vital part of the macro- and microscopic ecosystem, rhizosphere fungi play a key role in organic matter decomposition and relative abundance of plant species and have an impact on plant growth and development. Using Duchesnea indica as the host plant, we examined the rhizosphere soil fungal community patterns across the altitude gradient in 15 sites of Yunnan province by sequencing the fungal ITS2 region with the Illumina MiSeq platform. We determined the fungal community composition and structure. We found that, surprisingly, rhizosphere soil fungal diversity of D. indica increased with altitudinal gradient. There was a slight difference in diversity between samples from high- and medium-altitude sites, with medium-altitude sites having the greater diversity. Furthermore, the rhizosphere soil fungal community composition and structure kept changing along the altitudinal gradient. Taxonomic results showed that the extent of phylum diversity was greatest at high-altitude sites, with Ascomycota, Basidiomycota, Zygomycota, and Glomeromycota as the most dominant fungal phyla.
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Affiliation(s)
- Arslan Jamil
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Jun-Yu Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Dai-Fa Su
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Jiang-Yun Tong
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Shan-Yan Chen
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Zhi-Wei Luo
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Xue-Mei Shen
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Shi-Jie Wei
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
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33
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Chen J, Wang P, Wang C, Wang X, Miao L, Liu S, Yuan Q, Sun S. Distinct Assembly Mechanisms Underlie Similar Biogeographic Patterns of Rare and Abundant Bacterioplankton in Cascade Reservoirs of a Large River. Front Microbiol 2020; 11:158. [PMID: 32117173 PMCID: PMC7020914 DOI: 10.3389/fmicb.2020.00158] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/22/2020] [Indexed: 12/21/2022] Open
Abstract
Bacterioplankton communities commonly consist of few highly abundant species and a large number of rare species that play key roles in biogeochemical cycles of aquatic ecosystems. However, little is known about the biogeographic assemblies of these communities, especially in large rivers suffering from cascade dam regulation. Here, we used a 16S rRNA gene amplicon sequencing approach to investigate the biogeographic patterns and underlying assembly mechanisms of abundant and rare bacterioplankton taxa in cascade reservoirs of the Jinsha River in China. The results revealed species loss of bacterioplankton due to dam construction, which was more significant for rare taxa than for abundant ones. The distributions of abundant and rare taxa exhibited similar spatial and temporal patterns, which were significantly distinct between winter and summer and between upstream and downstream reservoirs. Both spatial (dispersal-related process) and environmental (selection process) factors seemed to together govern the assembly and biogeography of abundant and rare taxa, although both factors explained only a small fraction of variation in the rare taxa. More importantly, environmental factors explained more community variation in abundant sub-community than that in rare sub-community. Co-occurrence network analysis revealed that abundant species with closer interactions were more often located in a central position of the network compared with rare species. Nevertheless, half of the keystone species were rare species and may play important roles in maintaining the network stability. Overall, these findings indicate that distinct assembly mechanisms underlie the similar biogeography of rare and abundant bacteria in cascade reservoirs of a large river.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Shenghao Sun
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
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34
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Hu J, Zhou Y, Chen K, Li J, Wei Y, Wang Y, Wu Y, Ryder MH, Yang H, Denton MD. Large‐scale
Trichoderma
diversity was associated with ecosystem, climate and geographic location. Environ Microbiol 2019; 22:1011-1024. [DOI: 10.1111/1462-2920.14798] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/29/2019] [Accepted: 09/05/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Jindong Hu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yi Zhou
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
- School of Agriculture, Food and Wine The University of Adelaide SA Australia
| | - Kai Chen
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Jishun Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yanli Wei
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yilian Wang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yuanzheng Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Maarten H. Ryder
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
- School of Agriculture, Food and Wine The University of Adelaide SA Australia
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Matthew D. Denton
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
- School of Agriculture, Food and Wine The University of Adelaide SA Australia
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35
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Chen J, Wang P, Wang C, Wang X, Miao L, Liu S, Yuan Q, Sun S. Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river. Environ Microbiol 2019; 22:832-849. [DOI: 10.1111/1462-2920.14795] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 08/08/2019] [Accepted: 08/27/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Shenghao Sun
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
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36
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Feng M, Tripathi BM, Shi Y, Adams JM, Zhu Y, Chu H. Interpreting distance-decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales. Microbiologyopen 2019; 8:e00851. [PMID: 31074596 PMCID: PMC6741136 DOI: 10.1002/mbo3.851] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 11/08/2022] Open
Abstract
It has been widely accepted that there is a distance-decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance-decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize fields of Northeast China using Illumina MiSeq sequencing. Results showed that the processes governing spatial turnover in bacterial community composition shifted regularly with spatial scale, with homogenizing dispersal dominating at small spatial scales and variable selection dominating at larger scales, which in turn explained the distance-decay pattern that closer located sites tended to have higher community similarity. Together, homogenizing dispersal and dispersal limitation resulting from geographic factors governed about 33% of spatial turnover in bacterial community composition. Deterministic selection processes had the strongest influence, at 57%, with biotic factors and abiotic environmental filtering (mainly imposed by soil pH) respectively contributing about 37% and 63% of variation. Our results provided a novel and comprehensive way to explain the distance-decay pattern of soil microbiome via quantifying the assembly processes at multiple spatial scales, as well as the method to quantify the influence of abiotic, biotic, and geographic factors in shaping microbial community structure, thus enabling understanding of widely acknowledged microbial biogeographic patterns and microbial ecology.
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Affiliation(s)
- Maomao Feng
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil Science, Chinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Yu Shi
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil Science, Chinese Academy of SciencesNanjingChina
| | - Jonathan M. Adams
- School of Water, Energy and EnvironmentCranfield UniversityCranfieldUK
| | - Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil Science, Chinese Academy of SciencesNanjingChina
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37
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Zhang J, Tian H, Wang P, Xiao Q, Zhu S, Jiang H. Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:132-140. [PMID: 30889478 DOI: 10.1016/j.plaphy.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Substrates are fundamental prerequisites for growing grafted seedlings. In this study, substrates with different pH levels (5.0, 5.5, 6.0, 6.5, 7.0, and 8.0) were set up to elucidate the effect of pH on cadmium (Cd) uptake in grafted muskmelon (Cucumis melo L.) plants. Bacterial diversity was also investigated. Results showed that pH and high Cd concentration greatly affected the growth of grafted plants. The chlorophyll content of the muskmelon leaves decreased at 100 μM Cd. The majority of the Cd ions accumulated in the rootstock rather than in the shoot tissue in all of the treatments. The shoots and roots showed the highest Cd content at pH 5.5 and the lowest Cd content at pH 8.0 regardless of the Cd concentration. The operational taxonomic units belonging to Proteobacteria and Bacteroidetes were significantly (p < 0.05) enriched at different substrate pH levels compared with those at pH 5.0. The operational taxonomic units belonging to the phyla Firmicutes, Acidobacteria, and Chloroflexi were significantly decreased. The available nitrogen, phosphorus, Cd, and pH were strongly linked to bacterial community compositions. On the contrary, the available potassium was weakly correlated with the bacterial structure. This study demonstrates that pH greatly affects Cd uptake in grafted muskmelon plants and predicts microbial community structures in breeding substrates with different pH levels. Our results suggest that Cd accumulation in grafted plants can be reduced by setting the appropriate substrate pH. This work can serve as a reference for growing high-quality grafted plants and ensuring food safety in the presence of Cd contamination.
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Affiliation(s)
- Jian Zhang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China.
| | - Hongmei Tian
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China
| | - Pengcheng Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China.
| | - Qingqing Xiao
- Department of Biological and Environmental Engineering, Hefei University, 230601, Anhui Province, China
| | - Shoujing Zhu
- College of Life Science and Resources and Environment, Yichun University, Yichun, 336000, Jiangxi Province, China
| | - Haikun Jiang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China; School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui Province, China
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38
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Yang T, Tedersoo L, Soltis PS, Soltis DE, Gilbert JA, Sun M, Shi Y, Wang H, Li Y, Zhang J, Chen Z, Lin H, Zhao Y, Fu C, Chu H. Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. THE ISME JOURNAL 2019; 13:686-697. [PMID: 30353037 PMCID: PMC6461945 DOI: 10.1038/s41396-018-0303-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/26/2018] [Accepted: 09/30/2018] [Indexed: 12/19/2022]
Abstract
Recent studies have detected strong phylogenetic signals in tree-fungus associations for diseased leaves and mycorrhizal symbioses. However, the extent of plant phylogenetic constraints on the free-living soil mycobiome remains unknown, especially at broad geographic scales. Here, 343 soil samples were collected adjacent to individual tree trunks, representing 58 woody plant species located in five mountain forests of eastern China. Integrating plant species identity and phylogenetic information, we aimed to unravel the relative contributions of phylogenetic relationships among tree species, abiotic environmental filtering, and geographic isolation to the geographic distribution of soil mycobiome. We found that the community dissimilarities of total fungi and each dominant guild (viz. saprotrophs, plant pathogens, and ectomycorrhizal fungi) significantly increased with increasing plant phylogenetic distance. Plant phylogenetic eigenvectors explained 11.4% of the variation in community composition, whereas environmental and spatial factors explained 24.1% and 7.2% of the variation, respectively. The communities of ectomycorrhizal fungi and plant pathogens were relatively more strongly affected by plant phylogeny than those of saprotrophs (13.7% and 10.4% vs. 8.5%). Overall, our results demonstrate how plant phylogeny, environment, and geographic space contribute to forest soil fungal distributions and suggest that the influence of plant phylogeny on fungal association may differ by guilds.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, Tartu, 50411, Estonia
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, and Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Hongfei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hanyang Lin
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunpeng Zhao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China.
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39
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Kong X, Jin D, Wang X, Zhang F, Duan G, Liu H, Jia M, Deng Y. Dibutyl phthalate contamination remolded the fungal community in agro-environmental system. CHEMOSPHERE 2019; 215:189-198. [PMID: 30317089 DOI: 10.1016/j.chemosphere.2018.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/18/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
Dibutyl phthalate (DBP) is a typical soil contaminant that is widely used as plasticizer in modern agricultural production. In this study, an experiment was conducted to evaluate fungal community succession in a soil-vegetable ecosystem under different DBP concentrations. By using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region, it was shown that DBP contamination caused significant changes to the soil fungal community, in terms of both α and β diversities. The largest changes in fungal α and β diversities were detected under 50 mg/kg DBP concentration at the first day of addition. The bulk soils, rhizosphere soils and the phyllosphere harbored different fungal communities, while the abundance of saprotrophs and plant pathogens in the phyllosphere have been increased under DBP contamination. From correlation analysis and partial Mantel test, the change in fungal community α diversity was the result of multiple factors (DBP concentration, bacterial community and soil properties) while the β diversity of fungal community was mainly co-varied with the bacterial community after DBP contamination. Moreover, molecular ecological network analysis demonstrated that DBP contamination was detrimental to mutualistic relationships among fungal species and destabilized the network structure. Overall, the fungal communities in soils and around vegetables were largely remolded by DBP contamination that provides new insight into DBP contamination impacts on agricultural ecosystems.
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Affiliation(s)
- Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xinxin Wang
- China Offshore Environmental Service Co. Ltd., Tianjin 300452, China
| | - Fengsong Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Guilan Duan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijun Liu
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing 102206, China
| | - Minghong Jia
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing 102206, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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40
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Zhang J, Zhang B, Liu Y, Guo Y, Shi P, Wei G. Distinct large-scale biogeographic patterns of fungal communities in bulk soil and soybean rhizosphere in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:791-800. [PMID: 29990927 DOI: 10.1016/j.scitotenv.2018.07.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/27/2018] [Accepted: 07/01/2018] [Indexed: 05/20/2023]
Abstract
Fungi play a crucial role in the agroecological system; however, little is known about their large-scale biogeographical patterns and how various ecological processes contribute to community assembly, especially in the crop rhizosphere. In this study, we investigated the spatial distribution and community assembly of fungi in the bulk soil and rhizosphere of soybean collected from 43 sites across China using high-throughput sequencing. The alpha diversity of the rhizosphere was lower than that of bulk soil. The fungal community structures of the two soil compartments were distinct. Fungal communities in the rhizosphere had a steeper distance-decay relationship slope between sampled sites than those in bulk soil, suggesting a greater influence of historical processes (geographical separation) in the rhizosphere. The relative importance of dispersal limitation and environmental filtering for the fungal community composition differed between bulk soil and rhizosphere. Sloan neutral model analysis suggested that niche-based processes dominated the assemblage of fungal communities in the two soil compartments, while neutral processes had a weaker influence in the rhizosphere than in bulk soil. Additionally, we analyzed the structures of abundant and rare fungal sub-communities in each soil compartment. Rare sub-communities were more strongly influenced by dispersal limitation than abundant sub-communities. These results expand the current understanding of root-associated fungal community biogeography in agricultural soils on a large scale.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Baogang Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yao Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yanqing Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Peng Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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41
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Schröter K, Wemheuer B, Pena R, Schöning I, Ehbrecht M, Schall P, Ammer C, Daniel R, Polle A. Assembly processes of trophic guilds in the root mycobiome of temperate forests. Mol Ecol 2018; 28:348-364. [PMID: 30276908 DOI: 10.1111/mec.14887] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 01/09/2023]
Abstract
Root-associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.
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Affiliation(s)
- Kristina Schröter
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Martin Ehbrecht
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Peter Schall
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Christian Ammer
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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42
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Li P, Xue Y, Shi J, Pan A, Tang X, Ming F. The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties. MICROBIOME 2018; 6:184. [PMID: 30336777 PMCID: PMC6194802 DOI: 10.1186/s40168-018-0570-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/02/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear. RESULTS We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content. CONCLUSIONS In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.
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Affiliation(s)
- Peng Li
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Yong Xue
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jialiang Shi
- Dezhou Academy of Agricultural Sciences, Dezhou, 253000, China
| | - Aihu Pan
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Xueming Tang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Feng Ming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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43
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Chen Y, Yuan Z, Bi S, Wang X, Ye Y, Svenning JC. Macrofungal species distributions depend on habitat partitioning of topography, light, and vegetation in a temperate mountain forest. Sci Rep 2018; 8:13589. [PMID: 30206254 PMCID: PMC6134103 DOI: 10.1038/s41598-018-31795-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 08/28/2018] [Indexed: 11/09/2022] Open
Abstract
The habitat partitioning hypothesis provides a conceptual framework for explaining the maintenance of plant and animal diversity. Its central tenet assumes environmental conditions are spatially structured, and that this structure is reflected in species distributions through associations with different habitats. Studies confirming habitat partitioning effects have focused primarily on spatial distributions of plants and animals, with habitat partitioning hypothesis under explored for macrofungi. Here, we examined the sporocarps of macrofungi in a 5-ha forest dynamics plot in China. We used four different methods to define microhabitats for habitat partitioning analyses based on topography, understory light availability, plant community, or a combination of these factors, and analyzed the effect of microhabitat partitioning on epigeous macrofungal community. Our results showed that the characteristics of the macrofungal assemblages varied among the habitats. A total of 85 species examined were associated with one or more of the habitat types (85/125, 68%). The factors related to the sporocarp composition differed among the various microhabitats. Our findings suggest that different microhabitats favor occurrence of different macrofungal species, and sporocarps -environment relation varied among the different microhabitats at this temperate mountain forest locality. These findings shed new light to the biodiversity conservation in macrofungi in temperate deciduous broad-leaved forest and point to the potential importance of microhabitat partitioning for sporocarp formation.
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Affiliation(s)
- Yun Chen
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China.,Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Aarhus, Denmark
| | - Zhiliang Yuan
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China
| | - Shuai Bi
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China
| | - Xueying Wang
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China
| | - Yongzhong Ye
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China.
| | - Jens-Christian Svenning
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Aarhus, Denmark
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44
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Sun X, Zhou Y, Tan Y, Wu Z, Lu P, Zhang G, Yu F. Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:22106-22119. [PMID: 29802615 DOI: 10.1007/s11356-018-2244-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.
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Affiliation(s)
- Xiaoyan Sun
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China.
| | - Yanling Zhou
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Yinjing Tan
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Zhaoxiang Wu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Ping Lu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Guohua Zhang
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Faxin Yu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
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45
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Dhami MK, Hartwig T, Letten AD, Banf M, Fukami T. Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages. Mol Ecol 2018; 27:2067-2076. [PMID: 29446179 DOI: 10.1111/mec.14535] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 01/29/2023]
Abstract
Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M. reukaufii isolated from the floral nectar of hummingbird-pollinated shrub, Mimulus aurantiacus, along a 200-km coastline in California. Intraspecific genetic variation showed no detectable relationship with geographic distance, but could be grouped into three distinct lineages that correlated with metabolic ability and interspecific competitiveness. Despite ample evidence for strong competitive interactions within and among nectar yeasts, a full spectrum of the genotypic and phenotypic diversity observed across the 200-km coastline was represented even at a scale as small as 200 m. Further, more competitive strains were not necessarily more abundant. These results suggest that dispersal limitation and environmental sorting might not fully explain intraspecific diversity in this microbe and highlight the need to also consider other ecological factors such as trade-offs, source-sink dynamics and niche modification.
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Affiliation(s)
- Manpreet K Dhami
- Department of Biology, Stanford University, Stanford, CA, USA.,Landcare Research, Lincoln, New Zealand
| | - Thomas Hartwig
- Max Planck Institute for Plant Breeding Research, Köln, Germany.,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Andrew D Letten
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Biology, University of Canterbury, Christchurch, New Zealand
| | - Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Tadashi Fukami
- Department of Biology, Stanford University, Stanford, CA, USA
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