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Yang G, Jiang L, Li W, Li E, Lv G. Structural Characteristics and Assembly Mechanisms of Soil Microbial Communities under Water-Salt Gradients in Arid Regions. Microorganisms 2023; 11:microorganisms11041060. [PMID: 37110483 PMCID: PMC10142023 DOI: 10.3390/microorganisms11041060] [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: 03/13/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Exploring the structural characteristics of arid soil microbial communities and their assembly mechanisms is important for understanding the ecological characteristics of arid zone soils and promoting ecological restoration. In this study, we used Illumina high-throughput sequencing technology to study soils in the arid zone of the Lake Ebinur basin, determined the differences among soil microbial community structures in the study area under different water-salt gradients, and investigated the effects of environmental factors on microbial community structure and assembly mechanisms. The results show the following: the microbial community alpha diversity exhibited a significantly higher low water-salt gradient (L) than high water-salt gradient (H) and medium water-salt gradient (M). The pH was most strongly correlated with soil microbial community structure, where the alpha diversity indices of the bacterial community and fungal community were significantly negatively correlated with pH, and the Bray-Curtis distance of bacterial community was significantly positively correlated with pH (p < 0.05). The complexity of bacterial community co-occurrence networks showed a significantly higher L than H and M, and the complexity of fungal community co-occurrence network showed a significantly lower L than H and M. The cooperative relationship of H and M in the co-occurrence networks was stronger than that of the L, and the key species of the microbial co-occurrence network were different under different water-salt gradients. Stochastic processes dominated the assembly mechanism of the microbial community structure of soil, and the explanation rates of deterministic and stochastic processes were different under different water-salt gradients, with the highest explanation rate of stochastic processes on the L accounting for more than 90%. In summary, the soil microbial community structure and assembly mechanisms significantly differed across water-salt gradients, and these findings can help provide a reference for further research on soil microbiology in arid zones.
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Affiliation(s)
- Guang Yang
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Lamei Jiang
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Wenjing Li
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Eryang Li
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Guanghui Lv
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
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Ma J, Niu A, Liao Z, Qin J, Xu S, Lin C. Factors affecting N 2O fluxes from heavy metal-contaminated mangrove soils in a subtropical estuary. MARINE POLLUTION BULLETIN 2023; 186:114425. [PMID: 36462424 DOI: 10.1016/j.marpolbul.2022.114425] [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: 06/29/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
A 1-year field monitoring program was carried out to observe seasonal variation in N2O fluxes at two typical mangrove wetlands in a subtropical estuary. The soils in the island-type mangrove wetland had a higher level of heavy metal(loid) contamination and a lower level of salinity compared to the small bay-type mangrove wetland. While there was a high level of similarity in the seasonal variation pattern of N2O fluxes between the two investigated sites with both being significantly higher in summer than in other seasons, the average of N2O fluxes in the island-type mangrove wetland was 7.19 μg·m-2·h-1, which tended to be lower compared to the small bay-type mangrove wetland (15.63 μg·m-2·h-1). Overall, N2O flux was closely related to soil-borne heavy metal(loid)s, showing a trend to decrease with increasing concentration of these heavy metal(loid)s. The N2O fluxes increased with decreasing abundance of either denitrifiers or nitrifiers. But the opposite was observed for the anammox bacteria present in the soils. The anammox bacteria were more sensitive to heavy metal(loid) stress but more tolerated high salinity encountered in the investigated soils compared to the denitrifiers or nitrifiers. It appears that anammox reactions mediated by anammox bacteria played a key role in affecting the spatial variation in N2O fluxes from the mangrove soils in the study area. And an increased level of ammonium in soils tended to promote the activity of anammox bacteria and consequently enhanced N2O emission from the mangrove soils.
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Affiliation(s)
- Jiaojiao Ma
- School of Geography, South China Normal University, Guangzhou 510631, China; Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Anyi Niu
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Zhenni Liao
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Junhao Qin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Songjun Xu
- School of Geography, South China Normal University, Guangzhou 510631, China.
| | - Chuxia Lin
- Faculty of Science, Engineering and Built Environment, Deakin University, Burwood, VIC 3125, Australia.
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Hu W, Hou Q, Delgado-Baquerizo M, Stegen JC, Du Q, Dong L, Ji M, Sun Y, Yao S, Gong H, Xiong J, Xia R, Liu J, Aqeel M, Akram MA, Ran J, Deng J. Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol 2022; 24:5483-5497. [PMID: 35706137 DOI: 10.1111/1462-2920.16099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qingqing Hou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - James C Stegen
- Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Qiajun Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mingfei Ji
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuan Sun
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuran Yao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyang Gong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junlan Xiong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Rui Xia
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jiayuan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.,School of Economics, Lanzhou University, Lanzhou, China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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Marcos MS, González MC, Vallejos MB, Barrionuevo CG, Olivera NL. Impact of irrigation with fish-processing effluents on nitrification and ammonia-oxidizer abundances in Patagonian arid soils. Arch Microbiol 2021; 203:3945-3953. [PMID: 34021768 DOI: 10.1007/s00203-021-02358-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 11/24/2022]
Abstract
This study aimed to evaluate the short-term effects of irrigation with diluted fish-processing effluents on soil pH, electrical conductivity, nitrification rate and abundance of ammonia oxidizers. To accomplish that, we constructed microcosms of soil from an undisturbed arid ecosystem of Patagonia, and irrigated them for 2 months with diluted effluents from a fish-processing factory or with water as control. In the initial soil sample, and along the experiment, we determined soil pH, electrical conductivity, and the concentration of inorganic nitrogen forms, which we used to calculate the net nitrification rate. We further estimated the abundances of ammonia-oxidizing archaea and bacteria in the initial soil sample and at the end of the experiment, by qPCR of amoA genes. Soil pH decreased and electrical conductivity increased in both irrigation treatments, although the effect was higher in effluent-irrigated microcosms. Soil nitrate + nitrite concentration, and thus the nitrification rate, was higher in effluent than in water-irrigated microcosms. The abundance of archaeal amoA genes was higher under effluent than water-irrigation, but that of bacterial amoA genes did not vary significantly between treatments. Neither ammonia-oxidizing archaea nor bacteria were influenced by the changes in soil pH and electrical conductivity induced by effluent irrigation.
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Affiliation(s)
- Magalí S Marcos
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET, CCT CONICET-CENPAT), Boulevard Brown 2915, U9120ACD, Puerto Madryn, Argentina.
| | - M Candela González
- Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Puerto Madryn, Argentina
| | - M Belén Vallejos
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET, CCT CONICET-CENPAT), Boulevard Brown 2915, U9120ACD, Puerto Madryn, Argentina
| | - Cristian G Barrionuevo
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET, CCT CONICET-CENPAT), Boulevard Brown 2915, U9120ACD, Puerto Madryn, Argentina
| | - Nelda L Olivera
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET, CCT CONICET-CENPAT), Boulevard Brown 2915, U9120ACD, Puerto Madryn, Argentina
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5
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Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline. THE ISME JOURNAL 2021; 15:623-635. [PMID: 33067585 PMCID: PMC8027100 DOI: 10.1038/s41396-020-00801-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/11/2020] [Accepted: 09/30/2020] [Indexed: 01/30/2023]
Abstract
Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree health. Here, we combined high-throughput sequencing and qPCR analysis of key nitrification and denitrification genes with soil chemical analyses to characterise ammonia-oxidising bacteria (AOB), archaea (AOA) and denitrifying communities in soils associated with symptomatic (declining) and asymptomatic (apparently healthy) oak trees (Quercus robur and Q. petraea) in the United Kingdom. Asymptomatic trees were associated with a higher abundance of AOB that is driven positively by soil pH. No relationship was found between AOA abundance and tree health. However, AOA abundance was driven by lower concentrations of NH4+, further supporting the idea of AOA favouring lower soil NH4+ concentrations. Denitrifier abundance was influenced primarily by soil C:N ratio, and correlations with AOB regardless of tree health. These findings indicate that amelioration of soil acidification by balancing C:N may affect AOB abundance driving N transformations, reducing stress on declining oak trees.
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Zhang J, Cook J, Nearing JT, Zhang J, Raudonis R, Glick BR, Langille MGI, Cheng Z. Harnessing the plant microbiome to promote the growth of agricultural crops. Microbiol Res 2021; 245:126690. [PMID: 33460987 DOI: 10.1016/j.micres.2020.126690] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/11/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]
Abstract
The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world's rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant's rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.
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Affiliation(s)
- Janie Zhang
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Junzeng Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Halifax, NS, Canada
| | - Renee Raudonis
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada; Department of Pharmacology, Dalhousie University, Halifax, NS, Canada; CGEB-Integrated Microbiome Resource (IMR), Dalhousie University, Halifax, NS, Canada
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
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Hu HW, Trivedi P, He JZ, Singh BK. Microbial nitrous oxide emissions in dryland ecosystems: mechanisms, microbiome and mitigation. Environ Microbiol 2017; 19:4808-4828. [DOI: 10.1111/1462-2920.13795] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/01/2017] [Accepted: 05/05/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences; the University of Melbourne, Parkville; Victoria 3010, Australia
| | - Pankaj Trivedi
- Department of Bioagricultural Sciences and Pest Management; Colorado State University; Fort Collins CO USA
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences; the University of Melbourne, Parkville; Victoria 3010, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith South DC NSW 2751, Australia
- Global Centre for Land-Based Innovation; Western Sydney University; Penrith South DC NSW 2751, Australia
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Delgado-Baquerizo M, Maestre FT, Eldridge DJ, Singh BK. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients. Front Microbiol 2016; 7:505. [PMID: 27148194 PMCID: PMC4834304 DOI: 10.3389/fmicb.2016.00505] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 03/29/2016] [Indexed: 11/24/2022] Open
Abstract
Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered.
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Affiliation(s)
| | - Fernando T Maestre
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos Móstoles, Spain
| | - David J Eldridge
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, PenrithNSW, Australia; Global Centre for Land-Based Innovation, Western Sydney University, PenrithNSW, Australia
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Maestre FT, Bowker MA, Eldridge DJ, Cortina J, Lázaro R, Gallardo A, Delgado-Baquerizo M, Berdugo M, Castillo-Monroy AP, Valencia E. Biological Soil Crusts as a Model System in Ecology. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci U S A 2015; 112:15684-9. [PMID: 26647180 DOI: 10.1073/pnas.1516684112] [Citation(s) in RCA: 343] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.
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Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil. Sci Rep 2015; 5:11146. [PMID: 26053257 PMCID: PMC4459192 DOI: 10.1038/srep11146] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/14/2015] [Indexed: 11/10/2022] Open
Abstract
Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0–10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10–90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.
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Delgado‐Baquerizo M, Gallardo A, Covelo F, Prado‐Comesaña A, Ochoa V, Maestre FT. Differences in thallus chemistry are related to species‐specific effects of biocrust‐forming lichens on soil nutrients and microbial communities. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12403] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Manuel Delgado‐Baquerizo
- Departamento Sistemas Físicos, Químicos y Naturales Universidad Pablo de Olavide Carretera de Utrera km. 1 41013 Sevilla Spain
- Hawkesbury Institute for the Environment University of Western Sydney Penrith 2751 New South Wales Australia
| | - Antonio Gallardo
- Departamento Sistemas Físicos, Químicos y Naturales Universidad Pablo de Olavide Carretera de Utrera km. 1 41013 Sevilla Spain
| | - Felisa Covelo
- Departamento Sistemas Físicos, Químicos y Naturales Universidad Pablo de Olavide Carretera de Utrera km. 1 41013 Sevilla Spain
| | - Ana Prado‐Comesaña
- Departamento Sistemas Físicos, Químicos y Naturales Universidad Pablo de Olavide Carretera de Utrera km. 1 41013 Sevilla Spain
| | - Victoria Ochoa
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Física y Química Inorgánica Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos c/Tulipán s/n 28933 Móstoles Spain
| | - Fernando T. Maestre
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Física y Química Inorgánica Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos c/Tulipán s/n 28933 Móstoles Spain
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