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Jiao G, Huang Y, Tang H, Chen Y, Zhou D, Yu D, Ma Z, Ni S. Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175305. [PMID: 39117200 DOI: 10.1016/j.scitotenv.2024.175305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.
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Affiliation(s)
- Ganghui Jiao
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; Yunnan Earthquake Agency, Yunnan 650000, China; Observation Station for Field Scientific Research of Crustal Tectonic Activity in Northwest Yunnan, Dali 671000, China
| | - Yi Huang
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China.
| | - Hua Tang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Ying Chen
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
| | - Dan Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Daming Yu
- Pangang Group Company Limited, Sichuan 617050, China
| | - Zhongjian Ma
- Pangang Group Company Limited, Sichuan 617050, China
| | - Shijun Ni
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
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Luo Z, Wu S, Shi W, Hu H, Lin T, Zhao K, Hou G, Fan C, Li X, Chen G. Combined effects of cadmium and simulated acid rain on soil microbial communities in the early cultivation of Populus beijingensis seedlings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116583. [PMID: 38878333 DOI: 10.1016/j.ecoenv.2024.116583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 05/02/2024] [Accepted: 06/09/2024] [Indexed: 06/25/2024]
Abstract
The combined cadmium (Cd) and acid rain pollution poses a significant threat to the global ecological environment. Previous studies on the combined adverse effects have predominantly focused on the aboveground plant physiological responses, with limited reports on the microbial response in the rhizosphere soil. This study employed Populus beijingensis seedlings and potting experiments to simulate the impacts of combined mild acid rain (pH=4.5, MA) or highly strong acid rain (pH=3.0, HA), and soil Cd pollution on the composition and diversity of microbial communities, as well as the physiochemical properties in the rhizosphere soil. The results showed that Cd decreased the content of inorganic nitrogen, resulting in an overall decrease of 49.10 % and 46.67 % in ammonium nitrogen and nitrate nitrogen, respectively. Conversely, acid rain was found to elevate the content of total potassium and soil organic carbon by 4.68 %-6.18 % and 8.64-19.16 %, respectively. Additionally, simulated acid rain was observed to decrease the pH level by 0.29-0.35, while Cd increased the pH level by 0.11. Moreover, Cd alone reduced the rhizosphere bacterial diversity, however, when combined with acid rain, regardless of its intensity, Cd was observed to increase the diversity. Fungal diversity was not influenced by the acid rain, but Cd increased fungal diversity to some extend under HA as observed in bacterial diversity. In addition, composition of the rhizosphere bacterial community was primarily influenced by the inorganic nitrogen components, while the fungal community was driven mainly by soil pH. Furthermore, "Metabolism" was emerged as the most significant bacterial function, which was markedly affected by the combined pollution, while Cd pollution led to a shift from symbiotroph to other trophic types for fungi. These findings suggest that simulated acid rain has a mitigating effect on the diversity of rhizosphere bacteria affected by Cd pollution, and also alters the trophic type of these microorganisms. This can be attributed to the acid rain-induced direct acidic environment, as well as the indirect changes in the availability or sources of carbon, nitrogen, or potassium.
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Affiliation(s)
- Zhili Luo
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Siying Wu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Weijin Shi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongling Hu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiantian Lin
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China and Centre of Invasion Biology, Institute of Biodiversity, Yunnan University, Kunming 650504, China
| | - Kuangji Zhao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Guirong Hou
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Chuan Fan
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xianwei Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Chen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China.
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Lei S, Wang X, Wang J, Zhang L, Liao L, Liu G, Wang G, Song Z, Zhang C. Effect of aridity on the β-diversity of alpine soil potential diazotrophs: insights into community assembly and co-occurrence patterns. mSystems 2024; 9:e0104223. [PMID: 38059620 PMCID: PMC10804954 DOI: 10.1128/msystems.01042-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/23/2023] [Indexed: 12/08/2023] Open
Abstract
Microbial diversity plays a vital role in the maintenance of ecosystem functions. However, the current understanding of mechanisms that shape microbial diversity along environmental gradients at broad spatial scales is relatively limited, especially for specific functional groups, such as potential diazotrophs. Here, we conducted an aridity-gradient transect survey from 60 sites across the Tibetan Plateau, the largest alpine ecosystem of the planet, to investigate the ecological processes (e.g., local species pools, community assembly processes, and co-occurrence patterns) that underlie the β-diversity of alpine soil potential diazotrophic communities. We found that aridity strongly and negatively affected the abundance, richness, and β-diversity of soil diazotrophs. Diazotrophs displayed a distance-decay pattern along the aridity gradient, with organisms living in lower aridity habitats having a stronger distance-decay pattern. Arid habitats had lower co-occurrence complexity, including the number of edges and vertices, the average degree, and the number of keystone taxa, as compared with humid habitats. Local species pools explained limited variations in potential diazotrophic β-diversity. In contrast, co-occurrence patterns and stochastic processes (e.g., dispersal limitation and ecological drift) played a significant role in regulating potential diazotrophic β-diversity. The relative importance of stochastic processes and co-occurrence patterns changed with increasing aridity, with stochastic processes weakening whereas that of co-occurrence patterns enhancing. The genera Geobacter and Paenibacillus were identified as keystone taxa of co-occurrence patterns that are associated with β-diversity. In summary, aridity affects the co-occurrence patterns and community assembly by regulating soil and vegetation characteristics and ultimately shapes the β-diversity of potential diazotrophs. These findings highlight the importance of co-occurrence patterns in structuring microbial diversity and advance the current understanding of mechanisms that drive belowground communities.IMPORTANCERecent studies have shown that community assembly processes and species pools are the main drivers of β-diversity in grassland microbial communities. However, co-occurrence patterns can also drive β-diversity formation by influencing the dispersal and migration of species, the importance of which has not been reported in previous studies. Assessing the impact of co-occurrence patterns on β-diversity is important for understanding the mechanisms of diversity formation. Our study highlights the influence of microbial co-occurrence patterns on β-diversity and combines the drivers of community β-diversity with drought variation, revealing that drought indirectly affects β-diversity by influencing diazotrophic co-occurrence patterns and community assembly.
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Affiliation(s)
- Shilong Lei
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangtao Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Jie Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Lu Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Lirong Liao
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guobin Liu
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoliang Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Science, Yangling, Shaanxi, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Zhang
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
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Wang M, Pu W, Wang S, Zeng X, Sui X, Wang X. pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China. Microorganisms 2023; 11:2950. [PMID: 38138094 PMCID: PMC10745975 DOI: 10.3390/microorganisms11122950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.
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Affiliation(s)
- Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Wenmiao Pu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Shenzheng Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, China;
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xin Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
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Chen X, Xu G, Xiong P, Peng J, Fang K, Wan S, Wang B, Gu F, Li J, Xiong H. Dry and wet seasonal variations of the sediment fungal community composition in the semi-arid region of the Dali River, Northwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:123694-123709. [PMID: 37993647 DOI: 10.1007/s11356-023-31042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there has been a lack of research on the seasonal variation of sediment microorganisms in the sediments of small river basins in typical semi-arid region. In this study, high-throughput DNA sequencing was used to investigate the fungal community and its influencing factors in the sediment of the Dali River in the dry and wet seasons. The results showed that there were obvious seasonal differences in fungal alpha diversity. The diversity and richness of fungi in the dry season were greater than that in the wet season, but the evenness of fungi in the dry season was lower than that in the wet season. In addition, Ascomycota and Basidiomycota were the most important phyla in the Dali River fungal community, but their distributions showed clear seasonal differences. In the dry season, the relative abundance of Ascomycota and Basidiomycota were 12.34-46.42% and 17.59-27.20%, respectively. In the wet season, the relative abundances of these two phyla were 24.33-36.56% and 5.75-12.26%, respectively. PICRUSt2 was used to predict the metabolic function of fungal community in the sediment, and it was found that at the first level, the proportion of biosynthesis in the dry season was higher than that in the wet season. The ecological network structure showed that the fungal community in the wet season was more complex and stable than that in the dry season. The characteristic fungi in the dry season sediment were chytrid fungi in the family Rhizophydiaceae and the order Rhizophydiales, whereas those in the wet season sediment were in the orders Eurotiales and Saccharomycetales. Canonical correspondence analysis (CCA) showed that the physicochemical properties of water and sediment together explained a greater proportion of the dry-season fungal community changes than of the wet-season changes. In the dry season, temperature and ammonia nitrogen in the water were the main factors affecting the change of fungal community, whereas in the wet season, total nitrogen concentration of the water, electrical conductivity, total organic carbon and available phosphorus of the sediment, pH, and temperature were the main factors affecting the changes in fungal community composition. The results of this study enhanced our understanding of microbial communities in semi-arid river ecosystems, and highlight the importance of the management and protection in river ecosystems.
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Affiliation(s)
- Xin Chen
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Guoce Xu
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China.
| | - Ping Xiong
- Shaanxi Forestry Survey and Planning Institute, Xi'an, 710082, Shaanxi, China
| | - Jianbo Peng
- Shaanxi Forestry Survey and Planning Institute, Xi'an, 710082, Shaanxi, China
| | - Kang Fang
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Shun Wan
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Bin Wang
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Fengyou Gu
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Jing Li
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Haijing Xiong
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
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He P, Zhang Y, Shen Q, Ling N, Nan Z. Microbial carbon use efficiency in different ecosystems: A meta-analysis based on a biogeochemical equilibrium model. GLOBAL CHANGE BIOLOGY 2023; 29:4758-4774. [PMID: 37431700 DOI: 10.1111/gcb.16861] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/20/2023] [Accepted: 05/30/2023] [Indexed: 07/12/2023]
Abstract
Soil microbial carbon use efficiency (CUE) is a crucial parameter that can be used to evaluate the partitioning of soil carbon (C) between microbial growth and respiration. However, general patterns of microbial CUE among terrestrial ecosystems (e.g., farmland, grassland, and forest) remain controversial. To address this knowledge gap, data from 41 study sites (n = 197 soil samples) including 58 farmlands, 95 forests, and 44 grasslands were collected and analyzed to estimate microbial CUEs using a biogeochemical equilibrium model. We also evaluated the metabolic limitations of microbial growth using an enzyme vector model and the drivers of CUE across different ecosystems. The CUEs obtained from soils of farmland, forest, and grassland ecosystems were significantly different with means of 0.39, 0.33, and 0.42, respectively, illustrating that grassland soils exhibited higher microbial C sequestration potentials (p < .05). Microbial metabolic limitations were also distinct in these ecosystems, and carbon limitation was dominant exhibiting strong negative effects on CUE. Exoenzyme stoichiometry played a greater role in impacting CUE values than soil elemental stoichiometry within each ecosystem. Specifically, soil exoenzymatic ratios of C:phosphorus (P) acquisition activities (EEAC:P ) and the exoenzymatic ratio of C:nitrogen (N) acquisition activities (EEAC:N ) imparted strong negative effects on soil microbial CUE in grassland and forest ecosystems, respectively. But in farmland soils, EEAC:P exhibited greater positive effects, showing that resource constraints could regulate microbial resource allocation with discriminating patterns across terrestrial ecosystems. Furthermore, mean annual temperature (MAT) rather than mean annual precipitation (MAP) was a critical climate factor affecting CUE, and soil pH as a major factor remained positive to drive the changes in microbial CUE within ecosystems. This research illustrates a conceptual framework of microbial CUEs in terrestrial ecosystems and provides the theoretical evidence to improve soil microbial C sequestration capacity in response to global change.
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Affiliation(s)
- Peng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuntao Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Hou G, Wazir ZG, Liu J, Wang G, Rong F, Xu Y, Li M, Liu K, Liu A, Liu H, Wang F. Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils. Front Microbiol 2023; 14:1153199. [PMID: 37256053 PMCID: PMC10225667 DOI: 10.3389/fmicb.2023.1153199] [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: 01/29/2023] [Accepted: 03/10/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils. Methods In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences. Results The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type. Discussion Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.
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Affiliation(s)
- Guoqin Hou
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Zafran Gul Wazir
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Jing Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Guizhen Wang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Fangxu Rong
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Yuzhi Xu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Mingyue Li
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Kai Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Aijv Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Fayuan Wang
- School of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China
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8
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Tian Q, Jiang Q, Huang L, Li D, Lin Q, Tang Z, Liu F. Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient. MICROBIAL ECOLOGY 2023; 85:628-641. [PMID: 35083529 DOI: 10.1007/s00248-021-01949-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023]
Abstract
Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.
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Affiliation(s)
- Qiuxiang Tian
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qinghu Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lin Huang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, China
| | - Qiaoling Lin
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyao Tang
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes, Peking University, Beijing, China
| | - Feng Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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9
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Zhang ZY, Qiang FF, Liu GQ, Liu CH, Ai N. Distribution characteristics of soil microbial communities and their responses to environmental factors in the sea buckthorn forest in the water-wind erosion crisscross region. Front Microbiol 2023; 13:1098952. [PMID: 36704571 PMCID: PMC9871601 DOI: 10.3389/fmicb.2022.1098952] [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: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Soil microorganisms are an important part of forest ecosystems, and their community structure and ecological adaptations are important for explaining soil material cycles in the fragile ecological areas. We used high-throughput sequencing technology to examine the species composition and diversity of soil bacterial and fungal communities in sea buckthorn forests at five sites in the water-wind erosion crisscross in northern Shaanxi (about 400 km long). The results are described as follows: (1) The soil bacterial community of the sea buckthorn forest in the study region was mainly dominated by Actinobacteria, Proteobacteria, and Acidobacteria, and the fungi community was mainly dominated by Ascomycota. (2) The coefficient of variation of alpha diversity of microbial communities was higher in the 0-10 cm soil layer than in the 10-20 cm soil layer. (3) Soil electrical conductivity (36.1%), available phosphorous (AP) (21.0%), available potassium (16.2%), total nitrogen (12.7%), and the meteorological factors average annual maximum temperature (33.3%) and average annual temperature (27.1%) were identified as the main drivers of structural changes in the bacterial community. Available potassium (39.4%), soil organic carbon (21.4%), available nitrogen (AN) (13.8%), and the meteorological factors average annual maximum wind speed (38.0%) and average annual temperature (26.8%) were identified as the main drivers of structural changes in the fungal community. The explanation rate of soil factors on changes in bacterial and fungal communities was 26.6 and 12.0%, respectively, whereas that of meteorological factors on changes in bacterial and fungal communities was 1.22 and 1.17%, respectively. The combined explanation rate of environmental factors (soil and meteorological factors) on bacterial and fungal communities was 72.2 and 86.6%, respectively. The results of the study offer valuable insights into the diversity of soil microbial communities in the water-wind erosion crisscross region and the mechanisms underlying their interaction with environmental factors.
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Affiliation(s)
- Zhi-Yong Zhang
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Fang-Fang Qiang
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Guang-Quan Liu
- China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Chang-Hai Liu
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Ning Ai
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China,China Institute of Water Resources and Hydropower Research, Beijing, China,*Correspondence: Ning Ai, ✉
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10
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Ge W, Ren Y, Dong C, Shao Q, Bai Y, He Z, Yao T, Zhang Y, Zhu G, Deshmukh SK, Han Y. New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria. Front Microbiol 2023; 14:1074468. [PMID: 36876069 PMCID: PMC9978014 DOI: 10.3389/fmicb.2023.1074468] [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: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.
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Affiliation(s)
- Wei Ge
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yulian Ren
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yanmin Bai
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Zhaoying He
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Ting Yao
- Analysis and Test Center, Huangshan University, Huangshan, China
| | - Yanwei Zhang
- School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, China
| | - Guosheng Zhu
- Guizhou Key Laboratory of Edible Fungi Breeding, Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Sunil Kumar Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
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11
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Liao H, Li C, Ai S, Li X, Ai X, Ai Y. A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116672. [PMID: 36343402 DOI: 10.1016/j.jenvman.2022.116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH4 fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N2O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.
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Affiliation(s)
- Haijun Liao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China; CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Chaonan Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Shenghao Ai
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Xiaoyan Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
| | - Yingwei Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
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12
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Liu J, Gul Wazir Z, Hou GQ, Wang GZ, Rong FX, Xu YZ, Liu K, Li MY, Liu AJ, Liu HL. The dependent correlation between soil multifunctionality and bacterial community across different farmland soils. Front Microbiol 2023; 14:1144823. [PMID: 37125206 PMCID: PMC10132505 DOI: 10.3389/fmicb.2023.1144823] [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: 01/15/2023] [Accepted: 03/03/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Microorganisms play a critical role in soil biogeochemical cycles, but it is still debated whether they influence soil biogeochemical processes through community composition and diversity or not. This study aims to investigate variation in bacterial community structure across different soils and its correlation to soil multifunctionality. Soil samples were collected from five typical farmland zones along distinct climatic gradients in China. Methods The high-throughput sequencing (Illumina MiSeq) of 16S rRNA genes was employed to analyze bacterial community composition in each soil sample. Multivariate analysis was used to determine the difference in soil properties, microbial community and functioning, and their interactions. Results Cluster and discrimination analysis indicated that bacterial community composition was similar in five tested soil samples, but bacterial richness combined with soil enzyme activities and potential nitrification rate (PNR) contributed most to the differentiations of soil samples. Mantel test analysis revealed that bacterial community composition and richness were more significantly shaped by soil nutrient conditions and edaphic variables than bacterial diversity. As for soil multifunctionality, soil microbial community level physiological profiles were little affected by abiotic and biotic factors, while soil enzymes and PNR were also significantly related to bacterial community composition and richness, in addition to soil N and P availability. Conclusion Cumulatively, soil enzymes' activities and PNR were greatly dependent on bacterial community composition and richness not diversity, which in turn were greatly modified by soil N and P availability. Therefore, in the future it should be considered for the role of fertilization in the modification of bacterial community and the consequent control of nutrient cycling in soil.
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Affiliation(s)
- Jing Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Zafran Gul Wazir
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Guo-Qin Hou
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Gui-Zhen Wang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Fang-Xu Rong
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Yu-Zhi Xu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Kai Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Ming-Yue Li
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Ai-Ju Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
- *Correspondence: Ai-Ju Liu,
| | - Hong-Liang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
- Hong-Liang Liu,
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13
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Xu M, Su S, Zhang Z, Jiang S, Zhang J, Xu Y, Hu X. Two sides of the same coin: Meta-analysis uncovered the potential benefits and risks of traditional fermented foods at a large geographical scale. Front Microbiol 2022; 13:1045096. [PMID: 36406420 PMCID: PMC9668881 DOI: 10.3389/fmicb.2022.1045096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Traditional fermented foods, which are well-known microbial resources, are also bright national cultural inheritances. Recently, traditional fermented foods have received great attention due to their potential probiotic properties. Based on shotgun metagenomic sequencing data, we analyzed the microbial diversity, taxonomic composition, metabolic pathways, and the potential benefits and risks of fermented foods through a meta-analysis including 179 selected samples, as well as our own sequencing data collected from Hainan Province, China. As expected, raw materials, regions (differentiated by climatic zones), and substrates were the main driving forces for the microbial diversity and taxonomic composition of traditional fermented foods. Interestingly, a higher content of beneficial bacteria but a low biomass of opportunistic pathogens and antibiotic resistance genes were observed in the fermented dairy products, indicating that fermented dairy products are the most beneficial and reliable fermented foods. In contrast, despite the high microbial diversity found in the fermented soy products, their consumption risk was still high due to the enrichment of opportunistic pathogens and transferable antibiotic resistance genes. Overall, we provided the most comprehensive assessment of the microbiome of fermented food to date and generated a new view of its potential benefits and risks related to human health.
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Affiliation(s)
- Meng Xu
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Shunyong Su
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Zeng Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Shuaiming Jiang
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, China
| | - Yanqing Xu
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
- *Correspondence: Yanqing Xu,
| | - Xiaosong Hu
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Xiaosong Hu,
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14
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Kenya E, Kinyanjui G, Kipnyargis A, Kinyua F, Mwangi M, Khamis F, Mwirichia R. Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya. Heliyon 2022; 8:e11577. [PMID: 36411924 PMCID: PMC9674510 DOI: 10.1016/j.heliyon.2022.e11577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/14/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.
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Affiliation(s)
- Eucharia Kenya
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Grace Kinyanjui
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Alex Kipnyargis
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Franklin Kinyua
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Mary Mwangi
- Department of Biochemistry and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Fathiya Khamis
- International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi, Kenya
| | - Romano Mwirichia
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
- Corresponding author.
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15
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Wang X, Li Y, Yan Z, Hao Y, Kang E, Zhang X, Li M, Zhang K, Yan L, Yang A, Niu Y, Kang X. The divergent vertical pattern and assembly of soil bacterial and fungal communities in response to short-term warming in an alpine peatland. FRONTIERS IN PLANT SCIENCE 2022; 13:986034. [PMID: 36160969 PMCID: PMC9493461 DOI: 10.3389/fpls.2022.986034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Soil microbial communities are crucial in ecosystem-level decomposition and nutrient cycling processes and are sensitive to climate change in peatlands. However, the response of the vertical distribution of microbial communities to warming remains unclear in the alpine peatland. In this study, we examined the effects of warming on the vertical pattern and assembly of soil bacterial and fungal communities across three soil layers (0-10, 10-20, and 20-30 cm) in the Zoige alpine peatland under a warming treatment. Our results showed that short-term warming had no significant effects on the alpha diversity of either the bacterial or the fungal community. Although the bacterial community in the lower layers became more similar as soil temperature increased, the difference in the vertical structure of the bacterial community among different treatments was not significant. In contrast, the vertical structure of the fungal community was significantly affected by warming. The main ecological process driving the vertical assembly of the bacterial community was the niche-based process in all treatments, while soil carbon and nutrients were the main driving factors. The vertical structure of the fungal community was driven by a dispersal-based process in control plots, while the niche and dispersal processes jointly regulated the fungal communities in the warming plots. Plant biomass was significantly related to the vertical structure of the fungal community under the warming treatments. The variation in pH was significantly correlated with the assembly of the bacterial community, while soil water content, microbial biomass carbon/microbial biomass phosphorous (MBC/MBP), and microbial biomass nitrogen/ microbial biomass phosphorous (MBN/MBP) were significantly correlated with the assembly of the fungal community. These results indicate that the vertical structure and assembly of the soil bacterial and fungal communities responded differently to warming and could provide a potential mechanism of microbial community assembly in the alpine peatland in response to warming.
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Affiliation(s)
- Xiaodong Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Enze Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Yuechuan Niu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
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16
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Jia M, Sun X, Chen M, Liu S, Zhou J, Peng X. Deciphering the microbial diversity associated with healthy and wilted Paeonia suffruticosa rhizosphere soil. Front Microbiol 2022; 13:967601. [PMID: 36060757 PMCID: PMC9432862 DOI: 10.3389/fmicb.2022.967601] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Plant health is closely related to the soil, where microorganisms play a critical and unique role. For instance, Paeonia suffruticosa is an emerging woody oil crop in China with attractive development and utilization prospects. However, black root rot causes wilting of the aboveground plant parts, which significantly affected its seed yield and quality. Studies found that soil microorganisms are critical in maintaining plant health, but how changes in the soil microbial communities affect the healthy and diseased oil peony is unclear. Therefore, our present study used high throughput sequencing and BIOLOG to analyze the rhizosphere soil microbial communities of healthy and diseased oil peonies. Our results revealed that the physical and chemical properties of the soil of the diseased plants had changed, with the ability to metabolize the carbon source being enhanced. Moreover, our research highlighted that the oil peony-infecting fungal pathogenic genus (Fusarium, Cylindrocarpon, and Neocosmospora) was closely associated with oil peony yield reduction and disease aggravation. Further network analysis demonstrated that the bacterial and fungal networks of the diseased plants were more complex than those of the healthy plants. Finally, the inter-kingdom network among the diseased plants further indicated that the lesions destroyed the network and increased the intraspecific correlation between the fungal groups.
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Affiliation(s)
- Manman Jia
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xin Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Man Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shuang Liu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinxing Zhou
- Jianshui Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Xiawei Peng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
- *Correspondence: Xiawei Peng, ,
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17
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Wang Y, Tian S, Wu N, Liu W, Li L, Wang X. Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases. PLANT DISEASE 2022; 106:1882-1889. [PMID: 35021874 DOI: 10.1094/pdis-09-21-1974-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.
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Affiliation(s)
- Yajiao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China
| | - Shuping Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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18
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Lyu Q, Luo Y, Dong Y, Xiang Y, Zhao K, Chen G, Chen Y, Fan C, Li X. Effects of Forest Gaps on the Structure and Diversity of Soil Bacterial Communities in Weeping Cypress Forest Plantations. Front Microbiol 2022; 13:882949. [PMID: 35651493 PMCID: PMC9149315 DOI: 10.3389/fmicb.2022.882949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The decline in forest ecological function caused by pure forest plantations planted in the Yangtze River basin is becoming increasingly serious. To investigate this problem, we selected the local low-efficiency weeping cypress plantations for forest gap transformation. Three forest gap sizes, specifically large, medium, and small gaps, were established, and the effects of gap sizes on soil bacterial community structure and diversity in winter and summer were studied compared to no gaps (CK; control). Compared to CK, forest gaps had a significant effect on soil organic carbon (SOC) and soil total nitrogen (TN), and the highest values of SOC and soil TN under two seasons occurred in large forest gaps. The interactions of forest gap sizes and seasons had significant effects on pH, SOC, TN, and alpha diversity indices, including Simpson, Chao1, and ACE indices. Compared to winter, forest gaps significantly increased the soil bacterial community diversity indices in summer. Forest gap sizes significantly affected the composition of the bacterial community, but the composition of the dominant bacteria at the phyla and genera levels was similar. Linear discriminant effect size (LEfSe) analysis showed that there were 32 indicator bacterial species in two seasons. Co-occurrence network analysis revealed that the relationship of the soil bacterial community at the phyla level was complex, and there was a significant positive correlation among bacterial species. Soil bulk density (BD) and soil moisture (SM) significantly affected the soil bacterial alpha diversity indices. The composition of the dominant bacteria at the phyla level was significantly affected by soil microbial carbon (MBC), whereas the composition of dominant bacteria at the genera level was affected by soil hydrolysable nitrogen (AN) and the carbon/nitrogen (C/N) ratio. In this study, compared to the other forest gaps, large forest gaps were more conducive to the accumulation of soil nutrients, thus improving the structure of the soil bacterial community. Importantly, changes in the soil bacterial community structure due to gap formation may have profound effects on soil biogeochemical processes in weeping cypress forest plantations.
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Affiliation(s)
- Qian Lyu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yan Luo
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yuliang Dong
- Institute of Forest Genetics and Breeding, Sichuan Academy of Forestry, Chengdu, China
| | - Yongqi Xiang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Kuangji Zhao
- College of Forestry, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China.,Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Gang Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China.,Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yuqin Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China.,Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chuan Fan
- College of Forestry, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China.,Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianwei Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China.,Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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19
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Zou Z, Yuan K, Ming L, Li Z, Yang Y, Yang R, Cheng W, Liu H, Jiang J, Luan T, Chen B. Changes in Alpine Soil Bacterial Communities With Altitude and Slopes at Mount Shergyla, Tibetan Plateau: Diversity, Structure, and Influencing Factors. Front Microbiol 2022; 13:839499. [PMID: 35602088 PMCID: PMC9114662 DOI: 10.3389/fmicb.2022.839499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/14/2022] [Indexed: 01/10/2023] Open
Abstract
The alpine ecosystem as one of the most representative terrestrial ecosystems has been highly concerned due to its susceptibility to anthropogenic impacts and climatic changes. However, the distribution pattern of alpine soil bacterial communities and related deterministic factors still remain to be explored. In this study, soils were collected from different altitudes and slope aspects of the Mount (Mt.) Shergyla, Tibetan Plateau, and were analyzed using 16S rRNA gene-based bioinformatics approaches. Acidobacteriota and Proteobacteria were identified consistently as the two predominant phyla in all soil samples, accounting for approximately 74% of the bacterial community. The alpha diversity of the soil bacterial community generally increased as the vegetation changed with the elevated altitude, but no significant differences in alpha diversity were observed between the two slopes. Beta diversity analysis of bacterial community showed that soil samples from the north slope were always differentiated obviously from the paired samples at the south slope with the same altitude. The whole network constituted by soil bacterial genera at the Mt. Shergyla was parsed into eight modules, and Elev-16S-573, Sericytochromatia, KD4-96, TK10, Pedomicrobium, and IMCC26256 genera were identified as the “hubs” in the largest module. The distance-based redundancy analysis (db-RDA) demonstrated that variations in soil bacterial community thereof with the altitude and slope aspects at the Mt. Shergyla were closely associated with environmental variables such as soil pH, soil water content, metal concentrations, etc. Our results suggest that environmental variables could serve as the deterministic factors for shaping the spatial pattern of soil bacterial community in the alpine ecosystems.
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Affiliation(s)
- Zehao Zou
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ke Yuan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lili Ming
- Technical Center of Gongbei Customs District, Zhuhai, China
| | - Zhaohong Li
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Yang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ruiqiang Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Weibin Cheng
- Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Hongtao Liu
- Instrumental Analysis and Research Center, Sun Yat-sen University, Guangzhou, China
| | - Jie Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tiangang Luan
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China.,State Key Laboratory of Bioresource and Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
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20
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Huang A, Wu T, Wu X, Zhang B, Shen Y, Wang S, Song W, Ruan H. Analysis of Internal and External Microorganism Community of Wild Cicada Flowers and Identification of the Predominant Cordyceps cicadae Fungus. Front Microbiol 2021; 12:752791. [PMID: 34899639 PMCID: PMC8656164 DOI: 10.3389/fmicb.2021.752791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
The parasitoid fungus Cordyceps cicadae, whose fruiting bodies are known in China as “chan hua,” literally “cicada flower,” has been used as a traditional Chinese medicinal ingredient for centuries. However, systematic disclosure of the vital factors responsible for the formation of wild cicada flower is limited. Here, we determined the physicochemical properties of soil and simultaneously analyzed the diversities and the structures of microbial community inhabiting the coremia, sclerotia, and soil around wild cicada flowers through high-throughput sequencing. Our results indicated that cicada flower more preferentially occurred in acidic soil (pH 5.9) with abundant moisture content (MC), total nitrogen (TN), and organic matter (OM). The dominant fungal genera in soil mainly included Isaria, f__Clavariaceae_Unclassified, Umbelopsis, f__Chaetomiaceae_Unclassified, Mortierella, f__Sordariaceae_Unclassified, and Arcopilus. Among them, C. cicadae was the only fungus that was massively detected in both the coremia and sclerotia with abundance of 83.5 and 53.6%, respectively. Based on this, a C. cicadae strain named AH10-4 with excellent adenosine- and N6-(2-hydroxyethyl)-adenosine (HEA)-producing capability was successfully isolated. However, to the aspect of bacteria, Burkholderia–Caballeronia–Paraburkholderia, Bacillus, Acidibacter, f__Xanthobacteraceae_Unclassified, and Candidatus_Solibacter were the dominant genera in soil. Pedobacter, f__Enterobacteriaceae_Unclassified, Pandoraea, Achromobacter, Stenotrophomonas, Burkholderia–Caballeronia–Paraburkholderia, and Chitinophaga were the dominant genera in the coremia and sclerotia. Notably, Burkholderia–Caballeronia–Paraburkholderia was the shared bacteria among them with high abundance of 3.1, 11.4, and 5.2% in the sclerotia, coremia, and soil, respectively. However, the possible role of these bacteria to the occurrence of cicada flower has been unclear to our knowledge. By analyzing the correlation between physicochemical properties and microbial community of soil, we found that MC, Fe, and Zn were significantly negatively correlated with soil Isaria and that Cu was significantly negatively correlated with most dominant soil bacterial genera. But Mg was significantly positively correlated with most dominant taxa. This study provides new insight into the formation mechanisms of cicada flower and may contribute to the large-scale cultivation of cicada flowers.
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Affiliation(s)
- Ailin Huang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Tao Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Xiuyun Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Biao Zhang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Yuanyuan Shen
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Wenjun Song
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Haihua Ruan
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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21
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Zahid MS, Li D, Javed HU, Sabir IA, Wang L, Jiu S, Song S, Ma C, Wang D, Zhang C, Zhou X, Xu W, Wang S. Comparative fungal diversity and dynamics in plant compartments at different developmental stages under root-zone restricted grapevines. BMC Microbiol 2021; 21:317. [PMID: 34784893 PMCID: PMC8594160 DOI: 10.1186/s12866-021-02376-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The root-zone restriction cultivation technique is used to achieve superior fruit quality at the cost of limited vegetative and enhanced reproductive development of grapevines. Fungal interactions and diversity in grapevines are well established; however, our knowledge about fungal diversity under the root-zone restriction technique is still unexplored. To provide insights into the role of mycobiota in the regulation of growth and fruit quality of grapevine under root-zone restriction, DNA from rhizosphere and plant compartments, including white roots (new roots), leaves, flowers, and berries of root-zone restricted (treatment) and conventionally grown plants (control), was extracted at three growth stages (full bloom, veraison, and maturity). RESULTS Diversity analysis based on the ITS1 region was performed using QIIME2. We observed that the root-zone restriction technique primarily affected the fungal communities of the soil and plant compartments at different growth stages. Interestingly, Fusarium, Ilyonectria, Cladosporium and Aspergillus spp observed in the rhizosphere overlapped with the phyllosphere at all phenological stages, having distinctive abundance in grapevine habitats. Peak richness and diversity were observed in the rhizosphere at the full bloom stage of control plants, white roots at the veraison stage of treatment, leaves at the maturity stage of treatment, flowers at the full bloom stage and berries at the veraison stage of control plants. Except for white roots, the diversity of soil and plant compartments of treated plants tended to increase until maturity. At the maturity stage of the treated and control plants, the abundance of Aspergillus spp. was 25.99 and 29.48%, respectively. Moreover, the total soluble sugar content of berries was 19.03 obrix and 16 obrix in treated and control plants, respectively, at the maturity stage. CONCLUSIONS This is the first elucidative study targeting the fungal diversity of conventional and root-restricted cultivation techniques in a single vineyard. Species richness and diversity are affected by stressful cultivation known as root zone restriction. There is an association between the abundance of Aspergillus spp. and fruit quality because despite causing stress to the grapevine, superior quality of fruit is retrieved in root-zone restricted plants.
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Affiliation(s)
- Muhammad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dongmei Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hafiz Umer Javed
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dapeng Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xuhui Zhou
- Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241 China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
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22
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Responses of the Soil Microbial Community to Salinity Stress in Maize Fields. BIOLOGY 2021; 10:biology10111114. [PMID: 34827107 PMCID: PMC8614889 DOI: 10.3390/biology10111114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 01/13/2023]
Abstract
To investigate the diversity and structure of soil bacterial and fungal communities in saline soils, soil samples with three increasing salinity levels (S1, S2 and S3) were collected from a maize field in Yanqi, Xinjiang Province, China. The results showed that the K+, Na+, Ca2+ and Mg2+ values in the bulk soil were higher than those in the rhizosphere soil, with significant differences in S2 and S3 (p < 0.05). The enzyme activities of alkaline phosphatase (ALP), invertase, urease and catalase (CAT) were lower in the bulk soil than those in the rhizosphere. Principal coordinate analysis (PCoA) demonstrated that the soil microbial community structure exhibited significant differences between different salinized soils (p < 0.001). Data implied that the fungi were more susceptible to salinity stress than the bacteria based on the Shannon and Chao1 indexes. Mantel tests identified Ca2+, available phosphorus (AP), saturated electrical conductivity (ECe) and available kalium (AK) as the dominant environmental factors correlated with bacterial community structures (p < 0.001); and AP, urease, Ca2+ and ECe as the dominant factors correlated with fungal community structures (p < 0.001). The relative abundances of Firmicutes and Bacteroidetes showed positive correlations with the salinity gradient. Our findings regarding the bacteria having positive correlations with the level of salinization might be a useful biological indicator of microorganisms in saline soils.
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23
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Wang J, He N, Wang Y, Li J, Li M. Divergent drivers determine soil bacterial β-diversity of forest and grassland ecosystems in Northwest China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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24
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Tian Q, Jiang Y, Tang Y, Wu Y, Tang Z, Liu F. Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient. Front Microbiol 2021; 12:646124. [PMID: 34394018 PMCID: PMC8363232 DOI: 10.3389/fmicb.2021.646124] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Elevational gradients strongly affect the spatial distribution and structure of soil bacterial communities. However, our understanding of the effects and determining factors is still limited, especially in the deep soil layer. Here, we investigated the diversity and composition of soil bacterial communities in different soil layers along a 1,500-m elevational gradient in the Taibai Mountain. The variables associated with climate conditions, plant communities, and soil properties were analyzed to assess their contributions to the variations in bacterial communities. Soil bacterial richness and α-diversity showed a hump-shaped trend with elevation in both surface and deep layers. In the surface layer, pH was the main factor driving the elevational pattern in bacterial diversity, while in the deep layer, pH and soil carbon (C) availability were the two main predictors. Bacterial community composition differed significantly along the elevational gradient in all soil layers. In the surface layer, Acidobacteria, Delta-proteobacteria, and Planctomycetes were significantly more abundant in the lower elevation sites than in the higher elevation sites; and Gemmatimonadetes, Chloroflexi, and Beta-proteobacteria were more abundant in the higher elevation sites. In the deep layer, AD3 was most abundant in the highest elevation site. The elevational pattern of community composition co-varied with mean annual temperature, mean annual precipitation, diversity and basal area of trees, pH, soil C availability, and soil C fractions. Statistical results showed that pH was the main driver of the elevational pattern of the bacterial community composition in the surface soil layer, while soil C fractions contributed more to the variance of the bacterial composition in the deep soil layer. These results indicated that changes in soil bacterial communities along the elevational gradient were driven by soil properties in both surface and deep soil layers, which are critical for predicting ecosystem functions under future climate change scenarios.
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Affiliation(s)
- Qiuxiang Tian
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ying Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yanan Tang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyao Tang
- Key Laboratory for Earth Surface Processes, Department of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Feng Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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25
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Alown F, Alsharidah A, Shamsah S. Genotypic characterization of soil bacteria in the Umm Al-Namil Island, Kuwait. Saudi J Biol Sci 2021; 28:3847-3854. [PMID: 34220239 PMCID: PMC8241613 DOI: 10.1016/j.sjbs.2021.03.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/13/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Microflora is an integral part of soil ecosystem, in which bacteria are the largest group of soil microbes. This is a pioneer study for establishing baseline data on the diversity of soil bacteria among different regions in Kuwait. The aim is to understand biodiversity in different settings, how bacteria adapt to different niches in the environment as well as in different hosts. The identification of bacterial 16S rRNA molecules from environmental soil samples was investigated. Genomic Deoxyribonucleic acid DNA was extracted from 25 soil samples derived from five different test regions in the Umm Al-Namil Island, Kuwait. After amplification of bacterial 16S rRNA molecules by the Polymerase chain reaction PCR, the products were characterized and complex band patterns were obtained, indicating high bacterial diversity. A sample of the 16 s rRNA amplicons were sequenced in order to identify the species. The spatial distribution of bacterial taxa in the different soil samples was homogeneous, suggesting a stable and widespread community. Forty-nine isolates from Umm Al-Namil island were identified by comparative analysis of partial 16S rRNA gene sequences. Phylogenetic analysis was carried out in order to study the connection between the isolates to identify species. A large proportion of these isolates represent correspond to known or novel species within the Pseudomonus and Bacillus genera, which are common soil bacteria. Our results provided a reference for future studies to facilitate bacterial identification and ecological research in Kuwait.
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Affiliation(s)
- Fadaa Alown
- Public Authority for Training and Applied Education (PAAET), Department of Science-College of Basic Education, Kuwait
| | - Ahlam Alsharidah
- Public Authority for Training and Applied Education (PAAET), Department of Science-College of Basic Education, Kuwait
| | - Sara Shamsah
- Kuwait University, Department of Medical Laboratory Sciences, Kuwait
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26
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Wang C, Qu L, Yang L, Liu D, Morrissey E, Miao R, Liu Z, Wang Q, Fang Y, Bai E. Large-scale importance of microbial carbon use efficiency and necromass to soil organic carbon. GLOBAL CHANGE BIOLOGY 2021; 27:2039-2048. [PMID: 33559308 DOI: 10.1111/gcb.15550] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/21/2021] [Accepted: 01/30/2021] [Indexed: 05/18/2023]
Abstract
Optimal methods for incorporating soil microbial mechanisms of carbon (C) cycling into Earth system models (ESMs) are still under debate. Specifically, whether soil microbial physiology parameters and residual materials are important to soil organic C (SOC) content is still unclear. Here, we explored the effects of biotic and abiotic factors on SOC content based on a survey of soils from 16 locations along a ~4000 km forest transect in eastern China, spanning a wide range of climate, soil conditions, and microbial communities. We found that SOC was highly correlated with soil microbial biomass C (MBC) and amino sugar (AS) concentration, an index of microbial necromass. Microbial C use efficiency (CUE) was significantly related to the variations in SOC along this national-scale transect. Furthermore, the effect of climatic and edaphic factors on SOC was mainly via their regulation on microbial physiological properties (CUE and MBC). We also found that regression models on explanation of SOC variations with microbial physiological parameters and AS performed better than the models without them. Our results provide the empirical linkages among climate, microbial characteristics, and SOC content at large scale and confirm the necessity of incorporating microbial biomass and necromass pools in ESMs under global change scenarios.
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Affiliation(s)
- Chao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Lingrui Qu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liuming Yang
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Dongwei Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ember Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Renhui Miao
- International Joint Research Laboratory for Global Change Ecology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Ziping Liu
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
| | - Qingkui Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yunting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, China
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Dickey JR, Swenie RA, Turner SC, Winfrey CC, Yaffar D, Padukone A, Beals KK, Sheldon KS, Kivlin SN. The Utility of Macroecological Rules for Microbial Biogeography. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.633155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.
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A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils. Int J Mol Sci 2021; 22:ijms22073438. [PMID: 33810508 PMCID: PMC8036350 DOI: 10.3390/ijms22073438] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.
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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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Zeng Q, An S. Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau. Microorganisms 2021; 9:139. [PMID: 33435426 PMCID: PMC7827256 DOI: 10.3390/microorganisms9010139] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 01/06/2023] Open
Abstract
High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.
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Affiliation(s)
- Quanchao Zeng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
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Xia Z, Yang J, Sang C, Wang X, Sun L, Jiang P, Wang C, Bai E. Phosphorus Reduces Negative Effects of Nitrogen Addition on Soil Microbial Communities and Functions. Microorganisms 2020; 8:E1828. [PMID: 33233486 PMCID: PMC7699539 DOI: 10.3390/microorganisms8111828] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 01/21/2023] Open
Abstract
Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and P additions on soil bacterial and fungal communities and predicted their functional compositions in a temperate forest. We found that N addition significantly decreased soil bacterial diversity in the organic (O) horizon, but tended to increase bacterial diversity in the mineral (A) horizon soil. P addition alone did not significantly change soil bacterial diversity but mitigated the negative effect of N addition on bacterial diversity in the O horizon. Neither N addition nor P addition significantly influenced soil fungal diversity. Changes in soil microbial community composition under N and P additions were mainly due to the shifts in soil pH and NO3- contents. N addition can affect bacterial functional potentials, such as ureolysis, N fixation, respiration, decomposition of organic matter processes, and fungal guilds, such as pathogen, saprotroph, and mycorrhizal fungi, by which more C probably was lost in O horizon soil under increased N deposition. However, P addition can alleviate or switch the effects of increased N deposition on the microbial functional potentials in O horizon soil and may even be a benefit for more C sequestration in A horizon soil. Our results highlight the different responses of microorganisms to N and P additions between O and A horizons and provides an important insight for predicting the changes in forest C storage status under increasing N deposition in the future.
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Affiliation(s)
- Zongwei Xia
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
| | - Jingyi Yang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changpeng Sang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifei Sun
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
| | - Ping Jiang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
| | - Chao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
| | - Edith Bai
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (Z.X.); (J.Y.); (C.S.); (X.W.); (L.S.); (P.J.); (E.B.)
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
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Zi H, Jiang Y, Cheng X, Li W, Huang X. Change of rhizospheric bacterial community of the ancient wild tea along elevational gradients in Ailao mountain, China. Sci Rep 2020; 10:9203. [PMID: 32514187 PMCID: PMC7280300 DOI: 10.1038/s41598-020-66173-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/11/2020] [Indexed: 11/10/2022] Open
Abstract
The rhizospheric microbial community is one of the major environmental factors affecting the distribution and fitness of plants. Ancient wild tea plants are rare genetic resource distributed in Southwest China. In this study, we investigated that rhizospheric bacterial communities of ancient wild tea plants along the elevational gradients (2050, 2200, 2350 and 2500 m) in QianJiaZhai Reserve of Ailao Mountains. According to the Illumina MiSeq sequencing of 16 S rRNA gene amplicons, Proteobacteria, Acidobacteria and Actinobacteria were the dominant phyla with the relative abundance 43.12%, 21.61% and 14.84%, respectively. The Variibacter was the most dominant genus in rhizosphere of ancient wild tea plant. Phylogenetic null modeling analysis suggested that rhizospheric bacterial communities of ancient wild tea plants were more phylogenetically clustered than expected by chance. The bacterial community at 2050 m was unique with the highest alpha diversity, tend to cluster the nearest taxon and simple co-occurrence network structure. The unique bacterial community was correlated to multiple soil factors, and the content soil ammonium nitrogen (NH4+-N) was the key factor affecting the diversity and distribution of bacterial community along the elevational gradients. This study provided the necessary basic information for the protection of ancient tea trees and cultivation of tea plants.
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Affiliation(s)
- Haiyun Zi
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Xiaomao Cheng
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China
| | - Wanting Li
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China
| | - Xiaoxia Huang
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China.
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Water-soluble phosphorus contributes significantly to shaping the community structure of rhizospheric bacteria in rocky desertification areas. Sci Rep 2019; 9:18408. [PMID: 31804618 PMCID: PMC6895182 DOI: 10.1038/s41598-019-54943-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/21/2019] [Indexed: 02/01/2023] Open
Abstract
Microorganisms play important roles in soil improvement. Therefore, clarifying the contribution of environmental factors in shaping the microbial community structure is beneficial to improve soil fertility in karst rocky desertification areas. Here, the bacterial community structures of eight rhizospheric soil samples collected from perennial fruit plantations were analysed using an Illumina HiSeq2500 platform. The diversity and abundance of bacteria in rocky desertification areas were significantly lower than those in non-rocky desertification areas, while the bacterial community structure was not significantly different between root surface and non-root surface soils in the same rhizospheric soil samples. Proteobacteria predominated in rocky desertification areas, while Actinobacteria predominated in non-rocky desertification areas. Correlation analysis revealed that water-soluble phosphorus content (r2 = 0.8258), latitude (r2 = 0.7556), altitude (r2 = 0.7501), and the age of fruit trees (r2 = 0.7321) were positively correlated with the bacterial community structure, while longitude, pH, and total phosphorus content did not significantly influence the soil bacterial community structure. As water-soluble phosphorus content is derived from insoluble phosphorus minerals, supplementing phosphorus-solubilising bacteria to soils in rocky desertification areas is a feasible strategy for accelerating the dissolution of insoluble phosphorus minerals and improving agricultural production and environment ecology.
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Jeong S, Hong JK, Jho EH, Nam K. Interaction among soil physicochemical properties, bacterial community structure, and arsenic contamination: Clay-induced change in long-term arsenic contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2019; 378:120729. [PMID: 31202066 DOI: 10.1016/j.jhazmat.2019.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/23/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Pyrosequencing analyses to determine soil bacterial communities were conducted with forty-two soil samples collected from rice paddy and forest/farmland soils (Group A and B, respectively) at a long-term As-contaminated site. Soil physicochemical properties, such as the concentrations of As, Fe, Al, and Mn, pH, organic matter content, and clay content, were found to be significantly different with land use, and more importantly, strongly affected the bacterial community structure of the soil samples. When fitting the soil properties onto a nonmetric multidimensional scale plot of soil bacterial communities, clay content was found to be the most important factor in clustering the bacterial communities (R2 = 0.4831, p-value = 0.001). Phylum Chloroflexi (-1.03 of bioplot score) and Planctomycetes (1.31 of bioplot score) showed a significant relationship with clay content in soil samples. Interestingly, thebacterial phylotypes linked to clay content were only found in the soil samples of group B with low clay content, and had a strong relationship to As contamination in the redundancy analysis and the correlation analysis.Our results suggest that clay content seems to be negatively related to As contamination in soils, which, in turn, strongly influences the structure of bacterial communities in As-contaminated soil.
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Affiliation(s)
- Seulki Jeong
- Seoul Center, Korea Basic Science Institute, 6-7, Inchon-ro 22-gil, Seongbuk-gu, Seoul 02855, Republic of Korea
| | - Jin Kyung Hong
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeonmyeon, Cheoin-gu, Yongin-si, Gyeonggi-do 17035, Republic of Korea
| | - Eun Hea Jho
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeonmyeon, Cheoin-gu, Yongin-si, Gyeonggi-do 17035, Republic of Korea
| | - Kyoungphile Nam
- Department of Civil and Environmental Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea.
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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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37
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Zeng Q, An S, Liu Y, Wang H, Wang Y. Biogeography and the driving factors affecting forest soil bacteria in an arid area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 680:124-131. [PMID: 31100663 DOI: 10.1016/j.scitotenv.2019.04.184] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 05/24/2023]
Abstract
Bacteria are one of the most abundant and diverse groups and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large-scale biogeography patterns across longitude (east-west transect), and the processes that determine these patterns lags significantly behind that of macro-organisms. Here, we used 16S rRNA gene sequencing to evaluate the geographic distributions of bacterial diversity and their driving factors across different longitude sites along an 800-km east-west transect in the Loess Plateau. Twenty-four phyla were detected across all soil samples and the most sequence-abundant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Chloroflexi and Gemmatimonadetes (average relative abundance >5%). Soil bacterial α-diversity, expressed by the richness of soil bacterial communities and Shannon diversity, differed among climates (MAP) but showed strong correlations with MAP (r=-0.537 and r=-0.42, respectively; p<0.05 in both bacterial diversity indices). Variation partition analysis demonstrated that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 62% of the community variation. Soil properties contributed more to bacterial community variation than the combined geographic distance (historical contingencies) and climate factors. Among all environmental factors, soil pH exhibited a dominant role in structuring bacterial communities in this arid area. Our findings provide new evidence of bacterial biogeography patterns in an arid area (MAP ranged from 473mm to 547mm). Additionally, the results indicated a close linkage among soil bacterial community, climate and edaphic variables, which is critical for predicting promoting sustainable ecosystem services in the Loess Plateau.
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Affiliation(s)
- Quanchao Zeng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China.
| | - Yang Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - Honglei Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - Ying Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
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Liu D, Wang H, An S, Bhople P, Davlatbekov F. Geographic distance and soil microbial biomass carbon drive biogeographical distribution of fungal communities in Chinese Loess Plateau soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:1058-1069. [PMID: 30743903 DOI: 10.1016/j.scitotenv.2019.01.097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
Fungi are ecological drivers of carbon cycle in soils and also effectively mediate mineral nutrition for plants especially in the severely eroded Loess Plateau of China. However, factors determining variations in fungal diversity and their biogeographic patterns in this rigorously affected landscape area remain poorly understood. Therefore, we performed Illumina MiSeq high throughput sequencing of the fungal specific, internal transcribed spacer 2 (ITS2) region from 24 representative soils covering forest, grassland and agricultural lands from 8 distinct landscapes. Using this technique, we demonstrate that fungal members belonging to phylum Ascomycota dominated in all soils investigated in this study with an average relative abundance higher than 80%. High fungal richness in the Loess Plateau soils is ascribed to the retrieval of 1,822,499 quality sequences belonging to 13,533 different phylotypes. However, this richness/phylotype number decreased (from 779 to 561) with increasing longitudinal gradient through 107°39' to 109°36'. Interestingly, higher fungal diversity (in terms of presence of diverse fungal taxa) occurred as microbial biomass carbon (MBC) concentration decreased (approximately from 500 to 100mgkg-1) in soils. Variation partitioning analysis revealed that geographic distance contributed more to fungal community variation (38.3%) than soil properties (22.2%) at the landscape level (~400km). As indicated by non-metric multidimensional scaling (NMDS), among soil properties, concentrations of MBC primarily affected (significantly corrected with NMDS 1; r=0.620; p<0.01) fungal community structure in the current study. This study therefore constitutes an essential set of information and recommends usage of information on fungal community structure as a potential ecological indicator of the Loess Plateau region.
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Affiliation(s)
- Dong Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Honglei Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, PR China.
| | - Parag Bhople
- Faculty of Organic Agricultural Sciences, Department of Soil Biology and Plant Nutrition, University of Kassel, Germany
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Huang M, Chai L, Jiang D, Zhang M, Zhao Y, Huang Y. Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:699-707. [PMID: 30092526 DOI: 10.1016/j.scitotenv.2018.07.305] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/21/2018] [Accepted: 07/22/2018] [Indexed: 05/15/2023]
Abstract
Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.
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Affiliation(s)
- Muke Huang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- College of Environmental Science and Engineering, Peking University, Beijing 100871, 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, Beijing 100871, China
| | - Yanran Zhao
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China.
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40
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Liu D, Yang Y, An S, Wang H, Wang Y. The Biogeographical Distribution of Soil Bacterial Communities in the Loess Plateau as Revealed by High-Throughput Sequencing. Front Microbiol 2018; 9:2456. [PMID: 30405547 PMCID: PMC6200921 DOI: 10.3389/fmicb.2018.02456] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/25/2018] [Indexed: 02/01/2023] Open
Abstract
The rigorous environmental stress of the severely eroded Loess Plateau may have promoted specific soil bacterial communities in comparison to other eco-environmental regions. In order to unmask the bacterial diversity and most influential environmental parameters, Illumina MiSeq high throughput sequencing of 16S rRNA from 24 representative soil samples collected across south-east to north-west transect of the Loess Plateau in northern Shaanxi, China was conducted. This high-throughput sequencing revealed a total of 1,411,001 high quality sequences that classified into 38 phyla, 127 classes, >240 orders, and over 650 genera, suggesting a high bacterial richness across the Loess Plateau soils. The seven dominant groups were: Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, and Verrucomicrobi (relative abundance of >5%). Increasing/decreasing soil pH and geographic longitudinal distance correlated significantly with increasing/decreasing bacterial richness and diversity indices. Pairwise correlation analysis showed higher bacterial diversity at longitudinal gradients across 107°39'-109°15' (south-east to north-west) in our studied Chinese loess zone. Variation partitioning analysis indicated significant influence of soil characteristics (~40.4%) than geographical distance (at a landscape scale of ~400 km) that was responsible for 13.6% of variation in bacterial community structure from these soils. Overall, contemporary soil characteristics structure the bacterial community in Loess Plateau soil to a greater extent than the spatial distances along the loess transect.
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Affiliation(s)
- Dong Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China.,Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yang Yang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Honglei Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Ying Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
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41
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Soil Properties Drive Microbial Community Structure in a Large Scale Transect in South Eastern Australia. Sci Rep 2018; 8:11725. [PMID: 30082740 PMCID: PMC6078944 DOI: 10.1038/s41598-018-30005-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
Soil microbial communities directly affect soil functionality through their roles in the cycling of soil nutrients and carbon storage. Microbial communities vary substantially in space and time, between soil types and under different land management. The mechanisms that control the spatial distributions of soil microbes are largely unknown as we have not been able to adequately upscale a detailed analysis of the microbiome in a few grams of soil to that of a catchment, region or continent. Here we reveal that soil microbes along a 1000 km transect have unique spatial structures that are governed mainly by soil properties. The soil microbial community assessed using Phospholipid Fatty Acids showed a strong gradient along the latitude gradient across New South Wales, Australia. We found that soil properties contributed the most to the microbial distribution, while other environmental factors (e.g., temperature, elevation) showed lesser impact. Agricultural activities reduced the variation of the microbial communities, however, its influence was local and much less than the overall influence of soil properties. The ability to predict the soil and environmental factors that control microbial distribution will allow us to predict how future soil and environmental change will affect the spatial distribution of microbes.
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42
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Wei H, Peng C, Yang B, Song H, Li Q, Jiang L, Wei G, Wang K, Wang H, Liu S, Liu X, Chen D, Li Y, Wang M. Contrasting Soil Bacterial Community, Diversity, and Function in Two Forests in China. Front Microbiol 2018; 9:1693. [PMID: 30108560 PMCID: PMC6080587 DOI: 10.3389/fmicb.2018.01693] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/06/2018] [Indexed: 12/03/2022] Open
Abstract
Bacteria are the highest abundant microorganisms in the soil. To investigate bacteria community structures, diversity, and functions, contrasting them in four different seasons all the year round with/within two different forest type soils of China. We analyzed soil bacterial community based on 16S rRNA gene sequencing via Illumina HiSeq platform at a temperate deciduous broad-leaved forest (Baotianman, BTM) and a tropical rainforest (Jianfengling, JFL). We obtained 51,137 operational taxonomic units (OTUs) and classified them into 44 phyla and 556 known genera, 18.2% of which had a relative abundance >1%. The composition in each phylum was similar between the two forest sites. Proteobacteria and Acidobacteria were the most abundant phyla in the soil samples between the two forest sites. The Shannon index did not significantly differ among the four seasons at BTM or JFL and was higher at BTM than JFL in each season. The bacteria community at both BTM and JFL showed two significant (P < 0.05) predicted functions related to carbon cycle (anoxygenic photoautotrophy sulfur oxidizing and anoxygenic photoautotrophy) and three significant (P < 0.05) predicted functions related to nitrogen cycle (nitrous denitrificaton, nitrite denitrification, and nitrous oxide denitrification). We provide the basis on how changes in bacterial community composition and diversity leading to differences in carbon and nitrogen cycles at the two forests.
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Affiliation(s)
- Hua Wei
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,Medical College, Baoji Vocational Technology College, Baoji, China
| | - Changhui Peng
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,Départment des Sciences Biologiques, Institut des Sciences de l'Environnement, Université du Québec à Montréal, Montreal, QC, Canada
| | - Bin Yang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Hanxiong Song
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Quan Li
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Lin Jiang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Gang Wei
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Kefeng Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Hui Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Shirong Liu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiaojing Liu
- Baotianman Natural Reserve Administration, Neixiang, China
| | - Dexiang Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Yide Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun, China
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43
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Li J, Shen Z, Li C, Kou Y, Wang Y, Tu B, Zhang S, Li X. Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China. Front Microbiol 2018; 9:569. [PMID: 29636740 PMCID: PMC5880914 DOI: 10.3389/fmicb.2018.00569] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/13/2018] [Indexed: 11/24/2022] Open
Abstract
Ecological understandings of soil bacterial community succession and assembly mechanism along elevational gradients in mountains remain not well understood. Here, by employing the high-throughput sequencing technique, we systematically examined soil bacterial diversity patterns, the driving factors, and community assembly mechanisms along the elevational gradients of 1800–4100 m on Gongga Mountain in China. Soil bacterial diversity showed an extraordinary stair-step pattern along the elevational gradients. There was an abrupt decrease of bacterial diversity between 2600 and 2800 m, while no significant change at either lower (1800–2600 m) or higher (2800–4100 m) elevations, which coincided with the variation in soil pH. In addition, the community structure differed significantly between the lower and higher elevations, which could be primarily attributed to shifts in soil pH and vegetation types. Although there was no direct effect of MAP and MAT on bacterial community structure, our partial least squares path modeling analysis indicated that bacterial communities were indirectly influenced by climate via the effect on vegetation and the derived effect on soil properties. As for bacterial community assembly mechanisms, the null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region. In addition, variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the β-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations. Our results highlight the importance of environmental filtering, as well as elevation-related spatial attributes in structuring soil bacterial communities in mountain ecosystems.
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Affiliation(s)
- Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Zehao Shen
- Department of Ecology, Key Laboratory of Ministry of Education for Earth Surface Processes, Peking University, Beijing, China
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Yongping Kou
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Yansu Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Bo Tu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Shiheng Zhang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
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44
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Liu K, Ding X, Tang X, Wang J, Li W, Yan Q, Liu Z. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils. Front Microbiol 2018. [PMID: 29535703 PMCID: PMC5835090 DOI: 10.3389/fmicb.2018.00352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.
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Affiliation(s)
- Kaihui Liu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiaowei Ding
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiaofei Tang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiome Research Center and School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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45
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Liu S, Wang H, Deng Y, Tian P, Wang Q. Forest conversion induces seasonal variation in microbial β-diversity. Environ Microbiol 2018; 20:111-123. [DOI: 10.1111/1462-2920.14017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Shengen Liu
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Hang Wang
- National Plateau Wetlands Research Center; Southwest Forestry University; Kunming 650224 China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Science; Chinese Academy of Sciences; Beijing 100085 China
| | - Peng Tian
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Qingkui Wang
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
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46
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Xue L, Ren H, Li S, Leng X, Yao X. Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area. Front Microbiol 2017; 8:2377. [PMID: 29250053 PMCID: PMC5717032 DOI: 10.3389/fmicb.2017.02377] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
Vegetation restoration has been widely used in karst rocky desertification (KRD) areas of southwestern China, but the response of microbial community to revegetation has not been well characterized. We investigated the diversity, structure, and co-occurrence patterns of bacterial communities in soils of five vegetation types (grassland, shrubbery, secondary forest, pure plantation and mixed plantation) in KRD area using high-throughput sequencing of the 16S rRNA gene. Bray-Curtis dissimilarity analysis revealed that 15 bacterial community samples were clustered into five groups that corresponded very well to the five vegetation types. Shannon diversity was positively correlated with pH and Ca2+ content but negatively correlated with organic carbon, total nitrogen, and soil moisture. Redundancy analysis indicated that soil pH, Ca2+ content, organic carbon, total nitrogen, and soil moisture jointly influenced bacterial community structure. Co-occurrence network analysis revealed non-random assembly patterns of bacterial composition in the soils. Bryobacter, GR-WP33-30, and Rhizomicrobium were identified as keystone genera in co-occurrence network. These results indicate that diverse soil physicochemical properties and potential interactions among taxa during vegetation restoration may jointly affect the bacterial community structure in KRD regions.
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Affiliation(s)
- Liang Xue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Huadong Ren
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Sheng Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Xiuhui Leng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
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47
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Wang J, Zhang T, Li L, Li J, Feng Y, Lu Q. The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China. Front Microbiol 2017; 8:2126. [PMID: 29176963 PMCID: PMC5686094 DOI: 10.3389/fmicb.2017.02126] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/18/2017] [Indexed: 11/24/2022] Open
Abstract
Dryland ecosystems cover more than 30% of the terrestrial area of China, while processes that shape the biogeographic patterns of bacterial and fungal β-diversity have rarely been evaluated synchronously. To compare the biogeographic patterns and its drivers of bacterial and fungal β-diversity, we collected 62 soil samples from a typical dryland region of northwest China. We assessed bacterial and fungal communities by sequencing bacterial 16S rRNA gene and fungal ITS data. Meanwhile, the β-diversity was decomposed into two components: species replacement (species turnover) and nestedness to further explore the bacterial and fungal β-diversity patterns and its causes. The results show that both bacterial and fungal β-diversity were derived almost entirely from species turnover rather than from species nestedness. Distance-decay relationships confirmed that the geographic patterns of bacterial and fungal β-diversity were significantly different. Environmental factors had the dominant influence on both the bacterial and fungal β-diversity and species turnover, however, the role of geographic distance varied across bacterial and fungal communities. Furthermore, both bacterial and fungal nestedness did not significantly respond to the environmental and geographic distance. Our findings suggest that the different response of bacterial and fungal species turnover to dispersal limitation and other, unknown processes may result in different biogeographic patterns of bacterial and fungal β-diversity in the drylands of northwest China. Together, we highlight that the drivers of β-diversity patterns vary between bacterial and fungal communities, and microbial β-diversity are driven by multiple factors in the drylands of northwest China.
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Affiliation(s)
- Jianming Wang
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Tianhan Zhang
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Liping Li
- Institute of Remote Sensing and Digital Earth, Chinese Academy of Sciences, Beijing, China
| | - Jingwen Li
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yiming Feng
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Qi Lu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
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48
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Zhou Y, Zhu H, Fu S, Yao Q. Metagenomic evidence of stronger effect of stylo (legume) than bahiagrass (grass) on taxonomic and functional profiles of the soil microbial community. Sci Rep 2017; 7:10195. [PMID: 28860520 PMCID: PMC5579253 DOI: 10.1038/s41598-017-10613-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/07/2017] [Indexed: 12/21/2022] Open
Abstract
Plants are key determinants of soil microbial community (SMC). Legumes and grasses are distinct groups in various ecosystems; however, how they differentially shape SMC structure and functioning has yet to be explored. Here, we investigate SMC in soils grown with stylo (legume) or bahiagrass (grass). Soil metagenomic sequencing indicates that Archaea was more abundant in unplanted soils than in planted soils, and that stylo selected higher abundance of fungi than bahiagrass. When the stylo soils enriched Streptomyces, Frankia, Mycobacterium and Amycolatopsis, the bahiagrass soils enriched Sphingomonas and Sphingobium. NMDS reveals that the legume shaped SMC more greatly than the grass (P < 0.004). SMC functional profiles (KEGG and CAZy) were also greatly altered by plants with the legume being more effective (P < 0.000 and P < 0.000). The abundant microbial taxa contributed to the main community functions, with Conexibacter, Sphingomonas, and Burkholderia showing multifunctionality. Moreover, soil chemical property showed much higher direct effect on SMC structure and functional profiles than soil extracts, although the soil total nitrogen and some compounds (e.g. heptadecane, 1-pentadecyne and nonanoic acid) in soil extracts were best correlated with SMC structure and functional profiles. These findings are the first to suggest that legume species shape SMC more greatly than grass species.
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Affiliation(s)
- Yang Zhou
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, 510642, China
| | - Honghui Zhu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, 510070, China.
| | - Shenglei Fu
- College of Environment and Planning, Henan University, Kaifeng, 475004, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, 510642, China.
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49
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Jiang J, Song Z, Yang X, Mao Z, Nie X, Guo H, Peng X. Microbial community analysis of apple rhizosphere around Bohai Gulf. Sci Rep 2017; 7:8918. [PMID: 28827532 PMCID: PMC5566992 DOI: 10.1038/s41598-017-08398-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/12/2017] [Indexed: 11/21/2022] Open
Abstract
Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.
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Affiliation(s)
- Jihang Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotong Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271000, China
| | - Xiaohong Nie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xiawei Peng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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