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Cuartero J, Querejeta JI, Prieto I, Frey B, Alguacil MM. Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175006. [PMID: 39069184 DOI: 10.1016/j.scitotenv.2024.175006] [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: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.
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Affiliation(s)
- J Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland.
| | - J I Querejeta
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - I Prieto
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain; Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - B Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - M M Alguacil
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
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2
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Huang H, Lyu X, Xiao F, Fu J, Xu H, Wu J, Sun Y. Three-year field study on the temporal response of soil microbial communities and functions to PFOA exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135008. [PMID: 38943893 DOI: 10.1016/j.jhazmat.2024.135008] [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: 01/20/2024] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024]
Abstract
Contamination of per- and polyfluoroalkyl substances (PFAS) poses a significant threat to soil ecosystem health, yet there remains a lack of understanding regarding the responses of soil microbial communities to prolonged PFAS exposure in field conditions. This study involved a three-year field investigation to track changes in microbial communities and functions in soil subjected to the contamination of a primary PFAS, perfluorooctanoic acid (PFOA). Results showed that PFOA exposure altered soil bacterial and fungal communities in terms of diversity, composition, and structure. Notably, certain bacterial communities with a delayed reaction to PFOA contamination showed the most significant response after one year of exposure. Fungal communities were sensitive to PFOA in soil, exhibiting significant responses within just four months of exposure. After two years, the impact of PFOA on both bacterial and fungal communities was lessened, likely due to the long-term adaptation of microbial communities to PFOA. Moreover, PFOA exposure notably inhibited alkaline phosphatase activity and reduced certain phosphorus cycling-related functional genes after three years of exposure, suggesting potential disruptions in soil fertility. These new insights advance our understanding of the long-term effects of PFOA on soil microbial communities and functions at a field scale.
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Affiliation(s)
- Hai Huang
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China
| | - Xueyan Lyu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Feng Xiao
- Department of Civil and Environmental Engineering, University of Missouri, Columbia, MO 65211, USA
| | - Jiaju Fu
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China
| | - Hongxia Xu
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China
| | - Jichun Wu
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China; Technology Innovation Center for Ecological Monitoring & Restoration Project on Land (Arable), Nanjing 210018, China
| | - Yuanyuan Sun
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China; Technology Innovation Center for Ecological Monitoring & Restoration Project on Land (Arable), Nanjing 210018, China.
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3
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Tziros GT, Samaras A, Karaoglanidis GS. Soil Solarization Efficiently Reduces Fungal Soilborne Pathogen Populations, Promotes Lettuce Plant Growth, and Affects the Soil Bacterial Community. BIOLOGY 2024; 13:624. [PMID: 39194562 DOI: 10.3390/biology13080624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
Lettuce is the most cultivated leafy vegetable in Greece; however, due to the adopted intensive cropping system, its cultivation is susceptible to many soilborne pathogens that cause significant yield and quality losses. In the current study, the impact of various soil disinfestation methods such as solarization, chemical disinfestation, and application of a biofungicide were evaluated in a commercial field that has been repeatedly used for lettuce cultivation. The populations of soilborne pathogens Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Fusarium equiseti were measured via qPCR before and after the implementation of the specific disinfestation methods. Although all the tested methods significantly reduced the population of the four soilborne pathogens, soil solarization was the most effective one. In addition, solarization reduced the number of lettuce plants affected by the pathogens R. solani and F. equiseti, and at the same time, significantly influenced the growth of lettuce plants. Amplicon sequence analysis of 16S rRNA-encoding genes used to study the soil bacterial community structure showed that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla in soil samples. In general, solarization had positive effects on Firmicutes and negative effects on Proteobacteria and Actinobacteria; soil fumigation with dazomet increased the relative abundance of Firmicutes and Proteobacteria and reduced the corresponding values of Actinobacteria; and biofungicide had no significant effects on the three predominant bacterial phyla. The bacterial community composition and structure varied after the application of the soil disinfestation treatments since they imposed changes in the α- and β-diversity levels. The results of this study are expected to contribute towards implementing the most effective control method against the most common soilborne pathogens in intensively cultivated fields, such as those cultivated with leafy vegetables.
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Affiliation(s)
- George T Tziros
- Laboratory of Plant Pathology, Forestry and Natural Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, P.O. Box 269, 54124 Thessaloniki, Greece
| | - Anastasios Samaras
- Laboratory of Plant Pathology, Forestry and Natural Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, P.O. Box 269, 54124 Thessaloniki, Greece
| | - George S Karaoglanidis
- Laboratory of Plant Pathology, Forestry and Natural Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, P.O. Box 269, 54124 Thessaloniki, Greece
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4
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Doulcier G, Lambert A. Neutral diversity in experimental metapopulations. Theor Popul Biol 2024; 158:89-108. [PMID: 38493997 DOI: 10.1016/j.tpb.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial populations are grown in parallel serial transfers, in some cases with population-wide extinction and splitting events. We model bacterial growth by a birth-death process and use the theory of coalescent point processes. We show that there is a dilution factor that optimises the expected amount of neutral diversity for a given number of cycles, and study the power law behaviour of the mutation frequency spectrum for different experimental regimes. We also explore how neutral variation diverges between two recently split populations by establishing a new formula for the expected number of shared and private mutations. Finally, we show the interest of such a setup to select a phenotype of interest that requires multiple mutations.
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Affiliation(s)
- Guilhem Doulcier
- Macquarie University, Department of Philosophy, Sydney, Australia; Max Planck Institute for Evolutionary Biology, Department of Theoretical Biology, Plön, Germany.
| | - Amaury Lambert
- SMILE - Stochastic Models for the Inference of Life Evolution, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS UMR8197, INSERM U1024, France; Centre Interdisciplinaire de Recherche en Biologie (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, PSL Université, Paris, France.
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5
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Yates C, King WL, Richards SC, Wilson C, Viddam V, Blakney AJC, Eissenstat DM, Bell TH. Temperate trees locally engineer decomposition and litter-bound microbiomes through differential litter deposits and species-specific soil conditioning. THE NEW PHYTOLOGIST 2024; 243:909-921. [PMID: 38877705 DOI: 10.1111/nph.19900] [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: 01/15/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
Leaf decomposition varies widely across temperate forests, shaped by factors like litter quality, climate, soil properties, and decomposers, but forest heterogeneity may mask local tree influences on decomposition and litter-associated microbiomes. We used a 24-yr-old common garden forest to quantify local soil conditioning impacts on decomposition and litter microbiology. We introduced leaf litter bags from 10 tree species (5 arbuscular mycorrhizal; 5 ectomycorrhizal) to soil plots conditioned by all 10 species in a full-factorial design. After 6 months, we assessed litter mass loss, C/N content, and bacterial and fungal composition. We hypothesized that (1) decomposition and litter-associated microbiome composition would be primarily shaped by the mycorrhizal type of litter-producing trees, but (2) modified significantly by underlying soil, based on mycorrhizal type of the conditioning trees. Decomposition and, to a lesser extent, litter-associated microbiome composition, were primarily influenced by the mycorrhizal type of litter-producing trees. Interestingly, however, underlying soils had a significant secondary influence, driven mainly by tree species, not mycorrhizal type. This secondary influence was strongest under trees from the Pinaceae. Temperate trees can locally influence underlying soil to alter decomposition and litter-associated microbiology. Understanding the strength of this effect will help predict biogeochemical responses to forest compositional change.
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Affiliation(s)
- Caylon Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Cullen Wilson
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vedha Viddam
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew J C Blakney
- Department of Physical and Environmental Sciences, University of Toronto - Scarborough, Toronto, ON, M1A 1C4, Canada
| | - David M Eissenstat
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Physical and Environmental Sciences, University of Toronto - Scarborough, Toronto, ON, M1A 1C4, Canada
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6
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Laurich JR, Lash E, O'Brien AM, Pogoutse O, Frederickson ME. Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant. mBio 2024; 15:e0097224. [PMID: 38904411 PMCID: PMC11324027 DOI: 10.1128/mbio.00972-24] [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: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes. IMPORTANCE There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.
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Affiliation(s)
- Jason R. Laurich
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Emma Lash
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Anna M. O'Brien
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
- Department of
Molecular, Cellular, and Biomedical Sciences, University of New
Hampshire, Durham,
New Hampshire, USA
| | - Oxana Pogoutse
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Megan E. Frederickson
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
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Chen Y, Tao S, Ma J, Qu Y, Sun Y, Wang M, Cai Y. New insights into assembly processes and driving factors of urban soil microbial community under environmental stress in Beijing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174551. [PMID: 38972416 DOI: 10.1016/j.scitotenv.2024.174551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/21/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Rapid urbanization leads to drastic environmental changes, directly or indirectly affecting the structure and function of soil microbial communities. However, the ecological response of soil microbes to environmental stresses has not yet been fully explored. In this study, we used high-throughput sequencing to analyze the assembly mechanism and driving factors of soil microbial community under environmental stresses. The results indicated that environmental stresses significantly affected soil properties and the levels of beryllium, cobalt, antimony, and vanadium contamination in soil generally increased from the suburban areas toward the city core. The composition and distribution of soil microbial communities demonstrated clear differences under different levels of environmental stress, but there was no significant difference in microbial diversity. Random forest and partial least squares structural equation modeling results suggested that multiple factors influenced microbial diversity, but antimony was the key driver. The influence of environmental stress led to deterministic processes dominating microbial community assembly processes, which promoted the regional homogenization of soil microbes. Therefore, this study provides new insights into urban soil microbial management under environmental stresses.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shiyang Tao
- South China Institute of Environmental Science, Ministry of Ecological Environment, Guangzhou 510655, China
| | - Jin Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Yajing Qu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yi Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Meiying Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yuxuan Cai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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8
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Picariello E, De Nicola F. Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions. MICROBIAL ECOLOGY 2024; 87:86. [PMID: 38940921 PMCID: PMC11213729 DOI: 10.1007/s00248-024-02402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.
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Affiliation(s)
- Enrica Picariello
- Department of Sciences and Technologies, University of Sannio, 82100, Benevento, Italy.
| | - Flavia De Nicola
- Department of Sciences and Technologies, University of Sannio, 82100, Benevento, Italy
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Wang J, Jia M, Zhang L, Li X, Zhang X, Wang Z. Biodegradable microplastics pose greater risks than conventional microplastics to soil properties, microbial community and plant growth, especially under flooded conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172949. [PMID: 38703848 DOI: 10.1016/j.scitotenv.2024.172949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/10/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Biodegradable plastics (bio-plastics) are often viewed as viable option for mitigating plastic pollution. Nevertheless, the information regarding the potential risks of microplastics (MPs) released from bio-plastics in soil, particularly in flooded soils, is lacking. Here, our objective was to investigate the effect of polylactic acid MPs (PLA-MPs) and polyethylene MPs (PE-MPs) on soil properties, microbial community and plant growth under both non-flooded and flooded conditions. Our results demonstrated that PLA-MPs dramatically increased soil labile carbon (C) content and altered its composition and chemodiversity. The enrichment of labile C stimulated microbial N immobilization, resulting in a depletion of soil mineral nitrogen (N). This specialized environment created by PLA-MPs further filtered out specific microbial species, resulting in a low diversity and simplified microbial community. PLA-MPs caused an increase in denitrifiers (Noviherbaspirillum and Clostridium sensu stricto) and a decrease in nitrifiers (Nitrospira, MND1, and Ellin6067), potentially exacerbating the mineral N deficiency. The mineral N deficit caused by PLA-MPs inhibited wheatgrass growth. Conversely, PE-MPs had less effect on soil ecosystems, including soil properties, microbial community and wheatgrass growth. Overall, our study emphasizes that PLA-MPs cause more adverse effect on the ecosystem than PE-MPs in the short term, and that flooded conditions exacerbate and prolong these adverse effects. These results offer valuable insights for evaluating the potential threats of bio-MPs in both uplands and wetlands.
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Affiliation(s)
- Jie Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Minghao Jia
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China
| | - Long Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaona Li
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China
| | - Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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10
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Urbaniak M, Mierzejewska-Sinner E, Bednarek A, Krauze K, Włodarczyk-Marciniak R. Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172360. [PMID: 38614349 DOI: 10.1016/j.scitotenv.2024.172360] [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: 01/31/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years. Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H'), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H' and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity. The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.
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Affiliation(s)
- Magdalena Urbaniak
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Elżbieta Mierzejewska-Sinner
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Agnieszka Bednarek
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Kinga Krauze
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Lodz, Poland.
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Brindhadevi K, Chinnathambi A, Al Obaid S. An investigation on the conversion of infertile soil into fertile soil using crop waste as a remedial (compost) approach and its influence on Vigna mungo biometric and biomolecule profile. ENVIRONMENTAL RESEARCH 2024; 258:119351. [PMID: 38844030 DOI: 10.1016/j.envres.2024.119351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/17/2024]
Abstract
The sustainable management of huge volume of agricultural waste in India can be resolved through composting and used as soil amendment. Agriculture waste compost amendments can optimistically alter the physicochemical (pH, C, N, & P) as well as biological nature (microbial activity/biomass and enzymatic activity) of infertile soil. Hence this study, the agriculture wastes such as sugarcane trash, corn stover, and pearl millet stalks were converted to composite through decomposition pit. Interestingly, test crops residues individual composites and their mixed form contained considerable quantity of vital elements like TC, TN, TP, TK, and C:N ratio and can effectively convert infertile soil to fertile soil. These test crop composites also had a significant impact on MBN (42.3 μg g-1), MBC (198.4 μg g-1), and MBP (196.4 μg g-1) in test soil, as well as dehydrogenase and alkaline phosphatase enzyme activity. However, the mixed composite effects are significantly greater than the individual test crop composite effects. Furthermore, it effectively remediates/converts infertile soil to fertile soil, and it ultimately demonstrated positive effects on Vigna mungo biometric (SH, RH, WB, and DB) and biomolecule (total chlorophyll, total carbohydrate, and total proteins) profiles, followed by individual test crop composites. According to the findings of this study, the incorporation of crop residue-based mixed composite significantly transforms infertile soil into fertile soil and promotes the growth of V. mungo.
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Affiliation(s)
- Kathirvel Brindhadevi
- University Centre for Research & Development, Department of Chemistry, Chandigarh University, Mohali, 140103, India.
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451, Saudi Arabia
| | - Sami Al Obaid
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451, Saudi Arabia
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12
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Nolan TM, Martin NA, Reynolds LJ, Sala-Comorera L, O'Hare GMP, O'Sullivan JJ, Meijer WG. Agricultural and urban practices are correlated to changes in the resistome of riverine systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172261. [PMID: 38583611 DOI: 10.1016/j.scitotenv.2024.172261] [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: 11/13/2023] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
The objective of this study was to comprehensively characterise the resistome, the collective set of antimicrobial resistance genes in a given environment, of two rivers, from their source to discharge into the sea, as these flow through areas of different land use. Our findings reveal significant differences in the riverine resistome composition in areas of different land uses, with increased abundance and diversity of AMR in downstream agricultural and urban locations, with the resistome in urban areas more similar to the resistome in wastewater. The changes in resistome were accompanied by changes in microbial communities, with a reduction in microbial diversity in downstream agricultural and urban affected areas, driven mostly by increased relative abundance in the phyla, Bacteroidetes and Proteobacteria. These results provide insight into how pollution associated with agricultural and urban activities affects microbial communities and influences AMR in aquatic water bodies. These results add valuable insights to form effective strategies for mitigating and preserving aquatic ecosystems. Overall, our study highlights the critical role of the environment in the development and dissemination of AMR and underscores the importance of adopting a One Health approach to address this global public health threat.
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Affiliation(s)
- Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Gregory M P O'Hare
- School of Computer Science and Statistics, Trinity College Dublin, Dublin 2, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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13
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Fu Y, Tang X, Sun T, Lin L, Wu L, Zhang T, Gong Y, Li Y, Wu H, Xiong J, Tang R. Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems. Front Microbiol 2024; 15:1403338. [PMID: 38873152 PMCID: PMC11169858 DOI: 10.3389/fmicb.2024.1403338] [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: 03/19/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear. Methods Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level. Results Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%). Conclusion This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.
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Affiliation(s)
- Yue Fu
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Xiumei Tang
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
| | - Tingting Sun
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Litao Lin
- Center for Ecological Civilization Research, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Lixue Wu
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Tian Zhang
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Yifei Gong
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Yuting Li
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Haining Wu
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
| | - Jun Xiong
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
| | - Ronghua Tang
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
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14
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Lee J, Zhou X, Lee ST, Yang Y, Yun J, Lee HH, Kang H. Thinning enhances forest soil C storage by shifting the soil toward an oligotrophic condition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171745. [PMID: 38508257 DOI: 10.1016/j.scitotenv.2024.171745] [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: 08/08/2023] [Revised: 02/08/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Forests are significant carbon reservoirs, with approximately one-third of this carbon stored in the soil. Forest thinning, a prevalent management technique, is designed to enhance timber production, preserve biodiversity, and maintain ecosystem functions. Through its influence on biotic and abiotic factors, thinning can profoundly alter soil carbon storage. Yet, the full implications of thinning on forest soil carbon reservoirs and the mechanisms underpinning these changes remain elusive. In this study, we undertook a two-year monitoring initiative, tracking changes in soil extracellular enzyme activities (EEAs), microbial communities, and other abiotic parameters across four thinning intensities within a temperate pine forest. Our results show a marked increase in soil carbon stock following thinning. However, thinning also led to decreased dissolved organic carbon (DOC) content and a reduced DOC to soil organic carbon (SOC) ratio, pointing toward a decline in soil carbon lability. Additionally, fourier transform infrared spectroscopy (FTIR) analysis revealed an augmented relative abundance of aromatic compounds after thinning. There was also a pronounced increase in absolute EEAs (per gram of dry soil) post-thinning, implying nutrient limitations for soil microbes. Concurrently, the composition of bacterial and fungal communities shifted toward oligotrophic dominance post thinning. Specific EEAs (per gram of soil organic matter) exhibit a significant reduction following thinning, indicating a deceleration in organic matter decomposition rates. In essence, our findings reveal that thinning transitions soil toward an oligotrophic state, dampening organic matter decomposition, and thus bolstering the soil carbon storage potential of forest. This study provides enhanced insights into the nuanced relationship between thinning practices and forest soil carbon dynamics, serving as a robust foundation for enlightened forest management strategies.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; Climate and Environmental Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; College of Agricultural Science and Engineering, Hohai University, China
| | - Sang Tae Lee
- Forest Technology and Management Research Center, National Institute of Forest Science, Gyeonggi, Republic of Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Hyun Ho Lee
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; Institute of Microbiology, Leibniz University Hannover, Germany
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea.
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15
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Charalampous G, Fragkou E, Kalogerakis N, Antoniou E, Gontikaki E. Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea. MARINE POLLUTION BULLETIN 2024; 202:116275. [PMID: 38564821 DOI: 10.1016/j.marpolbul.2024.116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024]
Abstract
Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.
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Affiliation(s)
- Georgia Charalampous
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
| | - Efsevia Fragkou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Eleftheria Antoniou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; School of Mineral Resources Engineering, Technical University of Crete, Chania, Greece
| | - Evangelia Gontikaki
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
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16
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Li C, Lü F, Peng W, He PJ, Zhang H. Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6659-6669. [PMID: 38557040 DOI: 10.1021/acs.est.4c01227] [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: 04/04/2024]
Abstract
Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.
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Affiliation(s)
- Chao Li
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Fan Lü
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Wei Peng
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Pin-Jing He
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Hua Zhang
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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17
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Hu Z, Delgado-Baquerizo M, Fanin N, Chen X, Zhou Y, Du G, Hu F, Jiang L, Hu S, Liu M. Nutrient-induced acidification modulates soil biodiversity-function relationships. Nat Commun 2024; 15:2858. [PMID: 38570522 PMCID: PMC10991381 DOI: 10.1038/s41467-024-47323-3] [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: 08/18/2023] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Nutrient enrichment is a major global change component that often disrupts the relationship between aboveground biodiversity and ecosystem functions by promoting species dominance, altering trophic interactions, and reducing ecosystem stability. Emerging evidence indicates that nutrient enrichment also reduces soil biodiversity and weakens the relationship between belowground biodiversity and ecosystem functions, but the underlying mechanisms remain largely unclear. Here, we explore the effects of nutrient enrichment on soil properties, soil biodiversity, and multiple ecosystem functions through a 13-year field experiment. We show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon (C) availability, is the primary factor negatively affecting the relationship between soil diversity and ecosystem multifunctionality. Nitrogen and phosphorus additions significantly reduce soil pH, diversity of bacteria, fungi and nematodes, as well as an array of ecosystem functions related to C and nutrient cycling. Effects of nutrient enrichment on microbial diversity also have negative consequences at higher trophic levels on the diversity of microbivorous nematodes. These results indicate that nutrient-induced acidification can cascade up its impacts along the soil food webs and influence ecosystem functioning, providing novel insight into the mechanisms through which nutrient enrichment influences soil community and ecosystem properties.
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Affiliation(s)
- Zhengkun Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro‑Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
| | - Nicolas Fanin
- INRAE, Bordeaux Sciences Agro, UMR 1391 ISPA, Villenave-d'Ornon, France
| | - Xiaoyun Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuijin Hu
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Manqiang Liu
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro‑Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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18
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Darriaut R, Marzari T, Lailheugue V, Tran J, Martins G, Marguerit E, Masneuf-Pomarède I, Lauvergeat V. Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1358213. [PMID: 38628369 PMCID: PMC11018932 DOI: 10.3389/fpls.2024.1358213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.
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Affiliation(s)
- Romain Darriaut
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Tania Marzari
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Vincent Lailheugue
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Joseph Tran
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Guilherme Martins
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Isabelle Masneuf-Pomarède
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Virginie Lauvergeat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
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19
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Castellano-Hinojosa A, Karlsen-Ayala E, Boyd NS, Strauss SL. Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170659. [PMID: 38325480 DOI: 10.1016/j.scitotenv.2024.170659] [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: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA
| | - Elena Karlsen-Ayala
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA; Northern Research Station, United States Department of Agriculture, Forest Service, 51 Millpond Road, Hamden, CT 06517, USA
| | - Nathan S Boyd
- Gulf Coast Research and Education Center, Department of Horticulture, Institute of Food and Agricultural Sciences, University of Florida, 14625 C.R. 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
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20
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Li Y, Ma G, Xi Y, Wang S, Zeng X, Jia Y. Divergent adaptation strategies of abundant and rare bacteria to salinity stress and metal stress in polluted Jinzhou Bay. ENVIRONMENTAL RESEARCH 2024; 245:118030. [PMID: 38151148 DOI: 10.1016/j.envres.2023.118030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Understanding how abundant (AT) and rare (RT) taxa adapt to diverse environmental stresses is vital for assessing ecological processes, yet remains understudied. We collected sediment samples from Liaoning Province, China, representing rivers (upstream of wastewater outlet), estuaries (wastewater outlets), and Jinzhou Bay (downstream of wastewater outlets), to comprehensively evaluate AT and RT adaptation strategies to both natural stressors (salinity stress) and anthropogenic stressors (metal stress). Generally, RT displayed higher α- and β-diversities and taxonomic groups compared to AT. Metal and salinity stresses induced distinct α-diversity responses in AT and RT, while β-diversity remained consistent. Both subcommunities were dominated by Woeseia genus. Metal stress emerged as the primary driver of diversity and compositional discrepancies in AT and RT. Notably, AT responded more sensitively to salinity stress than RT. Stress increased topological parameters in the biotic network of AT subcommunities while decreasing values in RT subcommunities, concurrently loosening interactions of AT with other taxa and strengthening interactions of RT with others in biotic networks. RT generally exhibited greater diversity of metal resistance genes compared to AT. Greater numbers of genes related to salinity tolerance was observed for the RT than for AT. Compared to AT, RT demonstrated higher diversity of metal resistance genes and a greater abundance of genes associated with salinity tolerance. Additionally, deterministic processes governed AT community assembly, reinforced by salinity stress. However, the opposite trend was observed in the RT, where the importance of stochastic process gradually increased with metal stresses. The study is centered on exploring the adaptation strategies of both AT and RT to environmental stress. It underscores the importance of future research incorporating diverse ecosystems and a range of environmental stressors to draw broader and more reliable conclusions. This comprehensive approach is essential for gaining a thorough understanding of the adaptive mechanisms employed by these microorganisms.
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Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Guoqing Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yimei Xi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
| | - Shaofeng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xiangfeng Zeng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China.
| | - Yongfeng Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
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21
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Wei Z, Zhao L, Wang S, Chang L, Shi J, Kong X, Li M, Lin J, Zhang W, Bao Z, Ding W, Hu X. Paralytic shellfish toxins producing dinoflagellates cause dysbacteriosis in scallop gut microbial biofilms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116146. [PMID: 38412634 DOI: 10.1016/j.ecoenv.2024.116146] [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: 11/16/2023] [Revised: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Filter-feeding bivalves could accumulate paralytic shellfish toxins (PSTs) produced by harmful dinoflagellates through diet. Despite that bivalves are resistant to these neurotoxins due to possessing PST-resistant sodium channel, exposure to PSTs-producing dinoflagellates impair bivalve survival. We hypothesized that ingesting PSTs-producing dinoflagellates may influence the gut microbiota, and then the health of bivalves. To test this idea, we compared the gut microbiota of the scallop Patinopecten yessoensis, after feeding with PST-producing or non-toxic dinoflagellates. Exposure to PSTs-producing dinoflagellates resulted in a decline of gut microbial diversity and a disturbance of community structure, accompanied by a significant increase in the abundance and richness of pathogenic bacteria, represented by Vibrio. Moreover, network analysis demonstrated extensive positive correlations between pathogenic bacteria abundances and PSTs concentrations in the digestive glands of the scallops. Furthermore, isolation of a dominant Vibrio strain and its genomic analysis revealed a variety of virulence factors, including the tolC outer membrane exporter, which were expressed in the gut microbiota. Finally, the infection experiment demonstrated scallop mortality caused by the isolated Vibrio strain; further, the pathogenicity of this Vibrio strain was attenuated by a mutation in the tolC gene. Together, these findings demonstrated that the PSTs may affect gut microbiota via direct and taxa-specific interactions with opportunistic pathogens, which proliferate after transition from seawater to the gut environment. The present study has revealed novel mechanisms towards deciphering the puzzles in environmental disturbances-caused death of an important aquaculture species.
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Affiliation(s)
- Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Liang Zhao
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Shuaitao Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Lirong Chang
- Weihai Changqing Ocean Science & Technology Co. Ltd, Rongcheng, China
| | - Jiaoxia Shi
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiangfu Kong
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Jinshui Lin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yanan University, Yanan, China
| | - Weipeng Zhang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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22
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Sun X, Sitters J, Ruytinx J, Wassen MJ, Olde Venterink H. Microbial community composition in the dung of five sympatric European herbivore species. Ecol Evol 2024; 14:e11071. [PMID: 38481755 PMCID: PMC10933625 DOI: 10.1002/ece3.11071] [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: 06/27/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 06/21/2024] Open
Abstract
The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid-Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non-ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non-ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non-ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.
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Affiliation(s)
- Xingzhao Sun
- Research Group WILDVrije Universiteit BrusselBrusselsBelgium
| | - Judith Sitters
- Research Group WILDVrije Universiteit BrusselBrusselsBelgium
- B‐WARE Research CentreNijmegenThe Netherlands
| | - Joske Ruytinx
- Research Groups Microbiology and Plant GeneticsVrije Universiteit BrusselBrusselsBelgium
| | - Martin J. Wassen
- Environmental Sciences, Copernicus Institute of Sustainable DevelopmentUtrecht UniversityUtrechtThe Netherlands
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23
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Khatri-Chhetri U, Banerjee S, Thompson KA, Quideau SA, Boyce MS, Bork EW, Carlyle CN. Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169353. [PMID: 38104847 DOI: 10.1016/j.scitotenv.2023.169353] [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: 01/18/2023] [Revised: 05/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.
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Affiliation(s)
- Upama Khatri-Chhetri
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Karen A Thompson
- Trent School of Environment, Trent University, Peterborough, ON K9L 0G2, Canada
| | - Sylvie A Quideau
- Department of Renewable Resources, Earth Science Building University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Mark S Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Edward W Bork
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Cameron N Carlyle
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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24
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Liu Z, Zhang C, Ma J, Peng Q, Du X, Sun S, Cheng J, Peng W, Chen L, Gu Z, Zhang W, Su P, Zhang D. Extraction Methods Determine the Quality of Soil Microbiota Acquisition. Microorganisms 2024; 12:403. [PMID: 38399807 PMCID: PMC10891820 DOI: 10.3390/microorganisms12020403] [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: 01/16/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.
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Affiliation(s)
- Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Chi Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Qianze Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Xiaohua Du
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Shu'e Sun
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ju'e Cheng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weiye Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lijie Chen
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zepei Gu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weixing Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Pin Su
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
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25
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Paes da Costa D, das Graças Espíndola da Silva T, Sérgio Ferreira Araujo A, Prudêncio de Araujo Pereira A, William Mendes L, Dos Santos Borges W, Felix da França R, Alberto Fragoso de Souza C, Alves da Silva B, Oliveira Silva R, Valente de Medeiros E. Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil. Sci Rep 2024; 14:3919. [PMID: 38365962 PMCID: PMC10873301 DOI: 10.1038/s41598-024-54221-7] [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: 11/10/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.
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Affiliation(s)
- Diogo Paes da Costa
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil.
| | | | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Wisraiane Dos Santos Borges
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | - Rafaela Felix da França
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | | | - Bruno Alves da Silva
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | - Renata Oliveira Silva
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | - Erika Valente de Medeiros
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
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26
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Wang Y, Zhang L, Zhang S, Zhu S, Zhang F, Zhang G, Duan B, Ren R, Zhang H, Han M, Xu Y, Li Y. Regulating pathway for bacterial diversities toward improved ecological benefits of thiencarbazone-methyl·isoxaflutole application: A field experiment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120037. [PMID: 38194872 DOI: 10.1016/j.jenvman.2024.120037] [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: 08/23/2023] [Revised: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 01/11/2024]
Abstract
Herbicide abuse has a significantly negative impact on soil microflora and further influences the ecological benefit. The regulating measures and corresponding mechanisms mitigating the decreased bacterial diversity due to herbicide use have rarely been studied. A field experiment containing the application gradient of an efficient maize herbicide thiencarbazone-methyl·isoxaflutole was performed. The relationship between soil bacterial community and thiencarbazone-methyl·isoxaflutole use was revealed. Modified attapulgite was added to explore its impacts on soil microflora under the thiencarbazone-methyl·isoxaflutole application. Based on the analytic network process-entropy weighting method-TOPSIS method model, the ecological benefit focusing on microbial responses was quantitatively estimated along with technical effectiveness and economic benefit. The results showed that the diversity indices of soil microflora, especially the Inv_Simpson index, were reduced at the recommended, 5 and 10 times the recommended dosages of thiencarbazone-methyl·isoxaflutole use. The Flavisolibacter bacteria was negatively correlated with the residues in soils based on the random forest model and correlation analysis, indicating a potential degrader of thiencarbazone-methyl·isoxaflutole residues. The structural equation model further confirmed that the high soil water content and soil pH promoted the function of Flavisolibacter bacteria, facilitated the dissipation of thiencarbazone-methyl·isoxaflutole residues and further improved the diversity of soil microflora. In addition, the presence of modified attapulgite was found to increase the soil pH, which may improve bacterial diversity through the regulating pathway. This explained the high ecological benefits of the treatment where the thiencarbazone-methyl·isoxaflutole was applied at the recommended dosage rates in conjunction with modified attapulgite addition. Therefore, the comprehensive benefits of thiencarbazone-methyl·isoxaflutole application with a focus on ecological benefits can be improved by regulating the soil pH with modified attapulgite.
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Affiliation(s)
- Yonglu Wang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liyun Zhang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Shumin Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shiliang Zhu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fengsong Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an, 343000, China.
| | - Guixiang Zhang
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan, 030024, Shanxi Province, China
| | - Bihua Duan
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Rui Ren
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan, 030024, Shanxi Province, China
| | - Hongyu Zhang
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan, 030024, Shanxi Province, China
| | - Meng Han
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Yi Xu
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Yuyang Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
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27
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Nayak PK, Nayak AK, Panda BB, Senapati A, Panneerselvam P, Kumar A, Tripathi R, Poonam A, Shahid M, Mohapatra SD, Kaviraj M, Kumar U. Rice-based integrated farming system improves the soil quality, bacterial community structure and system productivity under sub-humid tropical condition. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:65. [PMID: 38321197 DOI: 10.1007/s10653-024-01863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024]
Abstract
Rice-based integrated farming system improves the productivity and profitability by recycling resources efficiently. In the sub-humid tropics, rice production without sufficient nutrient replenishment often leads to soil health and fertility degradation. There has been very limited research on soil health and fertility after adopting a multi-enterprising rice-based integrated farming system (IFS), notably in the rice-fish-livestock and agroforestry system, when compared to a conventional farming system (CS). Therefore, the present study analyzed the dynamics of soil properties, soil bacterial community structure and their possible interaction mechanisms, as well as their effect on regulating soil quality and production in IFS, IFSw (water stagnant area of IFS) and CS. The results indicated that soil nutrient dynamics, bacterial diversity indices (Shannon index, Simpson index, Chao 1, ACE and Fisher index) and system productivity were higher in IFSw and IFS compared to CS. Moreover, relative operational taxonomic units of dominant bacterial genera (Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, Cyanobacteria, Crenarchaeota and Gemmatimonadetes) were also higher in IFSw and IFS compared to CS. Mean soil quality index (SQI) was highest in IFSw (0.780 ± 0.201) followed by IFS (0.770 ± 0.080) and CS (0.595 ± 0.244). Moreover, rice equivalent yields (REY) and rice yields were well correlated with the higher levels of soil biological indices (SQIBiol) in IFS. Overall, our results revealed that rice-based IFS improved the soil health and fertility and ensuing crop productivity through positive interaction with soil bacterial communities and nutrient stoichiometry leading to agroecosystem sustainability.
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Affiliation(s)
| | - A K Nayak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - B B Panda
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Senapati
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - P Panneerselvam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - R Tripathi
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Poonam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - M Shahid
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S D Mohapatra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
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28
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Zeng K, Huang X, Guo J, Dai C, He C, Chen H, Xin G. Microbial-driven mechanisms for the effects of heavy metals on soil organic carbon storage: A global analysis. ENVIRONMENT INTERNATIONAL 2024; 184:108467. [PMID: 38310815 DOI: 10.1016/j.envint.2024.108467] [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: 09/07/2023] [Revised: 11/22/2023] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Heavy metal (HM) enrichment is closely related to soil organic carbon (SOC) pools in terrestrial ecosystems, which are deeply intertwined with soil microbial processes. However, the influence of HMs on SOC remains contentious in terms of magnitude and direction. A global analysis of 155 publications was conducted to integrate the synergistic responses of SOC and microorganisms to HM enrichment. A significant increase of 13.6 % in SOC content was observed in soils exposed to HMs. The response of SOC to HMs primarily depends on soil properties and habitat conditions, particularly the initial SOC content, mean annual precipitation (MAP), initial soil pH, and mean annual temperature (MAT). The presence of HMs resulted in significant decreases in the activities of key soil enzymes, including 31.9 % for soil dehydrogenase, 24.8 % for β-glucosidase, 35.8 % for invertase, and 24.3 % for cellulose. HMs also exerted inhibitory effects on microbial biomass carbon (MBC) (26.6 %), microbial respiration (MR) (19.7 %), and the bacterial Shannon index (3.13 %) but elevated the microbial metabolic quotient (qCO2) (20.6 %). The HM enrichment-induced changes in SOC exhibited positive correlations with the response of MBC (r = 0.70, p < 0.01) and qCO2 (r = 0.50, p < 0.01), while it was negatively associated with β-glucosidase activity (r = 0.72, p < 0.01) and MR (r = 0.39, p < 0.01). These findings suggest that the increase in SOC storage is mainly attributable to the inhibition of soil enzymes and microorganisms under HM enrichment. Overall, this meta-analysis highlights the habitat-dependent responses of SOC to HM enrichment and provides a comprehensive evaluation of soil carbon dynamics in an HM-rich environment.
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Affiliation(s)
- Kai Zeng
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xiaochen Huang
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Junjie Guo
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Chuanshun Dai
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Chuntao He
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Hao Chen
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Guorong Xin
- State Key Lab of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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Rzehak T, Praeg N, Zink H, Simon A, Geitner C, Illmer P. Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13215. [PMID: 38062558 PMCID: PMC10866079 DOI: 10.1111/1758-2229.13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/01/2023] [Indexed: 02/15/2024]
Abstract
Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.
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Affiliation(s)
- Theresa Rzehak
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Nadine Praeg
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Harald Zink
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Alois Simon
- Department of Forest PlanningOffice of the Tyrolean GovernmentInnsbruckAustria
| | - Clemens Geitner
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Paul Illmer
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
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Simon E, Guseva K, Darcy S, Alteio L, Pjevac P, Schmidt H, Jenab K, Ranits C, Kaiser C. Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates. THE ISME JOURNAL 2024; 18:wrae156. [PMID: 39105276 PMCID: PMC11325450 DOI: 10.1093/ismejo/wrae156] [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: 04/18/2024] [Revised: 06/29/2024] [Accepted: 08/05/2024] [Indexed: 08/07/2024]
Abstract
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.
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Affiliation(s)
- Eva Simon
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Ksenia Guseva
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Sean Darcy
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Lauren Alteio
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, 3430 Tulln, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Kian Jenab
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christian Ranits
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
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31
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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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Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Wang W, Wang X, Zhao Q, Wen L, Kong F, Xi M, He Q. Habitat-specific responses of soil organic matter decomposition to Spartina alterniflora invasion along China's coast. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2741. [PMID: 36103141 DOI: 10.1002/eap.2741] [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: 04/30/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Plant invasions cause a fundamental change in soil organic matter (SOM) turnover. Disentangling the biogeographic patterns and key drivers of SOM decomposition and its temperature sensitivity (Q10 ) under plant invasion is a prerequisite for making projections of global carbon feedback. We collected soil samples along China's coast across saltmarshes to mangrove ecosystems invaded by the smooth cordgrass (Spartina alterniflora Loisel.). Microcosm experiments were carried out to determine the patterns of SOM decomposition and its thermal response. Soil microbial biomass and communities were also characterized accordingly. SOM decomposition constant dramatically decreased along the mean annual temperature gradient, whereas the cordgrass invasion retarded this change (significantly reduced slope, p < 0.05). The response of Q10 to invasion and the soil microbial quotient peaked at midlatitude saltmarshes, which can be explained by microbial metabolism strategies. Climatic variables showed strong negative controls on the Q10 , whereas dissolved carbon fraction exerted a positive influence on its spatial variance. Higher microbial diversity appeared to weaken the temperature-related response of SOM decomposition, with apparent benefits for carbon sequestration. Inconsistent responses to invasion were exhibited among habitat types, with SOM accumulation in saltmarshes but carbon loss in mangroves, which were explained, at least in part, by the SOM decomposition patterns under invasion. This study elucidates the geographic pattern of SOM decomposition and its temperature sensitivity in coastal ecosystems and underlines the importance of interactions between climate, soil, and microbiota for stabilizing SOM under plant invasion.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, People's Republic of China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, People's Republic of China
| | | | - Laibin Huang
- Department of Land, Air and Water Resources, University of California-Davis, Davis, California, USA
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, People's Republic of China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, People's Republic of China
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, People's Republic of China
- Ecology Institute of Shandong Academy of Sciences, Ji'nan, People's Republic of China
| | - Lixiang Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, People's Republic of China
| | - Fanlong Kong
- College of Environmental Science and Engineering, Qingdao University, Qingdao, People's Republic of China
| | - Min Xi
- College of Environmental Science and Engineering, Qingdao University, Qingdao, People's Republic of China
| | - Qiang He
- Coastal Ecology Lab, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, National Observation and Research Station for Wetland Ecosystems of the Yangtze Estuary (Shanghai), School of Life Sciences, Fudan University, Shanghai, People's Republic of China
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Erhunmwunse AS, Guerra VA, Liu JC, Mackowiak CL, Blount ARS, Dubeux JCB, Liao HL. Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths. Microorganisms 2023; 11:3002. [PMID: 38138146 PMCID: PMC10745480 DOI: 10.3390/microorganisms11123002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant-soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3-V4 regions. We observed that a well-established RP-bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.
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Affiliation(s)
- Adesuwa Sylvia Erhunmwunse
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Victor Alonso Guerra
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Jung-Chen Liu
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Cheryl L. Mackowiak
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Ann Rachel Soffes Blount
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
| | - José Carlos Batista Dubeux
- North Florida Research and Education Center, University of Florida, 3925 Highway 71, Marianna, FL 32446, USA;
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
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Mukhopadhyay M, Mukherjee A, Ganguli S, Chakraborti A, Roy S, Choudhury SS, Subramaniyan V, Kumarasamy V, Sayed AA, El-Demerdash FM, Almutairi MH, Şuţan A, Dhara B, Mitra AK. Marvels of Bacilli in soil amendment for plant-growth promotion toward sustainable development having futuristic socio-economic implications. Front Microbiol 2023; 14:1293302. [PMID: 38156003 PMCID: PMC10752760 DOI: 10.3389/fmicb.2023.1293302] [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: 09/12/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023] Open
Abstract
Microorganisms are integral components of ecosystems, exerting profound impacts on various facets of human life. The recent United Nations General Assembly (UNGA) Science Summit emphasized the critical importance of comprehending the microbial world to address global challenges, aligning with the United Nations Sustainable Development Goals (SDGs). In agriculture, microbes are pivotal contributors to food production, sustainable energy, and environmental bioremediation. However, decades of agricultural intensification have boosted crop yields at the expense of soil health and microbial diversity, jeopardizing global food security. To address this issue, a study in West Bengal, India, explored the potential of a novel multi-strain consortium of plant growth promoting (PGP) Bacillus spp. for soil bioaugmentation. These strains were sourced from the soil's native microbial flora, offering a sustainable approach. In this work, a composite inoculum of Bacillus zhangzhouensis MMAM, Bacillus cereus MMAM3), and Bacillus subtilis MMAM2 were introduced into an over-exploited agricultural soil and implications on the improvement of vegetative growth and yield related traits of Gylcine max (L) Meril. plants were evaluated, growing them as model plant, in pot trial condition. The study's findings demonstrated significant improvements in plant growth and soil microbial diversity when using the bacterial consortium in conjunction with vermicompost. Metagenomic analyses revealed increased abundance of many functional genera and metabolic pathways in consortium-inoculated soil, indicating enhanced soil biological health. This innovative bioaugmentation strategy to upgrade the over-used agricultural soil through introduction of residual PGP bacterial members as consortia, presents a promising path forward for sustainable agriculture. The rejuvenated patches of over-used land can be used by the small and marginal farmers for cultivation of resilient crops like soybean. Recognizing the significance of multi-strain PGP bacterial consortia as potential bioinoculants, such technology can bolster food security, enhance agricultural productivity, and mitigate the adverse effects of past agricultural activities.
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Affiliation(s)
- Meenakshi Mukhopadhyay
- Department of Botany, Vivekananda College (Affiliated to University of Calcutta), Kolkata, West Bengal, India
| | - Ashutosh Mukherjee
- Department of Botany, Vivekananda College (Affiliated to University of Calcutta), Kolkata, West Bengal, India
| | - Sayak Ganguli
- Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India
| | - Archisman Chakraborti
- Department of Physics, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India
| | - Samrat Roy
- Depatrment of Commerce, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India
| | - Sudeshna Shyam Choudhury
- Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Vinoth Kumarasamy
- Department of Parasitology and Medical Entomology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Amany A. Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Fatma M. El-Demerdash
- Department of Environmental Studies, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Mikhlid H. Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anca Şuţan
- Department of Natural Sciences, Faculty of Science, Physical Education and Informatics, University of Pitești, Pitești, Romania
| | - Bikram Dhara
- Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Arup Kumar Mitra
- Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India
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35
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Pinheiro Alves de Souza Y, Schloter M, Weisser W, Schulz S. Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum. MICROBIAL ECOLOGY 2023; 86:2882-2893. [PMID: 37624441 PMCID: PMC10640511 DOI: 10.1007/s00248-023-02285-9] [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: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.
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Affiliation(s)
- Yuri Pinheiro Alves de Souza
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Wolfgang Weisser
- Technische Universität München, TUM School of Life Science, Chair of Terrestrial Ecology, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany.
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36
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Zhang G, Bai J, Jia J, Wang W, Wang D, Zhao Q, Wang C, Chen G. Soil microbial communities regulate the threshold effect of salinity stress on SOM decomposition in coastal salt marshes. FUNDAMENTAL RESEARCH 2023; 3:868-879. [PMID: 38933010 PMCID: PMC11197625 DOI: 10.1016/j.fmre.2023.02.024] [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: 05/25/2022] [Revised: 12/23/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Salinity stress is one of the critical environmental drivers of soil organic matter (SOM) decomposition in coastal ecosystems. Although the temperature sensitivity (Q10) of SOM decomposition has been widely applied in Earth system models to forecast carbon processes, the impact of salinity on SOM decomposition by restructuring microbial communities remains uncovered. Here, we conducted a microcosm experiment with soils collected from the coastal salt marsh in the Yellow River Estuary, which is subjected to strong dynamics of salinity due to both tidal flooding and drainage. By setting a gradient of salt solutions, soil salinity was adjusted to simulate salinity stress and soil carbon emission (CO2) rate was measured over the period. Results showed that as salinity increased, the estimated decomposition constants based on first-order kinetics gradually decreased at different temperatures. Below the 20‰ salinity treatments, which doubled the soil salinity, Q10 increased with increasing salinity; but higher salinity constrained the temperature-related response of SOM decomposition by inhibiting microbial growth and carbon metabolisms. Soil bacteria were more sensitive to salinity stress than fungi, which can be inferred from the response of microbial beta-diversity to changing salinity. Among them, the phylotypes assigned to Gammaproteobacteria and Bacilli showed higher salt tolerance, whereas taxa affiliated with Alphaproteobacteria and Bacteroidota were more easily inhibited by the salinity stress. Several fungal taxa belonging to Ascomycota had higher adaptability to the stress. As the substrate was consumed with the incubation, bacterial competition intensified, but the fungal co-occurrence pattern changed weakly during decomposition. Collectively, these findings revealed the threshold effect of salinity on SOM decomposition in coastal salt marshes and emphasized that salt stress plays a key role in carbon sequestration by regulating microbial keystone taxa, metabolisms, and interactions.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dawei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingqing Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Chen Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Guozhu Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Shi X, Tan W, Tang S, Ling Q, Tang C, Qin P, Luo S, Zhao Y, Yu F, Li Y. Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118766. [PMID: 37579601 DOI: 10.1016/j.jenvman.2023.118766] [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: 05/10/2023] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
Soil deficiency, cyclic erosion, and heavy metal pollution have led to fertility loss and ecological function decline in mining areas. Fertilization is an important way to rapidly replenish soil nutrients, which have a major influence on the soil nitrogen cycling process, but different fertilization regimes have different impacts on soil properties and microbial functional potentials. Here, metagenomic sequencing was used to investigate the different responses of key functional genes of microbial nitrogen cycling to fertilization regimes and explore the potential effects of soil physicochemical properties on the key functional genes. The results indicated that AC-HH (ammonium chloride-high frequency and concentration) treatment significantly increased the gene abundance of norC (13.40-fold), nirK (5.46-fold), and napA (5.37-fold). U-HH (urea-high frequency and concentration) treatment significantly increased the gene abundance of hao (6.24-fold), pmoA-amoA (4.32-fold) norC (7.00-fold), nosZ (3.69-fold), and nirK (6.88-fold). Functional genes were distributed differently among the 10 dominant phyla. The nifH and nifK genes were distributed only in Proteobacteria. The hao gene was distributed in Gemmatimonadetes, Nitrospirae and Proteobacteria. Fertilization regimes caused changes in functional redundancy in soil, and nirK and nirB, which are involved in denitrification, were present in different genera. Fertilization regimes with high frequency and high concentration were more likely to increase the gene abundance at the genus level. In summary, this study provides insights into the taxon-specific response of soil nitrogen cycling under different fertilization regimes, where changes in fertilization regimes affect microbial nitrogen cycling by altering soil physicochemical properties in a complex dynamic environment.
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Affiliation(s)
- Xinwei Shi
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Weilan Tan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Shuting Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Qiujie Ling
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Chijian Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Peiqing Qin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Shiyu Luo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Yinjun Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China.
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China.
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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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Kracmarova-Farren M, Papik J, Uhlik O, Freeman J, Foster A, Leewis MC, Creamer C. Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste. ENVIRONMENTAL MICROBIOME 2023; 18:74. [PMID: 37805609 PMCID: PMC10559404 DOI: 10.1186/s40793-023-00528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.
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Affiliation(s)
- Martina Kracmarova-Farren
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jakub Papik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - John Freeman
- Intrinsyx Environmental, Sunnyvale, CA, 94085, USA
| | | | - Mary-Cathrine Leewis
- U.S. Geological Survey, Menlo Park, CA, USA
- Agriculture and Agri-Food Canada, Quebec Research and Development Centre, Quebec, QC, Canada
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Zhou Z, Xia L, Wang X, Wu C, Liu J, Li J, Lu Z, Song S, Zhu J, Montes ML, Benzaazoua M. Coal slime as a good modifier for the restoration of copper tailings with improved soil properties and microbial function. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:109266-109282. [PMID: 37759064 DOI: 10.1007/s11356-023-30008-7] [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: 06/23/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
In recent years, the solid wastes from the coal industry have been widely used as soil amendments. Nevertheless, the impact of utilizing coal slime for copper tailing restoration in terms of plant growth, physicochemical characteristics of the tailing soil, and microbial succession remains uncertain.Herein, the coal slime was employed as a modifier into copper tailings. Their effect on the growth and physiological response of Ryegrass, and the soil physicochemical properties as well as the bacterial community structure were investigated. The results indicated that after a 30-day of restoration, the addition of coal slime at a ratio of 40% enhanced plant growth, with a 21.69% rise in chlorophyll content, and a 62.44% increase in peroxidase activity. The addition of 40% coal slime also increased the content of nutrient elements in copper tailings. Following a 20-day period of restoration, the concentrations of available copper and available zinc in the modified tailings decreased by 39.6% and 48.51%, respectively, with 40% of coal slime added. In the meantime, there was an observed augmentation in the species diversity of the bacterial community in the modified tailings. The alterations in both community structure and function were primarily influenced by variations in pH value, available nitrogen, phosphorus, potassium, and available copper. The addition of 40% coal slime makes the physicochemical properties and microbial community evolution of copper tailings reach a balance point. The utilization of coal slime has the potential to enhance the physicochemical characteristics of tailings and promote the proliferation of microbial communities, hence facilitating the soil evolution of two distinct solid waste materials. Consequently, the application of coal slime in the restoration of heavy metal tailings is a viable approach, offering both cost-effectiveness and efficacy as an enhancer.
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Affiliation(s)
- Zhou Zhou
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
| | - Ling Xia
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China.
| | - Xizhuo Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
| | - Chenyu Wu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
| | - Jiazhi Liu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
| | - Jianbo Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
- Instituto de Física de la Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000, San Luis Potosí, Mexico
| | - Zijing Lu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
| | - Shaoxian Song
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, 430070, Hubei, China
| | - Jiang Zhu
- Hubei Sanxin Gold Copper Limited Company, Huangshi, Hubei, China
| | | | - Mostafa Benzaazoua
- Mohammed VI Polytechnic University (UM6P), Geology and Sustainable Mining, Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco
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de Souza AJ, Santos E, Ribeiro FP, de Araújo Pereira AP, Viana DG, da Silva Coelho I, Filho FBE, Santaren KCF. Crotalaria juncea L. enhances the bioremediation of sulfentrazone-contaminated soil and promotes changes in the soil bacterial community. Braz J Microbiol 2023; 54:2319-2331. [PMID: 37578738 PMCID: PMC10485233 DOI: 10.1007/s42770-023-01064-5] [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: 01/04/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Sulfentrazone (STZ) is an efficient tool for the pre- and post-emergence control of monocotyledonous and dicotyledonous weeds in fields of crops such as pineapple, coffee, sugarcane, citrus, eucalyptus, tobacco, and soybean. However, this herbicide persists in the soil, causing phytotoxicity in the subsequent crop. Therefore, it is important to use efficient strategies for the remediation of STZ-contaminated areas. The aim of this study was to evaluate the effects of Crotalaria juncea L. on the remediation of STZ-contaminated soil and on the microbial activity and bacterial community structure therein. The study was conducted in three stages: (i) cultivation of C. juncea in soil contaminated with 200, 400, and 800 g ha-1 STZ; (ii) determination of the soil microbial activity (basal respiration, microbial biomass carbon, and bacterial community structure); and (iii) cultivation of a bioindicator species and determination of the residual fraction of STZ. The soil microbial activity was impacted by the soil type and STZ dose. Soil previously cultivated with C. juncea (rhizospheric soil) displayed higher CO2 and lower qCO2 values than non-rhizospheric soil (no previous C. juncea cultivation). Increasing doses of STZ reduced the activity and lowered the diversity indices of the soil microorganisms. The bacterial community structure was segregated between the rhizospheric and non-rhizospheric soils. Regardless of soil type, the bioindicator of remediation (Pennisetum glaucum R.Br.) grew only at the STZ dose of 200 g ha-1, and the plant intoxication level was also lower in rhizospheric soil treated with this herbicide dose. All P. glaucum plants died in the soils treated with 400 and 800 g ha-1 STZ. Previous cultivation of C. juncea in soils contaminated with 200, 400, and 800 g ha-1 STZ reduced the residual fraction of the herbicide by 4.8%, 12.5%, and 17.4%, respectively, compared with that in the non-rhizospheric soils. In conclusion, previous cultivation with C. juncea promoted increases in the soil bacterial activity and diversity indices, mitigated the deleterious effects of STZ on the bioindicator crop, and reduced the residual fraction of the herbicide in the soil.
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Affiliation(s)
| | - Esequiel Santos
- Federal University of Espírito Santo, Sao Mateus, Espírito Santo, Brazil
| | | | | | - Douglas Gomes Viana
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Sierocinski P, Stilwell P, Padfield D, Bayer F, Buckling A. The ecology of scale: impact of volume on coalescence and function in methanogenic communities. Interface Focus 2023; 13:20220089. [PMID: 37303743 PMCID: PMC10251116 DOI: 10.1098/rsfs.2022.0089] [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: 12/22/2022] [Accepted: 04/05/2023] [Indexed: 06/13/2023] Open
Abstract
Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.
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Affiliation(s)
- Pawel Sierocinski
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Peter Stilwell
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Daniel Padfield
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Florian Bayer
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Angus Buckling
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
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43
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Manfredini A, Malusà E, Pinzari F, Canfora L. Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil. J Appl Microbiol 2023; 134:lxad169. [PMID: 37516446 DOI: 10.1093/jambio/lxad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023]
Abstract
AIMS One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses. METHODS AND RESULTS We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties. CONCLUSIONS The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.
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Affiliation(s)
- Andrea Manfredini
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 00184 Roma, Italy
| | - Eligio Malusà
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, 31015 Conegliano, Italy
- National Institute of Horticultural Research, 96-100 Skierniewice, Poland
| | - Flavia Pinzari
- Institute for Biological Systems, Council of National Research of Italy (CNR), 00010 Montelibretti, Italy
- Life Sciences Department, Natural History Museum, Cromwell Road, SW7 5BD London, UK
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 00184 Roma, Italy
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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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Osburn ED, Yang G, Rillig MC, Strickland MS. Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress. ISME COMMUNICATIONS 2023; 3:66. [PMID: 37400524 PMCID: PMC10318037 DOI: 10.1038/s43705-023-00273-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
Ecosystem functions and services are under threat from anthropogenic global change at a planetary scale. Microorganisms are the dominant drivers of nearly all ecosystem functions and therefore ecosystem-scale responses are dependent on responses of resident microbial communities. However, the specific characteristics of microbial communities that contribute to ecosystem stability under anthropogenic stress are unknown. We evaluated bacterial drivers of ecosystem stability by generating wide experimental gradients of bacterial diversity in soils, applying stress to the soils, and measuring responses of several microbial-mediated ecosystem processes, including C and N cycling rates and soil enzyme activities. Some processes (e.g., C mineralization) exhibited positive correlations with bacterial diversity and losses of diversity resulted in reduced stability of nearly all processes. However, comprehensive evaluation of all potential bacterial drivers of the processes revealed that bacterial α diversity per se was never among the most important predictors of ecosystem functions. Instead, key predictors included total microbial biomass, 16S gene abundance, bacterial ASV membership, and abundances of specific prokaryotic taxa and functional groups (e.g., nitrifying taxa). These results suggest that bacterial α diversity may be a useful indicator of soil ecosystem function and stability, but that other characteristics of bacterial communities are stronger statistical predictors of ecosystem function and better reflect the biological mechanisms by which microbial communities influence ecosystems. Overall, our results provide insight into the role of microorganisms in supporting ecosystem function and stability by identifying specific characteristics of bacterial communities that are critical for understanding and predicting ecosystem responses to global change.
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Affiliation(s)
- Ernest D Osburn
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, USA.
| | - Gaowen Yang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
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Lü W, Ren H, Ding W, Li H, Yao X, Jiang X. The effects of climate warming on microbe-mediated mechanisms of sediment carbon emission. J Environ Sci (China) 2023; 129:16-29. [PMID: 36804232 DOI: 10.1016/j.jes.2022.09.016] [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: 08/13/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 06/18/2023]
Abstract
Due to significant differences in biotic and abiotic properties of soils compared to those of sediments, the predicted underlying microbe-mediated mechanisms of soil carbon emissions in response to warming may not be applicable for estimating similar emissions from inland water sediments. We addressed this issue by incubating different types of sediments, (including lake, small river, and pond sediments) collected from 36 sites across the Yangtze River basin, under short-term experimental warming to explore the effects of climate warming on sediment carbon emission and the underlying microbe-mediated mechanisms. Our results indicated that under climate warming CO2 emissions were affected more than CH4 emissions, and that pond sediments may yield a greater relative contribution of CO2 to total carbon emissions than lake and river sediments. Warming-induced CO2 and CH4 increases involve different microbe-mediated mechanisms; Warming-induced sediment CO2 emissions were predicted to be directly positively driven by microbial community network modularity, which was significantly negatively affected by the quality and quantity of organic carbon and warming-induced variations in dissolved oxygen, Conversely, warming-induced sediment CH4 emissions were predicted to be directly positively driven by microbial community network complexity, which was significantly negatively affected by warming-induced variations in pH. Our findings suggest that biotic and abiotic drivers for sediment CO2 and CH4 emissions in response to climate warming should be considered separately when predicting sediment organic carbon decomposition dynamics resulting from climate change.
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Affiliation(s)
- Weiwei Lü
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory of Lake Water Pollution Control and Ecological Restoration Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Haoyu Ren
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory of Lake Water Pollution Control and Ecological Restoration Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wanchang Ding
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory of Lake Water Pollution Control and Ecological Restoration Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - He Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory of Lake Water Pollution Control and Ecological Restoration Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xin Yao
- School of Environment and Planning, University of Liaocheng, Liaocheng 252000, China
| | - Xia Jiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory of Lake Water Pollution Control and Ecological Restoration Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Liu WS, Wei YX, Deng PP, Oladele OP, N'Dri Bohoussou Y, Dang YP, Zhao X, Zhang HL. Conservation tillage increases surface soil organic carbon stock by altering fungal communities and enzyme activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:80901-80915. [PMID: 37311861 DOI: 10.1007/s11356-023-28062-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
Fungal communities play a key role in the decomposition of crop residues and affect soil organic carbon (SOC) dynamics. Conservation tillage enhances SOC sequestration and mitigate global climate change. However, the impact of long-term tillage practices on fungal community diversity and its relation to SOC stock remains unclear. The objectives of this study were to evaluate the relationship between extracellular enzyme activities and fungal community diversity and SOC stock under different tillage practices. A field experiment was conducted with four tillage practices: (i) no-tillage with straw removal (NT0), (ii) no-tillage with straw retention (NTSR, conservation tillage), (iii) plough tillage with straw retention (PTSR), and (iv) rotary tillage with straw retention (RTSR). The results showed that the SOC stock in NTSR was higher than other treatments in the 0-10 cm soil layer. Compared to NT0, NTSR significantly increased soil β-glucosidase, xylosidase, cellobiohydrolase, and chitinase activities at 0-10 cm soil depth (P < 0.05). However, different tillage methods with straw returning had no significant effects on enzyme activity at 0-10 cm soil depth. The observed species and Chao1 index of the fungal communities under NTSR were 22.8% and 32.1% lower than under RTSR in the 0-10 cm soil layer, respectively. The composition, structure, and co-occurrence network of fungal communities differed across tillage practices. A partial least squares path model (PLS-PM) analysis indicated that C-related enzymes were the most influential factors associated with SOC stock. Soil physicochemical properties and fungal communities affected extracellular enzyme activities. Overall, conservation tillage can promote surface SOC stock, which was associated with increased enzyme activity.
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Affiliation(s)
- Wen-Sheng Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Yu-Xin Wei
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Ping-Ping Deng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Olatunde Pelumi Oladele
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Yves N'Dri Bohoussou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Yash Pal Dang
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, 4072, Australia
| | - Xin Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Hai-Lin Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China.
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China.
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Gonzalez JM, Santana MM, Gomez EJ, Delgado JA. Soil Thermophiles and Their Extracellular Enzymes: A Set of Capabilities Able to Provide Significant Services and Risks. Microorganisms 2023; 11:1650. [PMID: 37512823 PMCID: PMC10386326 DOI: 10.3390/microorganisms11071650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
During this century, a number of reports have described the potential roles of thermophiles in the upper soil layers during high-temperature periods. This study evaluates the capabilities of these microorganisms and proposes some potential consequences and risks associated with the activity of soil thermophiles. They are active in organic matter mineralization, releasing inorganic nutrients (C, S, N, P) that otherwise remain trapped in the organic complexity of soil. To process complex organic compounds in soils, these thermophiles require extracellular enzymes to break down large polymers into simple compounds, which can be incorporated into the cells and processed. Soil thermophiles are able to adapt their extracellular enzyme activities to environmental conditions. These enzymes can present optimum activity under high temperatures and reduced water content. Consequently, these microorganisms have been shown to actively process and decompose substances (including pollutants) under extreme conditions (i.e., desiccation and heat) in soils. While nutrient cycling is a highly beneficial process to maintain soil service quality, progressive warming can lead to excessive activity of soil thermophiles and their extracellular enzymes. If this activity is too high, it may lead to reduction in soil organic matter, nutrient impoverishment and to an increased risk of aridity. This is a clear example of a potential effect of future predicted climate warming directly caused by soil microorganisms with major consequences for our understanding of ecosystem functioning, soil health and the risk of soil aridity.
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Affiliation(s)
- Juan M Gonzalez
- Institute of Natural Resources and Agrobiology, IRNAS-CSIC, Avda. Reina Mercedes 10, E-41012 Sevilla, Spain
| | - Margarida M Santana
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Enrique J Gomez
- Institute of Natural Resources and Agrobiology, IRNAS-CSIC, Avda. Reina Mercedes 10, E-41012 Sevilla, Spain
| | - José A Delgado
- Department of Engineering, University of Loyola, Avda. de las Universidades, E-41704 Dos Hermanas, Spain
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Tang T, Wang F, Fang G, Mao T, Guo J, Kuang H, Sun G, Guo X, Duan Y, You J. Coptischinensis Franch root rot infection disrupts microecological balance of rhizosphere soil and endophytic microbiomes. Front Microbiol 2023; 14:1180368. [PMID: 37303806 PMCID: PMC10248259 DOI: 10.3389/fmicb.2023.1180368] [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: 03/06/2023] [Accepted: 04/21/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The ecological balance of the plant microbiome, as a barrier against pathogens, is very important for host health. Coptis chinensis is one of the important medicinal plants in China. In recent years, Illumina Miseq high-throughput sequencing technology was frequently used to analyze root rot pathogens and the effects of root rot on rhizosphere microorganisms of C. chinensis. But the effects of root rot infection on rhizosphere microecological balance of C. chinensis have received little attention. Methods In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the impact on microbial composition and diversity of C. chinensis by root rot. Results The results showed that root rot infection had significant impact on bacterial α-diversity in rhizome samples, but had no significant effect on that in leaf samples and rhizosphere soil samples, while root rot infection exhibited significant impact on the fungal α-diversity in leaf samples and rhizosphere soil samples, and no significant impact on that in rhizome samples. PCoA analysis showed that the root rot infection had a greater impact on the fungal community structure in the rhizosphere soil, rhizome, and leaf samples of C. chinensis than on the bacterial community structure. Root rot infection destroyed the microecological balance of the original microbiomes in the rhizosphere soil, rhizome, and leaf samples of C. chinensis, which may also be one of the reasons for the serious root rot of C. chinensis. Discussion In conclusion, our findings suggested that root rot infection with C. chinensis disrupts microecological balance of rhizosphere soil and endophytic microbiomes. The results of this study can provide theoretical basis for the prevention and control of C. chinensis root rot by microecological regulation.
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Affiliation(s)
- Tao Tang
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Fanfan Wang
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Guobin Fang
- Hubei Provincial Plant Protection Station, Wuhan, China
| | - Ting Mao
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
| | - Jie Guo
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Hui Kuang
- Hubei Provincial Plant Protection Station, Wuhan, China
| | | | - Xiaoliang Guo
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
| | - Yuanyuan Duan
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Jingmao You
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
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50
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Gonzalez-Gonzalez LM, de-Bashan LE. The Potential of Microalgae-Bacteria Consortia to Restore Degraded Soils. BIOLOGY 2023; 12:biology12050693. [PMID: 37237506 DOI: 10.3390/biology12050693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023]
Abstract
Soil restoration is one of the biggest challenges of this century. Besides the negative impacts of climate change, the current increase in food demands has put severe pressure on soil resources, resulting in a significant area of degraded land worldwide. However, beneficial microorganisms, such as microalgae and plant growth-promoting bacteria, have an outstanding ability to restore soil health and fertility. In this mini-review, we summarize state-of-the-art knowledge on these microorganisms as amendments that are used to restore degraded and contaminated soils. Furthermore, the potential of microbial consortia to maximize beneficial effects on soil health and boost the production of plant-growth-promoting compounds within a mutualistic interaction is discussed.
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Affiliation(s)
| | - Luz E de-Bashan
- The Bashan Institute of Science, 1730 Post Oak Ct, Auburn, AL 36830, USA
- Department of Entomology and Plant Pathology, Auburn University, 209 Life Sciences Building, Auburn, AL 36849, USA
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Avenida IPN 195, La Paz 23096, Mexico
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