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Ortúzar M, Riesco R, Criado M, Alonso MDP, Trujillo ME. Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174277. [PMID: 38944300 DOI: 10.1016/j.scitotenv.2024.174277] [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: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.
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Affiliation(s)
- Maite Ortúzar
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Marco Criado
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - María Del Pilar Alonso
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
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Xin G, Xiaohong S, Yujiao S, Wenbao L, Yanjun W, Zhimou C, Arvolab L. Characterization of bacterial community dynamics dominated by salinity in lakes of the Inner Mongolian Plateau, China. Front Microbiol 2024; 15:1448919. [PMID: 39234542 PMCID: PMC11371557 DOI: 10.3389/fmicb.2024.1448919] [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: 06/14/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024] Open
Abstract
Microorganisms in lakes are sensitive to salinity fluctuations. Despite extensive prior research on bacterial communities, our understanding of their characteristics and assembly mechanisms in lakes, especially in desert lakes with different salinities. To address this issue, we collected three samples from freshwater lakes, six from brackish lakes, and five from salt lakes in the Badanjilin Desert. The 16S rRNA gene sequencing was applied to investigate the bacterial interactions with rising salinity, community coexistence patterns, and assembly mechanisms. Our findings suggested that the increased lake salinity significantly reduces the bacterial community diversity and enhanced the community differentiation. Significant variations were observed in the contribution of biomarkers from Cyanobacteria, Chloroflexi, and Halobacterota to the composition of the lake bacterial communities. The bacterial communities in the salt lakes exhibited a higher susceptibility to salinity limitations than those in the freshwater and brackish lakes. In addition, the null modeling analyses confirmed the quantitative biases in the stochastic assembly processes of bacterial communities across freshwater, brackish, and saline lakes. With the increasing lake salinity, the significance of undominated and diffusion limitation decreased slightly, and the influence of homogenizing dispersal on community assembly increased. However, the stochasticity remained the dominant process across all lakes in the Badanjilin Desert. The analysis of co-occurring networks revealed that the rising salinity reduced the complexity of bacterial network structures and altered the interspecific interactions, resulting in the increased interspecies collaboration with increasing salinity levels. Under the influence of salinity stress, the key taxon Cyanobacteria in freshwater lakes (Schizothrix_LEGE_07164) was replaced by Proteobacteria (Thalassobaculum and Polycyclovorans) in brackish lakes, and Thermotogota (SC103) in salt lakes. The results indicated the symbiotic patterns of bacterial communities across varying salinity gradients in lakes and offer insights into potential mechanisms of community aggregation, thereby enhancing our understanding of bacterial distribution in response to salinity changes.
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Affiliation(s)
- Guo Xin
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Shi Xiaohong
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
- State Gauge and Research Station of Wetland Ecosystem, Wuliangsuhai Lake, Bayan Nur, China
| | - Shi Yujiao
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Li Wenbao
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Wang Yanjun
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Cui Zhimou
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Lauri Arvolab
- Lammi Biological Station, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, Helsinki University, Helsinki, Finland
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Sun J, Zhou H, Cheng H, Chen Z, Wang Y. Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106624. [PMID: 38943698 DOI: 10.1016/j.marenvres.2024.106624] [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: 04/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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Dong R, Wang X, Li Y, Zhang H, Li X, Song J, Chang F, Feng W, Pang H, Wang J. Soil bacterial diversity and community structure of Suaeda glauca vegetation in the Hetao Irrigation District, Inner Mongolia, China. Front Microbiol 2024; 15:1358783. [PMID: 38939186 PMCID: PMC11210291 DOI: 10.3389/fmicb.2024.1358783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/14/2024] [Indexed: 06/29/2024] Open
Abstract
Exploring the bacterial community in the S. glauca rhizosphere was of great value for understanding how this species adapted to the saline-alkali environment and for the rational development and use of saline-alkali soils. In this study, high-throughput sequencing technology was used to investigate the diversity characteristics and distribution patterns of soil bacterial communities in the rhizosphere of S.glauca-dominated communities in the Hetao Irrigation Distract, Inner Mongolia, China. The relationships among bacterial characteristics, soil physicochemical properties and vegetation in four sampling sites were analyzed. The soil bacterial communities in the rhizosphere of S. glauca-dominated communities were mainly composed of 16 phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, Saccharibacteria, Cyanobacteria, Nitrospirae, JL-ETNP-Z39, Parcubacteria and Chlorobi), and these populations accounted for more than 99% of the total bacterial community. At the genus level, the main bacterial communities comprised Halomonas, Nitriliruptor, Euzebya and Pelagibius, which accounted for 15.70% of the total bacterial community. An alpha diversity analysis indicated that the richness and diversity of rhizosphere soil bacteria differed significantly among the sampling sites, and the bacterial richness and diversity indices of severe saline-alkali land were higher than those of light and moderate saline-alkali land. The principal component analysis (PCA) and linear discriminant analysis effect size (LEfSe) showed significant differences in the species composition of the rhizosphere soil bacterial community among different sampling sites. A correlation analysis showed that the number of bacterial species exhibited the highest correlation with the soil water content (SWC). The richness and evenness indices were significantly correlated with the SWC and SO4 2-, K+ and Mg2+ concentrations. The electrical conductivity (EC), soluble ions (Na+, CO3 2- + HCO3 -, K+, Ca2+, Mg2+, and SO4 2+), SWC and vegetation coverage (VC) were the main drivers affecting the changes in its community structure. The bacterial community in the rhizosphere of S. glauca enhanced the adaptability of S. glauca to saline-alkali environment by participating in the cycling process of nutrient elements, the decomposition of organic matter and the production of plant growth regulating substances. These results provided a theoretical reference for further study on the relationship among rhizosphere soil microorganisms and salt tolerance in halophytes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jing Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences), Beijing, China
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Hao X, Gu Y, Zhang H, Wang X, Liu X, Chen C, Wang C, Zhang X, Liu X, Shen X. Synthetic Microbial Community Promotes Bacterial Communities Leading to Soil Multifunctionality in Desertified Land. Microorganisms 2024; 12:1117. [PMID: 38930499 PMCID: PMC11205429 DOI: 10.3390/microorganisms12061117] [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: 05/16/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Soil desertification is an important challenge in global soil management, and effectively and stably restoring soil function is an urgent problem. Using synthetic microbial communities (SynComs) is a burgeoning microbial strategy aimed at enhancing soil nutrients through functional synergies among diverse microorganisms; nevertheless, their effectiveness in restoring desertified soils remains unknown. In this study, we conducted a two-year field experiment using a SynCom constructed by in situ probiotic bacteria and set up control, chemical fertilizer, and combined SynCom-chemical fertilizer (combined fertilizer) treatments to investigate the linkage between microbial communities and soil multifunctionality in the soil surface layer (0-10 cm). Both the bacterial and fungal communities differed the most under the combined fertilizer treatment compared to the control. The bacterial communities differed more under treatments of the SynCom than the chemical fertilizer, while the fungal communities differed more under the chemical fertilizer treatment than the SynCom treatment. Regarding soil function, the SynCom strengthened the correlation between enzyme activities and both bacterial communities and functional properties. pH and available potassium were the main influencing factors under the chemical fertilizer and combined fertilizer treatments. The beta-diversity of the bacterial communities was significantly correlated with soil multifunctionality. Random forest analyses showed that the SynCom significantly enhanced the bacterial communities, driving soil multifunctionality, and that some potential microbial taxa drove multiple nutrient cycles simultaneously. In summary, the SynCom effectively increased the abundance of most carbon, nitrogen, and phosphorus functional genes as well as soil enzyme activities. The bacterial community composition contributed significantly to soil multifunctionality. Hence, the development of novel microbial agents holds significant potential for improving soil functionality and managing desertification.
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Affiliation(s)
- Xinwei Hao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Yazhou Gu
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd., Qingyang 745000, China; (Y.G.); (H.Z.)
| | - Hongzhi Zhang
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd., Qingyang 745000, China; (Y.G.); (H.Z.)
| | - Xiao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Xiaozhen Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010013, China; (X.L.); (X.Z.)
| | - Chunlei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Congcong Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Xiaoqing Zhang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010013, China; (X.L.); (X.Z.)
| | - Xingyu Liu
- State Key Laboratory of Geological Processes and Mineral Resources, Institute of Earth Sciences, China University of Geosciences, Beijing 100083, China;
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
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6
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Séré G, Le Guern C, Bispo A, Layet C, Ducommun C, Clesse M, Schwartz C, Vidal-Beaudet L. Selection of soil health indicators for modelling soil functions to promote smart urban planning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171347. [PMID: 38432376 DOI: 10.1016/j.scitotenv.2024.171347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
The contribution of soil health to global health receives a growing interest, especially in urban environment. Therefore, there is a true need to develop methods to evaluate ecological functions provided by urban soils in order to promote smart urban planning. This work aims first at identifying relevant soil indicators based either on in situ description, in situ measurement or lab analysis. Then, 9 soil functions and sub-functions were selected to meet the main expectations regarding soil health in urban contexts. A crucial step of the present research was then to select adequate indicators for each soil function and then to create adapted reference frameworks; they were in the form of 4 classes with scores ranging from 0 to 3. All the reference frameworks were developed to evaluate soil indicators in order to score soil functions, either by using existing scientific or technical standards or references or based on the expertise of the co-authors. Our model was later tested on an original database of 109 different urban soils located in 7 cities of Western Europe and under various land uses. The scores calculated for 8 soil functions of 109 soils followed a Gaussian distribution. The scoring successfully expressed the strong contrasts between the various soils; the lowest scores were calculated for sealed soils and soils located in urban brownfields, whereas the highest were found for soils located in city parks or urban agriculture. Despite requiring a soil expertise, the proposed approach is easy to implement and could help reveal the true potential of urban soils in order to promote smart urban planning and enhance their contribution to global health.
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Affiliation(s)
- Geoffroy Séré
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
| | | | | | - Clément Layet
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
| | | | - Margaux Clesse
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
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Fan Q, Liu K, Wang Z, Liu D, Li T, Hou H, Zhang Z, Chen D, Zhang S, Yu A, Deng Y, Cui X, Che R. Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits. Mol Ecol 2024; 33:e17302. [PMID: 38421102 DOI: 10.1111/mec.17302] [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: 08/27/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high-throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.
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Affiliation(s)
- Qiuping Fan
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Kaifang Liu
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Zelin Wang
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Dong Liu
- School of Life Sciences, Yunnan University, Kunming, China
| | - Ting Li
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Hou
- School of Ecology and Environment Science, Yunnan University, Kunming, China
| | - Zejin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Danhong Chen
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Song Zhang
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Anlan Yu
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Yongcui Deng
- School of Geography Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongxiao Che
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
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Xue P, Minasny B, Wadoux AMJC, Dobarco MR, McBratney A, Bissett A, de Caritat P. Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia. GLOBAL CHANGE BIOLOGY 2024; 30:e17216. [PMID: 38429628 DOI: 10.1111/gcb.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 03/03/2024]
Abstract
Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine-learning models, we generated high-resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes.
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Affiliation(s)
- Peipei Xue
- The University of Sydney, Sydney, New South Wales, Australia
| | - Budiman Minasny
- The University of Sydney, Sydney, New South Wales, Australia
| | - Alexandre M J-C Wadoux
- LISAH, University of Montpellier, AgroParisTech, INRAE, IRD, L'Institut Agro, Montpellier, France
| | | | - Alex McBratney
- The University of Sydney, Sydney, New South Wales, Australia
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Oliveira MCO, Ragonezi C, Valente S, de Freitas JGR, Pinheiro de Carvalho MAA. Microorganism community structure: A characterisation of agrosystems from Madeira Archipelago. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13227. [PMID: 38268303 PMCID: PMC10866076 DOI: 10.1111/1758-2229.13227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Microbial diversity profoundly influences soil ecosystem functions, making it vital to monitor community dynamics to comprehend its structure. Our study focused on six agrosystems in Madeira Archipelago, analysing bacteria, archaea, fungi and AMF through classical microbiology and molecular techniques. Despite distinct edaphoclimatic conditions and management practices, bacterial structures exhibited similarities, with Alphaproteobacteria at 18%-20%, Bacilli at 11%-18% and Clostridia at 9%-14%. The predominance of copiothrophic groups suggested that soil nutrient content was the driver of these communities. Regarding archaea, the communities changed among sites, and it was evident that agrosystems provided niches for methanogens. The Crenarchaeota varied between 15% and 29%, followed by two classes of Euryarchaeota, Methanomicrobia (17%-25%) and Methanococci (4%-32%). Fungal communities showed consistent composition at the class level but had differing diversity indices due to management practices and soil texture. Sordaryomycetes (21%-28%) and Agaricomycetes (15%-23%) were predominant. Conversely, AMF communities appeared to be also influenced by the agrosystem, with Glomus representing over 50% of the community in all agrosystems. These insights into microbial groups' susceptibilities to environmental conditions are crucial for maintaining healthy soil and predicting climate change effects on agrosystems' productivity, resilience and sustainability. Additionally, our findings enable the development of more robust prediction models for agricultural practices.
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Affiliation(s)
- Maria Cristina O. Oliveira
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
| | - Carla Ragonezi
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
- Centre for the Research and Technology of Agro‐Environmental and Biological Sciences (CITAB), Inov4Agro – Institute for Innovation, Capacity Building and Sustainability of Agri‐Food ProductionUniversity of Trás‐os‐Montes and Alto DouroVila RealPortugal
- Faculty of Life Sciences, Campus da PenteadaUniversity of MadeiraFunchalPortugal
| | - Sofia Valente
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
| | - José G. R. de Freitas
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
| | - Miguel A. A. Pinheiro de Carvalho
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
- Centre for the Research and Technology of Agro‐Environmental and Biological Sciences (CITAB), Inov4Agro – Institute for Innovation, Capacity Building and Sustainability of Agri‐Food ProductionUniversity of Trás‐os‐Montes and Alto DouroVila RealPortugal
- Faculty of Life Sciences, Campus da PenteadaUniversity of MadeiraFunchalPortugal
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10
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Yarahmadi A, Afkhami H. The role of microbiomes in gastrointestinal cancers: new insights. Front Oncol 2024; 13:1344328. [PMID: 38361500 PMCID: PMC10867565 DOI: 10.3389/fonc.2023.1344328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/20/2023] [Indexed: 02/17/2024] Open
Abstract
Gastrointestinal (GI) cancers constitute more than 33% of new cancer cases worldwide and pose a considerable burden on public health. There exists a growing body of evidence that has systematically recorded an upward trajectory in GI malignancies within the last 5 to 10 years, thus presenting a formidable menace to the health of the human population. The perturbations in GI microbiota may have a noteworthy influence on the advancement of GI cancers; however, the precise mechanisms behind this association are still not comprehensively understood. Some bacteria have been observed to support cancer development, while others seem to provide a safeguard against it. Recent studies have indicated that alterations in the composition and abundance of microbiomes could be associated with the progression of various GI cancers, such as colorectal, gastric, hepatic, and esophageal cancers. Within this comprehensive analysis, we examine the significance of microbiomes, particularly those located in the intestines, in GI cancers. Furthermore, we explore the impact of microbiomes on various treatment modalities for GI cancer, including chemotherapy, immunotherapy, and radiotherapy. Additionally, we delve into the intricate mechanisms through which intestinal microbes influence the efficacy of GI cancer treatments.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
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11
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Huang W, Zhao Y, Zhang L, Shi Y, Wang Z, Mai Y, Shu L. Soil physical structure drives N-glycan mediated trophic interactions in soil amoebae: Mechanisms and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167509. [PMID: 37788775 DOI: 10.1016/j.scitotenv.2023.167509] [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: 06/19/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
Soil protozoa are an essential part of the terrestrial ecosystem, playing a vital role in the global element cycling and energy flow. However, one research gap is what are the key factors driving their diversity and environmental fates. In this study, we hypothesized that soil texture could affect soil protozoa's predation and their interactions with environmental pollutants, and we tested it by using a soil amoeba Dictyostelium discoideum as a model system. We found that soil texture affected amoeba's growth and development. In addition, environmental factors cannot explain the variation of amoeba's fitness in different soil textures. Soil sandy particles and water content rather than particle size contribute to amoeba's fitness. Furthermore, different soil textures induced distinct transcriptional responses to amoebae, especially N-glycan-related and multiple signaling pathways and the expression of key genes (e.g., Ras superfamily, cxgE, trap1). The expression of N-glycan-related pathways, which is positively correlated with amoeba predation, was inhibited in sand soil, decreasing amoeba's fitness. Finally, the results showed that soil texture also affects amoeba's interaction with environmental pollutants. In conclusion, this study shows that soil physical structures affect amoeba's interactions with bacteria and environmental pollutants. SYNOPSIS: Soil texture affects soil protozoa's growth and development and their interactions with environmental pollutants.
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Affiliation(s)
- Wei Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanchen Zhao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yikun Shi
- Department of Mechanical and Electronic Engineering, Qingdao University of Technology, Qingdao 266520, China
| | - Zihe Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingwen Mai
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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12
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Christel A, Chemidlin Prevost-Bouré N, Dequiedt S, Saby N, Mercier F, Tripied J, Comment G, Villerd J, Djemiel C, Hermant A, Blondon M, Bargeot L, Matagne E, Horrigue W, Maron PA, Ranjard L. Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167454. [PMID: 37783435 DOI: 10.1016/j.scitotenv.2023.167454] [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: 07/20/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.
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Affiliation(s)
- A Christel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; AgroParisTech, 75732 Paris, France
| | | | - S Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Saby
- INRAE, US1106 Info&Sols, F-45075 Orleans, France
| | - F Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - J Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - G Comment
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - J Villerd
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - C Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - A Hermant
- Chambre d'agriculture de Côte d'Or, 1 rue des Coulots, 21110 Bretenière, France
| | - M Blondon
- Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - L Bargeot
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - E Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - W Horrigue
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - P A Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - L Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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13
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He H, Zhou J, Wang Y, Jiao S, Qian X, Liu Y, Liu J, Chen J, Delgado-Baquerizo M, Brangarí AC, Chen L, Cui Y, Pan H, Tian R, Liang Y, Tan W, Ochoa-Hueso R, Fang L. Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers. GLOBAL CHANGE BIOLOGY 2024; 30:e17028. [PMID: 37955302 DOI: 10.1111/gcb.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
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Affiliation(s)
- Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxiong Zhou
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Albert C Brangarí
- Institute for Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Renmao Tian
- Institute for Food Safety and Health (IFSH), Illinois Institute of Technology, Bedford Park, Illinois, USA
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, Cádiz, Spain
| | - Linchuan Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
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14
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Deshoux M, Sadet-Bourgeteau S, Gentil S, Prévost-Bouré NC. Effects of biochar on soil microbial communities: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166079. [PMID: 37553053 DOI: 10.1016/j.scitotenv.2023.166079] [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: 03/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.
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Affiliation(s)
- Maëlle Deshoux
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France; Groupe Bordet, Froidvent, F-21290 Leuglay, France.
| | - Sophie Sadet-Bourgeteau
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France
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15
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Jiraska L, Jones B, Knight SJ, Lennox J, Goddard MR. Soil and bark biodiversity forms discrete islands between vineyards that are not affected by distance or management regime. Environ Microbiol 2023; 25:3655-3670. [PMID: 37905675 DOI: 10.1111/1462-2920.16513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023]
Abstract
Within geographic regions, the existing data suggest that physical habitat (bark, soil, etc.) is the strongest factor determining agroecosystem microbial community assemblage, followed by geographic location (site), and then management regime (organic, conventional, etc.). The data also suggest community similarities decay with increasing geographic distance. However, integrated hypotheses for these observations have not been developed. We formalized and tested such hypotheses by sequencing 3.8 million bacterial 16S, fungal ITS2 and non-fungal eukaryotic COI barcodes deriving from 108 samples across two habitats (soil and bark) from six vineyards sites under conventional or conservation management. We found both habitat and site significantly affected community assemblage, with habitat the stronger for bacteria only, but there was no effect of management. There was no evidence for community similarity distance-decay within sites within each habitat. While communities significantly differed between vineyard sites, there was no evidence for between site community similarity distance-decay apart from bark bacterial communities, and no correlations with soil and bark pH apart from soil bacterial communities. Thus, within habitats, vineyard sites represent discrete biodiversity islands, and while bacterial, fungal and non-fungal eukaryotic biodiversity mostly differs between sites, the distance by which they are separated does not define how different they are.
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Affiliation(s)
- Lucie Jiraska
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Beatrix Jones
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sarah J Knight
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jed Lennox
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew R Goddard
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The School of Life and Environmental Sciences, University of Lincoln, Lincoln, UK
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16
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Pino V, Fajardo M, McBratney A, Minasny B, Wilson N, Baldock C. Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations. Mol Ecol 2023; 32:6243-6259. [PMID: 36862079 DOI: 10.1111/mec.16911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/05/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km2 ), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.
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Affiliation(s)
- Vanessa Pino
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Mario Fajardo
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Alex McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Neil Wilson
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
| | - Chris Baldock
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
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17
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Hao Y, Liu H, Li J, Mu L, Hu X. Environmental tipping points for global soil carbon fixation microorganisms. iScience 2023; 26:108251. [PMID: 37965139 PMCID: PMC10641746 DOI: 10.1016/j.isci.2023.108251] [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: 03/15/2023] [Revised: 07/18/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Carbon fixation microorganisms (CFMs) are important components of the soil carbon cycle. However, the global distribution of CFMs and whether they will exceed the environmental tipping points remain unclear. According to the machine learning models, total carbon content, nitrogen fertilizer, and precipitation play dominant roles in CFM abundance. Obvious stimulation and inhibition effects on CFM abundance only happened at low levels of total carbon and precipitation, where the tipping points were 6.1 g·kg-1 and 22.38 mm, respectively. The abundance of CFMs in response to nitrogen fertilizer changed from positive to negative (tipping point at 9.45 kg ha-1·y-1). Approximately 46% of CFM abundance decline happened in cropland at 2100. Our work presents the distribution of carbon-fixing microorganisms on a global scale and then points out the sensitive areas with significant abundance changes. The previously described information will provide references for future soil quality prediction and policy decision-making.
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Affiliation(s)
- Yueqi Hao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300080, China
| | - Hao Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300080, China
| | - Jiawei Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300080, China
| | - Li Mu
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety (Ministry of Agriculture and Rural Affairs), Tianjin Key Laboratory of Agro-environment and Safe-product, Institute of Agro-environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300080, China
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18
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Shu X, Liu W, Huang H, Ye Q, Zhu S, Peng Z, Li Y, Deng L, Yang Z, Chen H, Liu D, Shi J. Meta-Analysis of Organic Fertilization Effects on Soil Bacterial Diversity and Community Composition in Agroecosystems. PLANTS (BASEL, SWITZERLAND) 2023; 12:3801. [PMID: 38005698 PMCID: PMC10675672 DOI: 10.3390/plants12223801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023]
Abstract
Application of organic fertilizers or their combination with chemical fertilizers is a feasible practice for improving soil fertility and reducing soil degradation in agroecosystems, and these regulations are mainly mediated though soil microbial communities. Despite bacteria ranking among the most abundant and diverse groups of soil microorganisms, the effects of long-term organic fertilization (OF) and chemical-organic fertilization (COF) on soil bacterial diversity and community composition remain unclear. In this study, we conducted a meta-analysis and demonstrated that OF had no significant effect on bacterial alpha diversity. Application of chemical fertilizer and crop residue significantly decreased bacterial Richness index. Both OF and COF significantly altered bacterial community structure, with these changes being predominately attributed to shifts in soil pH. For bacterial phyla, both OF and COF significantly increased the relative abundance of Proteobacteria and Bacteroidetes, suggesting that OF and COF may cause the enrichment of copiotrophic taxa. In addition, COF significantly increased the relative abundance of Gammaproteobacteria but decreased the relative abundance of Acidobacteria. Overall, our results suggest that organic and chemical-organic fertilization can effectively maintain bacterial diversity and enhance soil fertility in agroecosystems, and the alteration of soil bacterial community structure is closely intertwined with soil pH.
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Affiliation(s)
- Xiangyang Shu
- Key Lab of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610068, China
| | - Weijia Liu
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Han Huang
- College of Economics and Management, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Qinxin Ye
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Shunxi Zhu
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Zhaohui Peng
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Yiding Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (L.D.)
| | - Liangji Deng
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (L.D.)
| | - Zepeng Yang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Z.Y.); (H.C.); (D.L.)
| | - Honglin Chen
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Z.Y.); (H.C.); (D.L.)
| | - Dinghui Liu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Z.Y.); (H.C.); (D.L.)
| | - Jialing Shi
- Chengdu Agricultural and Rural Bureau, Chengdu 610066, China;
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Rao G, Yan SZ, Song WL, Lin D, Chen YJ, Chen SL. Distribution, assembly, and interactions of soil microorganisms in the bright coniferous forest area of China's cold temperate zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165429. [PMID: 37437627 DOI: 10.1016/j.scitotenv.2023.165429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
The bright coniferous forest area in the cold temperate zone of China is a terrestrial ecosystem primarily dominated by low mountain Larix gmelinii trees. Limited information is available regarding the assembly mechanisms and interactions of microbial communities in the soil in this region. This study employed high-throughput techniques to obtain DNA from myxomycetes, bacteria, and fungi in the soil, evaluated their diversity in conjunction with environmental factors, associated them with the assembly process, and explored the potential interaction relationships between these microorganisms. The findings of our study showed that environmental factors had a more significant influence on the α and β diversity of bacteria compared to myxomycetes and fungi. Microbial communities were influenced by environmental selection and geographical diffusion, although environmental selection appeared to have a more significant impact than geographical diffusion. Our study suggested that different microorganisms exhibited unique evolutionary patterns and may have different assembly modes within phylogenetic groups. Myxomycetes and fungi exhibited a similar assembly process that was mainly influenced by stochastic dispersal limitation and drift. In contrast, bacteria's assembly process was primarily influenced by stochastic drift and deterministic homogeneous selection. The community of myxomycetes and fungi is greatly influenced by spatial distribution and random events, while bacteria have a relatively stable population composition in specific regions and may also be subject to environmental constraints. Finally, this study revealed that Humicolopsis cephalosporioides, a fungus that exclusively resided in cold environments, may play a critical role as a keystone species in maintaining molecular ecological networks and was considered a core member of the microbiome.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Di Lin
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Ya-Jing Chen
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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20
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Djemiel C, Dequiedt S, Bailly A, Tripied J, Lelièvre M, Horrigue W, Jolivet C, Bispo A, Saby N, Valé M, Maron PA, Ranjard L, Terrat S. Biogeographical patterns of the soil fungal:bacterial ratio across France. mSphere 2023; 8:e0036523. [PMID: 37754664 PMCID: PMC10597451 DOI: 10.1128/msphere.00365-23] [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: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Julie Tripied
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Mélanie Lelièvre
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | | | | | | | | | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
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21
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Lin Y, Tang KW, Ye G, Yang P, Hu HW, Tong C, Zheng Y, Feng M, Deng M, He ZY, He JZ. Community assembly of comammox Nitrospira in coastal wetlands across southeastern China. Appl Environ Microbiol 2023; 89:e0080723. [PMID: 37671870 PMCID: PMC10537594 DOI: 10.1128/aem.00807-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023] Open
Abstract
Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.
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Affiliation(s)
- Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Kam W. Tang
- Department of Biosciences, Swansea University, Swansea, United Kingdom
| | - Guiping Ye
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, Fujian, China
| | - Ping Yang
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
- Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou, Fujian, China
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chuan Tong
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
- Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou, Fujian, China
| | - Yong Zheng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Mengmeng Feng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Milin Deng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Zi-Yang He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Ji-Zheng He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne, Victoria, Australia
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22
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Hou M, Zhao X, Wang Y, Lv X, Chen Y, Jiao X, Sui Y. Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain. Sci Rep 2023; 13:14555. [PMID: 37666914 PMCID: PMC10477331 DOI: 10.1038/s41598-023-41401-0] [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: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.
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Affiliation(s)
- Meng Hou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xiaorui Zhao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Yao Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xuemei Lv
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China
| | - Yimin Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Xiaoguang Jiao
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China.
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China.
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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23
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Amon CER, Fossou RK, Ebou AET, Koua DK, Kouadjo CG, Brou YC, Voko Bi DRR, Cowan DA, Zézé A. The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones. Front Microbiol 2023; 14:1220655. [PMID: 37692382 PMCID: PMC10483230 DOI: 10.3389/fmicb.2023.1220655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.
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Affiliation(s)
- Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Anicet E. T. Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Dominiqueua K. Koua
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Claude Ghislaine Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, Abidjan, Côte d’Ivoire
| | - Yao Casimir Brou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Don Rodrigue Rosin Voko Bi
- Unité de Formation et de Recherche en Agroforesterie, Université Jean Lorougnon Guédé, Daloa, Côte d’Ivoire
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
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24
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Cantoran A, Maillard F, Baldrian P, Kennedy PG. Defining a core microbial necrobiome associated with decomposing fungal necromass. FEMS Microbiol Ecol 2023; 99:fiad098. [PMID: 37656873 DOI: 10.1093/femsec/fiad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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Affiliation(s)
- Anahi Cantoran
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Microbial Ecology Group, Department of Biology, Lund University, Naturvetarvägen 22362, Lund, Sweden
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídenská 1083, Prague 142 20, Czech Republic
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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25
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Zhao S, Zhao X, Li Y, Zhang R, Zhao Y, Fang H, Li W. Impact of altered groundwater depth on soil microbial diversity, network complexity and multifunctionality. Front Microbiol 2023; 14:1214186. [PMID: 37601343 PMCID: PMC10434790 DOI: 10.3389/fmicb.2023.1214186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Understanding the effects of groundwater depth on soil microbiota and multiple soil functions is essential for ecological restoration and the implementation of groundwater conservation. The current impact of increased groundwater levels induced by drought on soil microbiota and multifunctionality remains ambiguous, which impedes our understanding of the sustainability of water-scarce ecosystems that heavily rely on groundwater resources. This study investigated the impacts of altered groundwater depths on soil microbiota and multifunctionality in a semi-arid region. Three groundwater depth levels were studied, with different soil quality and soil moisture at each level. The deep groundwater treatment had negative impacts on diversity, network complexity of microbiota, and the relationships among microbial phylum unites. Increasing groundwater depth also changed composition of soil microbiota, reducing the relative abundance of dominant phyla including Proteobacteria and Ascomycota. Increasing groundwater depth led to changes in microbial community characteristics, which are strongly related to alterations in soil multifunctionality. Overall, our results suggest that groundwater depth had a strongly effect on soil microbiota and functionality.
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Affiliation(s)
- Siteng Zhao
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueyong Zhao
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Rui Zhang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Yanming Zhao
- Tongliao Hydrology and Water Resources Sub-center, Tongliao, China
| | - Hong Fang
- Tongliao Hydrology and Water Resources Sub-center, Tongliao, China
| | - Wenshuang Li
- Tongliao Hydrology and Water Resources Sub-center, Tongliao, China
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26
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Deng W, Zhang F, Li YP, Zhang X, Fornacca D, Yang XY, Xiao W. Uncovering the biogeographic pattern of the widespread nematode-trapping fungi Arthrobotrys oligospora: watershed is the key. Front Microbiol 2023; 14:1152751. [PMID: 37152762 PMCID: PMC10156993 DOI: 10.3389/fmicb.2023.1152751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Studies of biogeographic patterns of fungi have long been behind those of plants and animals. The presence of worldwide species, the lack of systematic sampling design and adequate sampling effort, and the lack of research units are responsible for this status. This study investigates the biogeographical patterns of Arthrobotrys oligospora, the most widespread globally distributed nematode-trapping fungi (NTF), by stratified collecting and analyzing 2,250 samples from 228 sites in Yunnan Province, China. The A. oligospora was isolated, and 149 strains were subjected to ITS, TUB, TEF and RPB2 gene sequencing and multi-gene association phylogeographic analysis. The results show that at population level A. oligospora is randomly distributed throughout Yunnan Province and has no biogeographical distribution pattern. At the genetic level, the phylogenetic tree of A. oligospora diverges into five major evolutionary clades, with a low degree of gene flow between the five clades. However, the correlation between the phylogenetic diversity of A. oligospora and geographical factors was low. There was no clear pattern in the phylogenetic clades distribution of A. oligospora either without dividing the study unit or when the grid was used as the study unit. When watersheds were used as the study unit, 67.4%, 63.3%, 65.9%, 83.3%, and 66.7% of clade 1-5 strains were distributed in the Jinsha river, Red river, Peal river, Lancang river, and Nujiang-Irawaddy river watersheds, respectively. The clades distribution of A. oligospora was highly consistent with the watersheds distribution. Training predictions of the clades distributions using randomly generated polygons were also less accurate than watersheds. These results suggest that watersheds are key to discovering the biogeographic distribution patterns of A. oligospora. The A. oligospora populations are blocked by mountains in the watershed, and gene flow barriers have occurred, which may have resulted in the formation of multiple cryptic species. Watersheds are also ideal for understanding such speciation processes, explaining factors affecting biodiversity distribution and coupling studies of plant and animal and microbial diversity.
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Affiliation(s)
- Wei Deng
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Yan-Peng Li
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali, Yunnan, China
| | - Xin Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Davide Fornacca
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali, Yunnan, China
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Mukhtar H, Wunderlich RF, Muzaffar A, Ansari A, Shipin OV, Cao TND, Lin YP. Soil microbiome feedback to climate change and options for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163412. [PMID: 37059149 DOI: 10.1016/j.scitotenv.2023.163412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO2 and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.
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Affiliation(s)
- Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | | | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Oleg V Shipin
- School of Environmental Engineering and Management, Asian Institute of Technology, Thailand
| | - Thanh Ngoc-Dan Cao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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Xiong G, Zhu X, Wu J, Liu M, Yang Y, Zeng X. Seawater intrusion alters nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions: Based on Bayesian isotope mixing model and microbial functional network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161368. [PMID: 36621512 DOI: 10.1016/j.scitotenv.2022.161368] [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: 10/17/2022] [Revised: 12/07/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Seawater intrusion is a global coastal environmental issue of great concern and significantly impacts the regional biogeochemical environment and material cycles, including nitrogen cycling. To reveal the mechanism of seawater intrusion altering nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions, the Bayesian mixing model (δ15N-NO3- and δ18O-NO3-) and 16S rDNA gene amplicon sequencing are used to establish nitrogen cycling pathways and microbial functional network. The results show that the nitrate in the coastal groundwater is from manure and septic waste (M&S, over 44 %), soil organic nitrogen (SON, over 20 %), and nitrogen fertilizer (FN, over 16 %). The hydrological interaction has promoted the coupling between material cycling and microbial community in the coastal groundwater systems. Among them, precipitation infiltration has caused the gradual decrease of specific microbes along the flow direction, such as Lactobacillus, Acinetobacter, Bifidobacterium, etc. And seawater intrusion has caused the mutations of specific microbes (Planktomarina, Clade_Ia, Wenyingzhuangia, Glaciecola, etc.) and convergence of microbial community at the salt-freshwater interface in the aquifer. In the coastal intruded aquifer systems, the nitrogen cycling pattern can be divided into oxidation and reduction processes. The oxidation process involves the enhancement of nitrification while the weakening of denitrification and anammox with the increase of aquifer depth. The reduction process consists of the enhancement of denitrification and anammox while the erosion of nitrification and ammonification with increased seawater intrusion. In addition, seawater intrusion can mitigate nitrate contamination by promoting denitrification and anammox in coastal areas.
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Affiliation(s)
- Guiyao Xiong
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaobin Zhu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Mengwen Liu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Yun Yang
- School of Earth Sciences and Engineering, Hohai University, Nanjing 211100, China
| | - Xiankui Zeng
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
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Qu S, Shen C, Zhang L, Wang J, Zhang LM, Chen B, Sun GX, Ge Y. Dispersal limitation and host selection drive geo-specific and plant-specific differentiation of soil bacterial communities in the Tibetan alpine ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160944. [PMID: 36526178 DOI: 10.1016/j.scitotenv.2022.160944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soil bacteria, which are active in shrub encroachment, play key roles in regulating ecosystem structure and function. However, the differentiation characteristics and assembly process of bacterial communities in scrubbed grasslands remain unknown. Taking the Qinghai-Tibet Plateau, a hotspot of shrub encroachment, as the study area, we collected 192 soils near nine natural typical shrubs' roots on a trans-longitude transect (about 1800 km) and investigated the bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial communities exhibited plant-specific and geographic-specific differentiation. On the one hand, bacterial communities differed significantly across plant species, with widely distributed shrubs harboring high diversity communities but few plant-specific taxa, and narrowly distributed shrubs possessing low diversity communities but more plant-specific taxa. Besides, there was a significant negative correlation between bacterial community similarity and plant phylogenetic distance. On the other hand, bacterial communities differed across geographic sites, with a significant decay in bacterial community similarity with geographic distance. The bacterial alpha diversity varied in an inverted V-shape from west to east, peaking at 91°E, which could be largely driven by mean annual temperature, soil pH and soil total carbon content. Community differentiation increased with the heterogeneity degree of assembly processes, and the dominant assembly process in these two specific differentiations differed. Dominated by stochastic and deterministic forces, respectively, geography diverged bacterial communities primarily through increased dispersal limitation, whereas plants diverged bacterial communities primarily through increased variable selection. Our study provides new insight into the characteristics and mechanisms of root-surrounding soil bacteria differentiation in scrubbed grasslands, contributing to the scientific management of degraded grasslands and the prediction of bacterial community structure and ecosystem function in response to global change.
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Affiliation(s)
- Sai Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Gruet C, Abrouk D, Börner A, Muller D, Moënne-Loccoz Y. Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere. PLANT, CELL & ENVIRONMENT 2023; 46:1018-1032. [PMID: 36494920 DOI: 10.1111/pce.14508] [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: 08/07/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by quantitative polymerase chain reaction their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Wang Y, Dang N, Feng K, Wang J, Jin X, Yao S, Wang L, Gu S, Zheng H, Lu G, Deng Y. Grass-microbial inter-domain ecological networks associated with alpine grassland productivity. Front Microbiol 2023; 14:1109128. [PMID: 36760496 PMCID: PMC9905801 DOI: 10.3389/fmicb.2023.1109128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Associations between grasses and soil microorganisms can strongly influence plant community structures. However, the associations between grass productivity and diversity and soil microbes, as well as the patterns of co-occurrence between grass and microbes remain unclear. Here, we surveyed grass productivity and diversity, determined soil physicochemical, and sequenced soil archaea, bacteria and fungi by metabarcoding technology at 16 alpine grasslands. Using the Distance-decay relationship, Inter-Domain Ecological Network (IDEN), and Mantel tests, we investigated the relationship between grass productivity, diversity and microbial diversity, and the patterns of co-occurrence between grass and microbial inter-domain network in alpine grassland. We found the archaea richness, bacteria richness and Shannon, and fungi α-diversity were significantly negatively correlation with grass diversity, but archaea and bacteria diversity were positively correlation with grass productivity. Moreover, an increase in microbial β-diversity was observed along with increased discrepancy in grass diversity and productivity and soil variables. Variance partitioning analysis suggested that the contribution of grass productivity on microbial community was higher than that of soil variables and grass diversity, which implies that microbial community was more related to grass productivity. Inter-Domain Ecological Network showed that the grass species formed complex and stable ecological networks with some bacterial, archaeal, and fungal species, and the grass-fungal ecological networks showed the highest robustness, which indicated that soil fungi could better co-coexist with aboveground grass in alpine grasslands. Besides, the connectivity degrees of the grass-microbial network were significantly positively correlated with grass productivity, suggesting that the coexistence pattern of grasses and microbes had a positive feedback effect on the grass productivity. The results are important for establishing the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.
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Affiliation(s)
- Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China,CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ning Dang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Junbang Wang
- National Ecosystem Science Data Center, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Xin Jin
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Shiting Yao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Linlin Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Hua Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guangxin Lu
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China,*Correspondence: Guangxin Lu ✉
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China,Ye Deng ✉
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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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Li Q, Qiu J, Liang Y, Lan G. Soil bacterial community changes along elevation gradients in karst graben basin of Yunnan-Kweichow Plateau. Front Microbiol 2022; 13:1054667. [PMID: 36620048 PMCID: PMC9813600 DOI: 10.3389/fmicb.2022.1054667] [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: 09/27/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Elevation gradients could provide natural experiments to examine geomorphological influences on biota ecology and evolution, however little is known about microbial community structures with soil depths along altitudinal gradients in karst graben basin of Yunnan-Kweichow Plateau. Here, bulk soil in A layer (0 ~ 10 cm) and B layer (10 ~ 20 cm) from two transect Mounts were analyzed by using high-throughput sequencing coupled with physicochemical analysis. It was found that the top five phyla in A layer were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia, and the top five phyla in B layer were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi in a near-neutral environment. Edaphic parameters were different in two layers along altitudinal gradients. Besides that, soil microbial community compositions varied along altitudinal gradient, and soil organic carbon (SOC) and total nitrogen (TN) increased monotonically with increasing elevation. It was further observed that Shannon indexes with increasing altitudes in two transect Mounts decreased monotonically with significant difference (p = 0.001), however beta diversity followed U-trend with significant difference (p = 0.001). The low proportions of unique operational taxonomic units (OTUs) appeared at high altitude areas which impact the widely accepted elevation Rapoport's rules. The dominant Bradyrhizobium (alphaproteobacterial OTU 1) identified at high altitudes in two layers constitutes the important group of free-living diazotrophs and could bring fixed N into soils, which simultaneously enhances SOC and TN accumulation at high altitudes (p < 0.01). Due to different responses of bacterial community to environmental changes varying with soil depths, altitudinal gradients exerted negative effects on soil bacterial communities via soil physical properties and positive effects on soil bacterial diversities via soil chemical properties in A layer, however the results in B layer were opposite. Overall, our study is the first attempt to bring a deeper understanding of soil microbial structure patterns along altitudinal gradients at karst graben basin areas.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China,*Correspondence: Qiang Li, ✉
| | - Jiangmei Qiu
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Yueming Liang
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Gaoyong Lan
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
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Wang Y, He Y, Ding M, Wang Z, Zhou S. Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest. Curr Microbiol 2022; 79:368. [PMID: 36253615 DOI: 10.1007/s00284-022-03049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022]
Abstract
Understanding plant-microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.
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Affiliation(s)
- Yukun Wang
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Yuran He
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Mao Ding
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Zhi Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, Nanjing, 210042, China
| | - Shoubiao Zhou
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China.
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, 241002, China.
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Durán P, Ellis TJ, Thiergart T, Ågren J, Hacquard S. Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations. THE NEW PHYTOLOGIST 2022; 236:608-621. [PMID: 35794837 DOI: 10.1111/nph.18357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Disentangling the contribution of climatic and edaphic factors to microbiome variation and local adaptation in plants requires an experimental approach to uncouple their effects and test for causality. We used microbial inocula, soil matrices and plant genotypes derived from two natural Arabidopsis thaliana populations in northern and southern Europe in an experiment conducted in climatic chambers mimicking seasonal changes in temperature, day length and light intensity of the home sites of the two genotypes. The southern A. thaliana genotype outperformed the northern genotype in the southern climate chamber, whereas the opposite was true in the northern climate chamber. Recipient soil matrix, but not microbial composition, affected plant fitness, and effects did not differ between genotypes. Differences between chambers significantly affected rhizosphere microbiome assembly, although these effects were small in comparison with the shifts induced by physicochemical differences between soil matrices. The results suggest that differences in seasonal changes in temperature, day length and light intensity between northern and southern Europe have strongly influenced adaptive differentiation between the two A. thaliana populations, whereas effects of differences in soil factors have been weak. By contrast, below-ground differences in soil characteristics were more important than differences in climate for rhizosphere microbiome differentiation.
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Affiliation(s)
- Paloma Durán
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- LIPME, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Castanet-Tolosan, 31326, France
| | - Thomas James Ellis
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
- Gregor Mendel Institute of Molecular Plant Sciences, Austrian Academy of Sciences, Doktor-Bohr-Gasse 3, 1030, Vienna, Austria
| | - Thorsten Thiergart
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jon Ågren
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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Zhang D, Tang Y, Zhang C, Huhe F, Wu B, Gong X, Chuang SSC, Zheng J. Formulating Zwitterionic, Responsive Polymers for Designing Smart Soils. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203899. [PMID: 35996809 DOI: 10.1002/smll.202203899] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The design of new remediation strategies and materials for treating saline-alkaline soils is of fundamental and practical importantance for many applications. Conventional soil remediation strategies mainly focus on the development of fertilizers or additives for water, nutrient, and heavy metal managements in soils, but they often overlook a soil sensing function for early detection of salinization/alkalization levels toward optimal and timely soil remediation. Here, new smart soils, structurally consisting of the upper signal soil and the bottom hygroscopic bed and chemically including zwitterionic, thermo-responsive poly(NIPAM-co-VPES) and poly(NIPAM-co-SBAA) aerogels in each soil layer are formulated. Upon salinization, the resultant smart soils exhibit multiple superior capacities for reducing the soil salinity and alkalinity through ion exchange, controlling the water cycling, modulating the degradation of pyridine-base ligands into water-soluble, nitrogenous salts-rich ingredients for soil fertility, and real-time monitoring salinized soils via pH-induced allochroic color changes. Further studies of plant growth in smart soils with or without salinization treatments confirm a synergy effect of soil remediation and soil sensing on facilitating the growth of plants and increasing the saline-alkaline tolerance of plants. The esign concept of smart soils can be further expanded for soil remediation and assessment.
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Affiliation(s)
- Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Chang Zhang
- Ningbo Institute of Material Technology and Engineering, Chinese Academy of Sciences, Zhongguan West Road 1219, Ningbo, 315201, China
| | - Fnu Huhe
- School of Polymer Science and Polymer Engineering, The University of Akron, 170 University Avenue, Akron, OH, 44325, USA
| | - Baoyi Wu
- Ningbo Institute of Material Technology and Engineering, Chinese Academy of Sciences, Zhongguan West Road 1219, Ningbo, 315201, China
| | - Xiong Gong
- School of Polymer Science and Polymer Engineering, The University of Akron, 170 University Avenue, Akron, OH, 44325, USA
| | - Steven S C Chuang
- School of Polymer Science and Polymer Engineering, The University of Akron, 170 University Avenue, Akron, OH, 44325, USA
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
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38
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Cowan DA, Lebre PH, Amon C, Becker RW, Boga HI, Boulangé A, Chiyaka TL, Coetzee T, de Jager PC, Dikinya O, Eckardt F, Greve M, Harris MA, Hopkins DW, Houngnandan HB, Houngnandan P, Jordaan K, Kaimoyo E, Kambura AK, Kamgan-Nkuekam G, Makhalanyane TP, Maggs-Kölling G, Marais E, Mondlane H, Nghalipo E, Olivier BW, Ortiz M, Pertierra LR, Ramond JB, Seely M, Sithole-Niang I, Valverde A, Varliero G, Vikram S, Wall DH, Zeze A. Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes. MICROBIOME 2022; 10:131. [PMID: 35996183 PMCID: PMC9396824 DOI: 10.1186/s40168-022-01297-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/15/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - P H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Cer Amon
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
| | - R W Becker
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - H I Boga
- Taita Taveta University, Voi, Kenya
| | - A Boulangé
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
- UMR InterTryp, CIRAD-IRD, 34398, Montpellier, France
| | - T L Chiyaka
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - T Coetzee
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - P C de Jager
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - O Dikinya
- Department of Environmental Science, University of Botswana, Gaborone, Botswana
| | - F Eckardt
- Department of Geography, University of Cape Town, Cape Town, South Africa
| | - M Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M A Harris
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - D W Hopkins
- Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - H B Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - P Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - K Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - E Kaimoyo
- University of Zambia, Lusaka, Zambia
| | | | - G Kamgan-Nkuekam
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - T P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - E Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - H Mondlane
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - E Nghalipo
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - B W Olivier
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - L R Pertierra
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - J-B Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - M Seely
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - I Sithole-Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - A Valverde
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - S Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - D H Wall
- Department of Biology, Colorado State University, Fort Collins, USA
| | - A Zeze
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
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Wu MH, Xue K, Wei PJ, Jia YL, Zhang Y, Chen SY. Soil microbial distribution and assembly are related to vegetation biomass in the alpine permafrost regions of the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155259. [PMID: 35452733 DOI: 10.1016/j.scitotenv.2022.155259] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/09/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
It is generally believed that there is a vegetation succession sequence from alpine marsh meadow to desert in the alpine ecosystem of the Qinghai-Tibet Plateau. However, we still have a limited understanding about distribution patterns and community assemblies of microorganisms' response to such vegetation changes. Hence, across a gradient represented by three types of alpine vegetation from swamp meadow to meadow to steppe, the soil bacterial, fungal and archaeal diversity was evaluated and then associated with their assembly processes, and glacier foreland vegetation was also surveyed as a case out of this gradient. Vegetation biomass was found to decrease significantly along the vegetation gradient. In contrast to irregular shifts in alpha diversity, bacterial and fungal beta diversities that were dominated by species replacement components (71.07-79.08%) significantly increased with the decreasing gradient in vegetation biomass (P < 0.05). These trends of increase were also found in the extent of stochastic bacterial and fungal assembly. Moreover, an increase in microbial beta diversity but a decrease in beta nearest taxon index were observed along with increased discrepancy in vegetation biomass (P < 0.001). Stepwise regression analyses and structural equation models suggested that vegetation biomass was the major variable that was related to microbial distribution and community assembly, and there might be associations between the dominance of species replacements and stochastic assembly. These findings enhanced our recognition of the relationship between vegetation and soil microorganisms and would facilitate the development of vegetation-microbe feedback models in alpine ecosystems.
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Affiliation(s)
- Ming-Hui Wu
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Jie Wei
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Lan Jia
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- Long-term National Scientific Research Base of the Qilian Mountain National Park, Xining, Qinghai 810000, China
| | - Sheng-Yun Chen
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; Long-term National Scientific Research Base of the Qilian Mountain National Park, Xining, Qinghai 810000, China.
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40
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Song M, Zhang X, Yang J, Gao C, Wei Y, Chen S, Liesche J. Arabidopsis plants engineered for high root sugar secretion enhance the diversity of soil microorganisms. Biotechnol J 2022; 17:e2100638. [PMID: 35894173 DOI: 10.1002/biot.202100638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/06/2022]
Abstract
Plants secrete sugars from their roots into the soil, presumably to support beneficial plant-microbe interactions. Accordingly, manipulation of sugar secretion might be a viable strategy to enhance plant health and productivity. To evaluate the effect of increased root sugar secretion on plant performance and the soil microbiome, we overexpressed glucose and sucrose-specific membrane transporters in root epidermal cells of the model plant Arabidopsis thaliana. These plants showed strongly increased rates of sugar secretion in a hydroponic culture system. When grown on soil, the transporter-overexpressor plants displayed a higher photosynthesis rate, but reduced shoot growth compared to the wild-type control. Amplicon sequencing and qPCR analysis of rhizosphere soil samples indicated a limited effect on the total abundance of bacteria and fungi, but a strong effect on community structure in soil samples associated with the overexpressors. Notable changes included the increased abundance of bacteria belonging to the genus Rhodanobacter and the fungi belonging to the genus Cutaneotrichosporon, while Candida species abundance was reduced. The potential influences of the altered soil microbiome on plant health and productivity are discussed. The results indicate that the engineering of sugar secretion can be a viable pathway to enhancing the carbon sequestration rate and optimizing the soil microbiome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Min Song
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Xingjian Zhang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Jintao Yang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Chen Gao
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Yahong Wei
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China
| | - Johannes Liesche
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
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Shu X, He J, Zhou Z, Xia L, Hu Y, Zhang Y, Zhang Y, Luo Y, Chu H, Liu W, Yuan S, Gao X, Wang C. Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154627. [PMID: 35306065 DOI: 10.1016/j.scitotenv.2022.154627] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/22/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Fertilization plays an important role in changing soil microbial diversity, which is essential for determining crop yields. Yet, the influence of organic amendments on microbial diversity remains uncertain, and few studies have addressed the relative importance of microbial diversity versus other drivers of crop yields. Here, we synthesize 219 studies worldwide and found that organic amendments significantly increased microbial diversity components (i.e., Shannon, richness, and phylogenetic diversity) and shifted microbial community structure compared to mineral-only fertilization. The performance of microbial alpha diversity varied substantially with organic amendment types, microbial groups and changes in soil pH. Both microbial diversity and community structure exhibited significantly positive relationships with microbial functionality and crop yields. In addition, soil abiotic properties and microbial functionality had a much stronger impact on crop yields than microbial diversity and climate factors. Partial least squares path modeling showed that soil microbial diversity was an important underlying factor driving crop yields via boosting soil microbial functionality. Overall, our findings provide robust evidence for the positive diversity-functions relationships, emphasizing that substituting mineral fertilizers with organic amendments is a promising way to conserve microbial diversity and promote soil microbial functions and crop yields.
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Affiliation(s)
- Xiangyang Shu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia He
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenghu Zhou
- Center for Ecological Research, Northeast Forestry University, Harbin 150040, China
| | - Longlong Xia
- Institute for Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany
| | - Yufu Hu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yulin Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China
| | - Weijia Liu
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuesong Gao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
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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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Legeay J, Hijri M. A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02060-2. [PMID: 35739325 DOI: 10.1007/s00248-022-02060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.
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Affiliation(s)
- Jean Legeay
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
| | - Mohamed Hijri
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Institut de La Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montreal, QE, H1X 2B2, Canada
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Fall F, Sanguin H, Fall D, Tournier E, Bakhoum N, Ndiaye C, Diouf D, Bâ AM. Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient. MICROBIAL ECOLOGY 2022; 83:886-898. [PMID: 34245330 DOI: 10.1007/s00248-021-01779-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.
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Affiliation(s)
- Fatoumata Fall
- LCM Laboratoire Commun de Microbiologie, IRD, ISRA, UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal
- LAPSE Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux, Dakar, Senegal
| | - Hervé Sanguin
- CIRAD, UMR PHIM, 34090, Montpellier, France.
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, Univ Montpellier, Montpellier, France.
| | - Dioumacor Fall
- LCM Laboratoire Commun de Microbiologie, IRD, ISRA, UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal
- Institut Sénégalais de Recherches Agricoles (ISRA), Centre National de Recherches Agronomiques (CNRA), Bambey, Senegal
| | - Estelle Tournier
- CIRAD, UMR PHIM, 34090, Montpellier, France
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | - Niokhor Bakhoum
- LCM Laboratoire Commun de Microbiologie, IRD, ISRA, UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal
- LAPSE Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux, Dakar, Senegal
- Département Environnement, Biodiversité Et Développement Durable, Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), Kaolack, Senegal
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Diégane Diouf
- Département Environnement, Biodiversité Et Développement Durable, Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), Kaolack, Senegal
| | - Amadou Mustapha Bâ
- Laboratoire de Biologie Et Physiologie Végétales, Université Des Antilles, Guadeloupe, France
- LSTM, CIRAD, INRAE, IRD, Institut Agro, Univ Montpellier, Montpellier, France
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Calderón‐Sanou I, Zinger L, Hedde M, Martinez‐Almoyna C, Saillard A, Renaud J, Gielly L, Khedim N, Lionnet C, Ohlmann M, Consortium O, Münkemüller T, Thuiller W. Energy and physiological tolerance explain multi‐trophic soil diversity in temperate mountains. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Irene Calderón‐Sanou
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Lucie Zinger
- Département de biologie Institut de Biologie de l’ENS (IBENS) École normale supérieure CNRS INSERM Université PSL Paris France
| | - Mickael Hedde
- Eco&Sols Univ Montpellier CIRAD INRA IRD Montpellier SupAgro Montpellier France
| | - Camille Martinez‐Almoyna
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Amelie Saillard
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Julien Renaud
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Norine Khedim
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
- Univ. Savoie Mont‐Blanc Univ. Grenoble Alpes CNRS EDYTEM Chambéry France
| | - Clement Lionnet
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Marc Ohlmann
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | | | - Tamara Münkemüller
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
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46
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Bahram M, Espenberg M, Pärn J, Lehtovirta-Morley L, Anslan S, Kasak K, Kõljalg U, Liira J, Maddison M, Moora M, Niinemets Ü, Öpik M, Pärtel M, Soosaar K, Zobel M, Hildebrand F, Tedersoo L, Mander Ü. Structure and function of the soil microbiome underlying N 2O emissions from global wetlands. Nat Commun 2022; 13:1430. [PMID: 35301304 PMCID: PMC8931052 DOI: 10.1038/s41467-022-29161-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 02/23/2022] [Indexed: 01/16/2023] Open
Abstract
Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.
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Affiliation(s)
- Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. .,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Pärn
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kuno Kasak
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Liira
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kaido Soosaar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, Norfolk, UK.,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Leho Tedersoo
- College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Bernard L, Basile‐Doelsch I, Derrien D, Fanin N, Fontaine S, Guenet B, Karimi B, Marsden C, Maron P. Advancing the mechanistic understanding of the priming effect on soil organic matter mineralisation. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laetitia Bernard
- IRD UMR Eco&Sols INRAE, CIRAD Institut Agro Univ Montpellier 2 place Viala Bt12 34060 Montpellier France
| | | | | | - Nicolas Fanin
- INRAE UMR 1391 ISPA, Bordeaux Sciences Agro 71 Avenue Edouard Bourlaux, CS 20032 Villenave‐d’Ornon Cedex F33882 France
| | - Sébastien Fontaine
- INRAE Université Clermont Auvergne VetAgro Sup UMR Ecosystème Prairial 63000 Clermont Ferrand France
| | - Bertrand Guenet
- Laboratoire de Géologie Ecole Normale Supérieure/CNRS UMR8538 IPSL PSL Research University Paris France
| | | | - Claire Marsden
- Institut Agro UMR Eco&Sols, IRD, INRAE, CIRAD Univ Montpellier 2 place Viala Bt12 34060
| | - Pierre‐Alain Maron
- INRAE UMR AgroEcologie AgroSup Dijon, BP 87999, CEDEX 21079 Dijon France
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Comprehensive assessment of harmful heavy metals in contaminated soil in order to score pollution level. Sci Rep 2022; 12:3552. [PMID: 35241759 PMCID: PMC8894455 DOI: 10.1038/s41598-022-07602-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
Soil-related problems have grown up to be a major threat to human society. Scientific evaluation is helpful to understand the status of soil pollution and provide reference to further work. In this situation, Liaoning Province, a typical industrial and agricultural province in Northeast China, was selected as a case study region. It reviewed 200 studies published between 2010 and 2020 and recorded related data of soil heavy metal. It used model method and index method to evaluate the agricultural region. The comprehensive assessment score of Liaoning pollution level was 0.8998. Dalian was 0.9536, ranking first among the 14 cities. Huludao and Jinzhou were 0.7594 respectively, ranked the last. Heavy metal accumulation in different cities stemmed from different sources, including weathering of parent materials, industrial wastes, sewage irrigation, and mining activities. In general, the pollution level of heavy metal in Liaoning was at low risk level, but it still needs to pay attention to the health risk of heavy metal and the input of heavy metal into the soil, especially cadmium (Cd). This study provides a comprehensive assessment of soil heavy metal pollution in Liaoning, while identifying policy recommendations for pollution mitigation and environmental management.
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49
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Soil Type Influences Rhizosphere Bacterial Community Assemblies of Pecan Plantations, a Case Study of Eastern China. FORESTS 2022. [DOI: 10.3390/f13030363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The rhizosphere microbiome is closely related to forest health and productivity. However, whether soil type affects pecan (Carya illinoinensis) rhizosphere microbiomes is unclear. We aimed to explore the diversity and structural characteristics of rhizosphere bacteria associated with pecan plantations grown in three soil types (Luvisols, Cambisols, Solonchaks) in Eastern China and analyze their potential functions through high-throughput sequencing. The results showed that the diversity and community structure of rhizosphere bacteria in pecan plantations were significantly affected by soil type and the pH, available phosphorus content, electrical conductivity, soil moisture, and ammonium nitrogen contents were the main factors. At the phylum level, the rhizosphere bacterial community composition was consistent, mainly included Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi. At the family level, the pecan plantations formed different rhizosphere enriched biomarkers due to the influence of soil type, with functional characteristics such as plant growth promotion and soil nutrient cycling. In addition, there existed low abundance core species such as Haliangiaceae, Bryobacteraceae, and Steroidobacteraceae. They played important roles in the rhizosphere environments through their functional characteristics and community linkages. Overall, this study provides a basis for the study of the rhizosphere microbiome in different soil types of pecan plantations, and plays an important role in the sustainable management of forest soil.
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50
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Gschwend F, Hartmann M, Mayerhofer J, Hug AS, Enkerli J, Gubler A, Meuli RG, Frey B, Widmer F. Site and land-use associations of soil bacteria and fungi define core and indicative taxa. FEMS Microbiol Ecol 2022; 97:fiab165. [PMID: 34940884 PMCID: PMC8752248 DOI: 10.1093/femsec/fiab165] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.
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Affiliation(s)
- Florian Gschwend
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, CH-8092 Zürich, Switzerland
| | - Johanna Mayerhofer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Anna-Sofia Hug
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Andreas Gubler
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Reto G Meuli
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
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