51
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Zhu D, Delgado-Baquerizo M, Su JQ, Ding J, Li H, Gillings MR, Penuelas J, Zhu YG. Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7445-7455. [PMID: 33977709 DOI: 10.1021/acs.est.1c00811] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.
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Affiliation(s)
- Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Manuel Delgado-Baquerizo
- 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
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jing Ding
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Bellaterra, Barcelona, Catalonia 08193, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia 08193, Spain
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
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52
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Baruch Z, Liddicoat C, Cando-Dumancela C, Laws M, Morelli H, Weinstein P, Young JM, Breed MF. Increased plant species richness associates with greater soil bacterial diversity in urban green spaces. ENVIRONMENTAL RESEARCH 2021; 196:110425. [PMID: 33157108 DOI: 10.1016/j.envres.2020.110425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
The vegetation and soil microbiome within urban green spaces is increasingly managed to help conserve biodiversity and improve human health concurrently. However, the effects of green space management on urban soil ecosystems is poorly understood, despite their importance. Across 40 urban green spaces in metropolitan Adelaide, South Australia, we show that soil bacterial communities are strongly affected by urban green space type (incl. sport fields, community gardens, parklands and revegetated areas), and that plant species richness is positively associated with soil bacterial diversity. Importantly, these microbiome trends were not affected by geographic proximity of sample sites. Our results provide early evidence that urban green space management can have predictable effects on the soil microbiome, at least from a diversity perspective, which could prove important to inform policy development if urban green spaces are to be managed to optimise population health benefits.
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Affiliation(s)
- Zdravko Baruch
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Craig Liddicoat
- School of Public Health, University of Adelaide, Adelaide, SA, 5005, Australia; College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia
| | | | - Mark Laws
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Hamish Morelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Philip Weinstein
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia; School of Public Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia.
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53
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Cui J, Glatzel S, Bruckman VJ, Wang B, Lai DYF. Long-term effects of biochar application on greenhouse gas production and microbial community in temperate forest soils under increasing temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:145021. [PMID: 33636794 DOI: 10.1016/j.scitotenv.2021.145021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 06/12/2023]
Abstract
Biochar management has been proposed as a promising strategy to mitigate climate change. However, the long-term effects of biochar amendment on soil greenhouse gas (GHG) production and microbial community in forest ecosystems under projected warming remain highly uncertain. In this study, we conducted a 49-day incubation experiment to investigate the impact of biochar application on soil physico-chemical properties, GHG production rates, and microbial community at three temperature levels using a temperate forest soil amended with spruce biochar four years ago. Our results showed that temperature exerted a positive effect on soil CO2, CH4 and N2O production, leading to an increase in total global warming potential by 169% and 87% as temperature rose from 5 to 15 °C and from 15 to 25 °C, respectively, and thus a positive feedback to warming. Moreover, warming was found to reduce soil microbial biomass significantly, but at the same time promote the selection of an activated microbial community towards some phyla, e.g. Acidobacteria and Actinobacteria. We observed that biochar amendment reduced soil CH4 consumption and N2O production in the absence of litter by 106% and 94%, respectively, but did not affect soil CO2 production. While biochar had no significant influence of total global warming potential of forest soil, it could promote climate change mitigation by increasing the total soil carbon content by 26% in the presence of litter. In addition, biochar application was shown to enhance soil available phosphorus and dissolved organic carbon concentrations, as well as soil microbial biomass under a warmer environment. Our findings highlighted the potential of spruce biochar as a soil amendment in improving soil fertility and carbon sequestration in temperate forest over the long term, without creating any adverse climatic impacts associated with soil GHG production.
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Affiliation(s)
- Jinglan Cui
- Department of Geography and Resource Management, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Stephan Glatzel
- Department of Geography and Regional Research, Geoecology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Viktor J Bruckman
- Commission for Interdisciplinary Ecological Studies, Austrian Academy of Sciences, Dr. Ignaz Seipel-Platz 2, 1010 Vienna, Austria
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Derrick Y F Lai
- Department of Geography and Resource Management, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Environmental Policy and Resource Management, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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54
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Bui A, Orr D, Lepori-Bui M, Konicek K, Young HS, Moeller HV. Soil fungal community composition and functional similarity shift across distinct climatic conditions. FEMS Microbiol Ecol 2021; 96:5909968. [PMID: 32960210 DOI: 10.1093/femsec/fiaa193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/18/2020] [Indexed: 11/15/2022] Open
Abstract
A large part of ecosystem function in woodland systems depends on soil fungal communities. However, global climate change has the potential to fundamentally alter these communities as fungal species are filtered with changing environmental conditions. In this study, we examined the potential effects of climate on host-associated (i.e. tree-associated) soil fungal communities at climatically distinct sites in the Tehachapi Mountains in California, where more arid conditions represent likely regional climate futures. We found that soil fungal community composition changes strongly across sites, with species richness and diversity being highest at the most arid site. However, host association may buffer the effects of climate on community composition, as host-associated fungal communities are more similar to each other across climatically distinct sites than the whole fungal community. Lastly, an examination of functional traits for ectomycorrhizal fungi, a well-studied guild of fungal mutualist species, showed that stress-tolerant traits were more abundant at arid sites than mesic sites, providing a mechanistic understanding of these community patterns. Taken together, our results indicate that fungal community composition will likely shift with future climate change but that host association may buffer these effects, with shifts in functional traits having implications for future ecosystem function.
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Affiliation(s)
- An Bui
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Devyn Orr
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Michelle Lepori-Bui
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Kelli Konicek
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Hillary S Young
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Holly V Moeller
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
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55
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Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile. Nat Commun 2021; 12:2089. [PMID: 33828081 PMCID: PMC8027381 DOI: 10.1038/s41467-021-22408-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.
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56
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Wan W, Liu S, Li X, Xing Y, Chen W, Huang Q. Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation. mSystems 2021; 6:e01221-20. [PMID: 33785569 PMCID: PMC8547000 DOI: 10.1128/msystems.01221-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/03/2021] [Indexed: 01/09/2023] Open
Abstract
Bacterial diversity and ecosystem multifunctionality (EMF) vary along environmental gradients. However, little is known about interconnections between EMF and taxonomic and phylogenetic diversities of rare and abundant bacteria. Using MiSeq sequencing and multiple statistical analyses, we evaluated the maintenance of taxonomic and phylogenetic diversities of rare and abundant bacteria and their contributions to EMF in salinized agricultural soils (0.09 to 19.91 dS/m). Rare bacteria exhibited closer phylogenetic clustering and broader environmental breadths than abundant ones, while abundant bacteria showed higher functional redundancies and stronger phylogenetic signals of ecological preferences than rare ones. Variable selection (86.7%) dominated rare bacterial community assembly, and dispersal limitation (54.7%) and variable selection (24.5%) determined abundant bacterial community assembly. Salinity played a decisive role in mediating the balance between stochastic and deterministic processes and showed significant effects on functions and diversities of both rare and abundant bacteria. Rare bacterial taxonomic α-diversity and abundant bacterial phylogenetic α-diversity contributed significantly to EMF, while abundant bacterial taxonomic α-diversity and rare bacterial phylogenetic α-diversity did not. Additionally, abundant rather than rare bacterial community function had a significant effect on soil EMF. These findings extend our knowledge of environmental adaptation of rare and abundant bacteria and highlight different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF.IMPORTANCE Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality. Our sequence-based data showed differences in environmental adaptations of rare and abundant bacteria at taxonomic and phylogenetic levels, which led to different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. Studying the diversity of rare and abundant bacteria and their contributions to EMF in salinized soils is critical for guiding soil restoration.
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Affiliation(s)
- Wenjie Wan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yonghui Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, People's Republic of China
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57
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Wang C, Morrissey EM, Mau RL, Hayer M, Piñeiro J, Mack MC, Marks JC, Bell SL, Miller SN, Schwartz E, Dijkstra P, Koch BJ, Stone BW, Purcell AM, Blazewicz SJ, Hofmockel KS, Pett-Ridge J, Hungate BA. The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization. ISME JOURNAL 2021; 15:2738-2747. [PMID: 33782569 DOI: 10.1038/s41396-021-00959-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 03/04/2021] [Indexed: 11/09/2022]
Abstract
Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.
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Affiliation(s)
- Chao Wang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.,CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Juan Piñeiro
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheryl L Bell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA.,Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Jennifer Pett-Ridge
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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58
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Wan W, Gadd GM, Yang Y, Yuan W, Gu J, Ye L, Liu W. Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:2390-2403. [PMID: 33714213 DOI: 10.1111/mec.15882] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/03/2023]
Abstract
Disentangling the biogeographic patterns of rare and abundant microbes is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbes across large spatial-scale wetlands. Using Illumina sequencing and multiple statistical analyses, we characterized the taxonomic and phylogenetic diversity of rare and abundant bacteria and fungi in Qinghai-Tibet Plateau wetland soils. Abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare ones. By contrast, rare taxa showed higher sensitivity to environmental changes and closer phylogenetic clustering than abundant ones. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated community assemblies of abundant bacteria, and rare and abundant fungi, while variable selection belonging to deterministic process governed community assembly of rare bacteria. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbes were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbes. Abundant microbes may have better environmental adaptation potential and are less dispersed by environmental changes than rare ones. Our findings extend knowledge of the adaptation of rare and abundant microbes to ongoing environmental change and could facilitate prediction of biodiversity loss caused probably by climate change and human activity in the Qinghai-Tibet Plateau wetlands.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, UK.,State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jidong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Environmental Engineering, Guangdong Technion Israel Institute of Technology, Guangdong, China
| | - Luping Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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59
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Saia SM, Carrick HJ, Buda AR, Regan JM, Walter MT. Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2722-2742. [PMID: 33559467 DOI: 10.1021/acs.est.0c03566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite ongoing management efforts, phosphorus (P) loading from agricultural landscapes continues to impair water quality. Wastewater treatment research has enhanced our knowledge of microbial mechanisms influencing P cycling, especially regarding microbes known as polyphosphate accumulating organisms (PAOs) that store P as polyphosphate (polyP) under oxic conditions and release P under anoxic conditions. However, there is limited application of PAO research to reduce agricultural P loading and improve water quality. Herein, we conducted a meta-analysis to identify articles in Web of Science on polyP and its use by PAOs across five disciplines (i.e., wastewater treatment, terrestrial, freshwater, marine, and agriculture). We also summarized research that provides preliminary support for PAO-mediated P cycling in natural habitats. Terrestrial, freshwater, marine, and agriculture disciplines had fewer polyP and PAO articles compared to wastewater treatment, with agriculture consistently having the least. Most meta-analysis articles did not overlap disciplines. We found preliminary support for PAOs in natural habitats and identified several knowledge gaps and research opportunities. There is an urgent need for interdisciplinary research linking PAOs, polyP, and oxygen availability with existing knowledge of P forms and cycling mechanisms in natural and agricultural environments to improve agricultural P management strategies and achieve water quality goals.
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Affiliation(s)
- Sheila M Saia
- Depatment of Biological and Agricultural Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Hunter J Carrick
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Anthony R Buda
- Pasture Systems and Watershed Management Research Unit, Agricultural Research Service, United States Department of Agriculture, University Park, Pennsylvania 16802, United States
| | - John M Regan
- Department of Civil and Environmental Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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60
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Zhu H, Gong L, Ding Z, Li Y. Effects of litter and root manipulations on soil carbon and nitrogen in a Schrenk's spruce (Picea schrenkiana) forest. PLoS One 2021; 16:e0247725. [PMID: 33630965 PMCID: PMC7906406 DOI: 10.1371/journal.pone.0247725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Plant detritus represents the major source of soil carbon (C) and nitrogen (N), and changes in its quantity can influence below-ground biogeochemical processes in forests. However, we lack a mechanistic understanding of how above- and belowground detrital inputs affect soil C and N in mountain forests in an arid land. Here, we explored the effects of litter and root manipulations (control (CK), doubled litter input (DL), removal of litter (NL), root exclusion (NR), and a combination of litter removal and root exclusion (NI)) on soil C and N concentrations, enzyme activity and microbial biomass during a 2-year field experiment. We found that DL had no significant effect on soil total organic carbon (SOC) and total nitrogen (TN) but significantly increased soil dissolved organic carbon (DOC), microbial biomass C, N and inorganic N as well as soil cellulase, phosphatase and peroxidase activities. Conversely, NL and NR reduced soil C and N concentrations and enzyme activities. We also found an increase in the biomass of soil bacteria, fungi and actinomycetes in the DL treatment, while NL reduced the biomass of gram-positive bacteria, gram-negative bacteria and fungi by 5.15%, 17.50% and 14.17%, respectively. The NR decreased the biomass of these three taxonomic groups by 8.97%, 22.11% and 21.36%, respectively. Correlation analysis showed that soil biotic factors (enzyme activity and microbial biomass) and abiotic factors (soil moisture content) significantly controlled the change in soil C and N concentrations (P < 0.01). In brief, we found that the short-term input of plant detritus could markedly affect the concentrations and biological characteristics of the C and N fractions in soil. The removal experiment indicated that the contribution of roots to soil nutrients is greater than that of the litter.
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Affiliation(s)
- Haiqiang Zhu
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
- Ministry of Education, Key Laboratory of Oasis Ecology, Urumqi, China
| | - Lu Gong
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
- Ministry of Education, Key Laboratory of Oasis Ecology, Urumqi, China
| | - Zhaolong Ding
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
- Ministry of Education, Key Laboratory of Oasis Ecology, Urumqi, China
| | - Yuefeng Li
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
- Ministry of Education, Key Laboratory of Oasis Ecology, Urumqi, China
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61
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Wan W, Grossart HP, He D, Yuan W, Yang Y. Stronger environmental adaptation of rare rather than abundant bacterioplankton in response to dredging in eutrophic Lake Nanhu (Wuhan, China). WATER RESEARCH 2021; 190:116751. [PMID: 33348071 DOI: 10.1016/j.watres.2020.116751] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Deciphering responses of rare versus abundant bacterioplankton to environmental change, crucial for understanding and mitigating of cyanobacterial blooms, is an important but poorly investigated subject. Using MiSeq sequencing, we investigated the taxonomic and phylogenetic diversity of rare and abundant bacterioplankton in eutrophic Lake Nanhu before and after dredging. We estimated environmental breadths and phylogenetic signals of ecological preferences of rare and abundant bacterioplankton, and investigated community function and bacterioplankton assembly processes. Both taxonomic and phylogenic distances of rare and abundant bacterioplankton communities were significantly positively correlated with the dissimilarity of environmental factors. Threshold indicator taxa analysis and Blomberg's K statistic indicated that rare taxa held broader environmental thresholds and stronger phylogenetic signals for ecological traits than abundant taxa. Environmental adaptations of both rare and abundant taxa exhibited distinct changes after dredging. Higher functional redundancy occurred in the abundant compared to the rare bacterioplankton, with functions of rare bacterioplankton decreasing and for the abundant ones increasing after dredging. The null model revealed that dispersal limitation belonging to stochastic processes determined the abundant bacterioplankton community assembly, whereas variable selection belonging to deterministic processes drove the rare one. Rare bacterioplankton was more environmentally constrained than the abundant one. Dissolved oxygen was the decisive factor in determining the balance between stochasticity and determinism in both rare and abundant bacterioplankton. Our study extends our knowledge of environmental adaptation of rare versus abundant bacterioplankton to massive disturbing measures, i.e. dredging, and allows to estimate dredging performance for mitigating cyanobacterial blooms from a molecular ecology viewpoint.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Hans-Peter Grossart
- Leibniz-Institude of Freshwater Ecology and Inland Fisheries (IGB), 16775, Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan 430070, PR China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China.
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62
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Landis EA, Oliverio AM, McKenney EA, Nichols LM, Kfoury N, Biango-Daniels M, Shell LK, Madden AA, Shapiro L, Sakunala S, Drake K, Robbat A, Booker M, Dunn RR, Fierer N, Wolfe BE. The diversity and function of sourdough starter microbiomes. eLife 2021; 10:e61644. [PMID: 33496265 PMCID: PMC7837699 DOI: 10.7554/elife.61644] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- North Carolina Museum of Natural SciencesRaleighUnited States
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Nicole Kfoury
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | | | - Leonora K Shell
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Lori Shapiro
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | | | - Kinsey Drake
- Department of Biology, Tufts UniversityMedfordUnited States
| | - Albert Robbat
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | - Matthew Booker
- Department of History, North Carolina State UniversityRaleighUnited States
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- Danish Natural History Museum, University of CopenhagenCopenhagenDenmark
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
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63
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Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient. mSystems 2020; 5:5/6/e01150-20. [PMID: 33361326 PMCID: PMC7762797 DOI: 10.1128/msystems.01150-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora, was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata. Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes. IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes.
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64
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Hermans SM, Buckley HL, Curran-Cournane F, Taylor M, Lear G. Temporal variation in soil bacterial communities can be confounded with spatial variation. FEMS Microbiol Ecol 2020; 96:5909033. [PMID: 32949457 DOI: 10.1093/femsec/fiaa192] [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: 06/23/2020] [Accepted: 09/17/2020] [Indexed: 11/12/2022] Open
Abstract
Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.
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Affiliation(s)
- Syrie M Hermans
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Fiona Curran-Cournane
- Ministry for the Environment-Manatū Mō Te Taiao, 45 Queen Street, Auckland 1010, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 401 Grey Street, Hamilton 3216, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
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65
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The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities. mBio 2020; 11:mBio.01718-20. [PMID: 33109755 PMCID: PMC7593963 DOI: 10.1128/mbio.01718-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.
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66
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Chua CY, Wong CMVL. Effects of simulated warming on bacterial diversity and abundance in tropical soils from East Malaysia using open top chambers. Can J Microbiol 2020; 67:64-74. [PMID: 33084348 DOI: 10.1139/cjm-2019-0461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effects of global warming are increasingly evident, where global surface temperatures and atmospheric concentration of carbon dioxide have increased in past decades. Given the role of terrestrial bacteria in various ecological functions, it is important to understand how terrestrial bacteria would respond towards higher environmental temperatures. This study aims to determine soil bacterial diversity in the tropics and their response towards in situ warming using an open-top chamber (OTC). OTCs were set up in areas exposed to sunlight throughout the year in the tropical region in Malaysia. Soil samples were collected every 3 months to monitor changes in bacterial diversity using V3-V4 16S rDNA amplicon sequencing inside the OTCs (treatment plots) and outside the OTCs (control plots). After 12 months of simulated warming, an average increase of 0.81 to 1.15 °C was recorded in treatment plots. Significant changes in the relative abundance of bacterial phyla such as Bacteroidetes and Chloroflexi were reported. Increases in the relative abundance of Actinobacteria were also observed in treatment plots after 12 months. Substantial changes were observed at the genus level, where most bacterial genera decreased in relative abundance after 12 months. This study demonstrated that warming can alter soil bacteria in tropical soils from Kota Kinabalu.
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Affiliation(s)
- Chuen Yang Chua
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.,Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Clemente Michael Vui Ling Wong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.,Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
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67
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Soriano-Lerma A, Pérez-Carrasco V, Sánchez-Marañón M, Ortiz-González M, Sánchez-Martín V, Gijón J, Navarro-Mari JM, García-Salcedo JA, Soriano M. Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples. Sci Rep 2020; 10:13637. [PMID: 32788589 PMCID: PMC7423937 DOI: 10.1038/s41598-020-70141-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023] Open
Abstract
Next generation sequencing methods are widely used in evaluating the structure and functioning of microbial communities, especially those centered on 16S rRNA subunit. Since Illumina Miseq, the most used sequencing platform, does not allow the full sequencing of 16S rRNA gene, this study aims to evaluate whether the choice of different target regions might affect the outcome of microbiome studies regarding soil and saliva samples. V1V3, V3V4, V4V5 and V6V8 domains were studied, finding that while some regions showed differences in the detection of certain bacterial taxa and in the calculation of alpha diversity, especially in soil samples, the overall effect did not compromise the differentiation of any sample type in terms of taxonomic analysis at the genus level. 16S rRNA target regions did affect the detection of specific bacteria related to soil quality and development, and microbial genera used as health biomarkers in saliva. V1V3 region showed the closest similarity to internal sequencing control mock community B, suggesting it might be the most preferable choice regarding data reliability.
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Affiliation(s)
- Ana Soriano-Lerma
- Department of Physiology (Faculty of Pharmacy, Campus Universitario de Cartuja), Institute of Nutrition and Food Technology "José Mataix", University of Granada, 18071, Granada, Spain
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Virginia Pérez-Carrasco
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, 18014, Granada, Spain
| | - Manuel Sánchez-Marañón
- Department of Soil Science and Agricultural Chemistry, University of Granada, 18071, Granada, Spain
| | - Matilde Ortiz-González
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Center for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almeria, 04001, Almería, Spain
| | - Victoria Sánchez-Martín
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, 18014, Granada, Spain
| | - Juan Gijón
- Department of Periodontics, School of Dentistry, University of Granada, Granada, Spain
| | - José María Navarro-Mari
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, 18014, Granada, Spain
| | - José Antonio García-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain.
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, 18014, Granada, Spain.
| | - Miguel Soriano
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain.
- Center for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almeria, 04001, Almería, Spain.
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68
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Jiao S, Lu Y. Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields. GLOBAL CHANGE BIOLOGY 2020; 26:4506-4520. [PMID: 32324306 DOI: 10.1111/gcb.15130] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how communities assemble in response to environmental change is of great ecological importance. Little is known about the assembly processes governing abundant and rare fungal communities across agro-ecosystems, particularly with regard to their environmental adaptation. By considering abundant and rare taxa, we tested the environmental thresholds and phylogenetic signals for ecological preferences of fungal communities across complex environmental gradients to reflect their environmental adaptation, and explored the factors influencing their assembly based on the large-scale soil survey in agricultural fields across eastern China. We found that the abundant taxa exhibited remarkably broader response thresholds and stronger phylogenetic signals for the ecological preferences across environmental gradients compared to the rare taxa. Neutral processes played a key role in shaping the abundant subcommunity compared to the rare subcommunity. Null model analysis revealed that the abundant subcommunity was less clustered phylogenetically and governed primarily by dispersal limitation, while homogeneous selection was the major assembly process in the rare subcommunity. Soil available sulfur was the major factor mediating the balance between stochastic and deterministic processes of both the abundant and rare subcommunities, as indicated by an increase in stochasticity with higher available sulfur concentration. Based on macroecological spatial scale datasets, our study revealed the potential broader environmental adaptation of abundant fungal taxa compared to rare fungal taxa, and identified the factors mediating their distinct community assembly processes in agricultural fields. These results contribute to our understanding of the mechanisms underlying the generation and maintenance of fungal diversity in response to global environmental change.
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Affiliation(s)
- Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, P. R. China
- College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, P. R. China
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69
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Hallin S, Bodelier PLE. Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry. Front Microbiol 2020; 11:981. [PMID: 32499774 PMCID: PMC7243610 DOI: 10.3389/fmicb.2020.00981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/23/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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70
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Abstract
Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation. The relative importance of spatial and temporal variability in shaping the distribution of soil microbial communities at a large spatial scale remains poorly understood. Here, we explored the relative importance of space versus time when predicting the distribution of soil bacterial and fungal communities across North China Plain in two contrasting seasons (summer versus winter). Although we found that microbial alpha (number of phylotypes) and beta (changes in community composition) diversities differed significantly between summer and winter, space rather than season explained more of the spatiotemporal variation of soil microbial alpha and beta diversities. Environmental covariates explained some of microbial spatiotemporal variation observed, with fast-changing environmental covariates—climate variables, soil moisture, and available nutrient—likely being the main factors that drove the seasonal variation found in bacterial and fungal beta diversities. Using random forest modeling, we further identified a group of microbial exact sequence variants (ESVs) as indicators of summer and winter seasons and for which relative abundance was associated with fast-changing environmental variables (e.g., soil moisture and dissolved organic nitrogen). Together, our empirical field study’s results suggest soil microbial seasonal variation could arise from the changes of fast-changing environmental variables, thus providing integral support to the large emerging body of snapshot studies related to microbial biogeography. IMPORTANCE Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.
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71
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Isobe K, Bouskill NJ, Brodie EL, Sudderth EA, Martiny JBH. Phylogenetic conservation of soil bacterial responses to simulated global changes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190242. [PMID: 32200749 PMCID: PMC7133522 DOI: 10.1098/rstb.2019.0242] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 01/03/2023] Open
Abstract
Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nicholas J. Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L. Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Erika A. Sudderth
- Center for Environmental Studies, Brown University, Providence, RI, USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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72
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Chu H, Gao GF, Ma Y, Fan K, Delgado-Baquerizo M. Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives. mSystems 2020; 5:e00803-19. [PMID: 32317392 PMCID: PMC7174637 DOI: 10.1128/msystems.00803-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.
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Affiliation(s)
- Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
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73
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Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. CHEMOSPHERE 2020; 243:125242. [PMID: 31995861 DOI: 10.1016/j.chemosphere.2019.125242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/13/2019] [Accepted: 10/26/2019] [Indexed: 05/18/2023]
Abstract
Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
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Affiliation(s)
- Eglantina Lopez-Echartea
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Shinjini Mukherjee
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belgium
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kim Yrjälä
- University of Helsinki, Department of Forest Sciences, Helsinki, Finland; Zhejiang A&F University, State Key Laboratory of Subtropical Silviculture, Zhejiang, China.
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74
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Reese AT, Madden AA, Joossens M, Lacaze G, Dunn RR. Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread. mSphere 2020; 5:e00950-19. [PMID: 31941818 PMCID: PMC6968659 DOI: 10.1128/msphere.00950-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022] Open
Abstract
Sourdough starters are naturally occurring microbial communities in which the environment, ingredients, and bakers are potential sources of microorganisms. The relative importance of these pools remains unknown. Here, bakers from two continents used a standardized recipe and ingredients to make starters that were then baked into breads. We characterized the fungi and bacteria associated with the starters, bakers' hands, and ingredients using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing and then measured dough acidity and bread flavor. Starter communities were much less uniform than expected, and this variation manifested in the flavor of the bread. Starter communities were most similar to those found in flour but shared some species with the bakers' skin. While humans likely contribute microorganisms to the starters, the reverse also appears to be true. This bidirectional exchange of microorganisms between starters and bakers highlights the importance of microbial diversity on bodies and in our environments as it relates to foods.IMPORTANCE Sourdough starters are complex communities of yeast and bacteria which confer characteristic flavor and texture to sourdough bread. The microbes present in starters can be sourced from ingredients or the baking environment and are typically consistent over time. Herein, we show that even when the recipe and ingredients for starter and bread are identical, different bakers around the globe produce highly diverse starters which then alter bread acidity and flavor. Much of the starter microbial community comes from bread flour, but the diversity is also associated with differences in the microbial community on the hands of bakers. These results indicate that bakers may be a source for yeast and bacteria in their breads and/or that bakers' jobs are reflected in their skin microbiome.
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Affiliation(s)
- Aspen T Reese
- Society of Fellows, Harvard University, Cambridge, Massachusetts, USA
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Marie Joossens
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Science, Ghent University, Ghent, Belgium
| | - Guylaine Lacaze
- Puratos Center for Bread Flavour, Puratos Corporation, Vith, Belgium
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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75
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Nottingham AT, Whitaker J, Ostle NJ, Bardgett RD, McNamara NP, Fierer N, Salinas N, Ccahuana AJQ, Turner BL, Meir P. Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient. Ecol Lett 2019; 22:1889-1899. [DOI: 10.1111/ele.13379] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/12/2019] [Accepted: 07/20/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Andrew T. Nottingham
- School of Geosciences University of Edinburgh Crew Building, Kings Buildings Edinburgh EH9 3FFUK
- Smithsonian Tropical Research Institute Apartado 0843‐03092Balboa, Ancon Republic of Panama
| | - Jeanette Whitaker
- Centre for Ecology & Hydrology Lancaster Environment Centre Lancaster LA1 4APUK
| | - Nick J. Ostle
- Lancaster Environment Centre Lancaster University Library Avenue Lancaster LA1 4YQUK
| | - Richard D. Bardgett
- School of Earth and Environmental Sciences Michael Smith Building, The University of Manchester Oxford Road Manchester M13 9PTUK
| | - Niall P. McNamara
- Centre for Ecology & Hydrology Lancaster Environment Centre Lancaster LA1 4APUK
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder CO USA
| | - Norma Salinas
- Seccion Química, Pontificia Universidad Católica del Peru Lima Peru
| | - Adan J. Q. Ccahuana
- Facultad de Biología Universidad Nacional de San Antonio Abad del Cusco Cusco Peru
| | - Benjamin L. Turner
- Smithsonian Tropical Research Institute Apartado 0843‐03092Balboa, Ancon Republic of Panama
| | - Patrick Meir
- School of Geosciences University of Edinburgh Crew Building, Kings Buildings Edinburgh EH9 3FFUK
- Research School of Biology Australian National University Canberra ACT 2601Australia
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76
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Koyama A, Steinweg JM, Haddix ML, Dukes JS, Wallenstein MD. Soil bacterial community responses to altered precipitation and temperature regimes in an old field grassland are mediated by plants. FEMS Microbiol Ecol 2019; 94:4628037. [PMID: 29145592 DOI: 10.1093/femsec/fix156] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 01/10/2023] Open
Abstract
The structure and function of soil microbiomes often change in response to experimental climate manipulations, suggesting an important role in ecosystem feedbacks. However, it is difficult to know if microbes are responding directly to environmental changes or are more strongly impacted by plant responses. We investigated soil microbial responses to precipitation and temperature manipulations at the Boston-Area Climate Experiment in Massachusetts, USA, in both vegetated and bare plots to parse direct vs. plant-mediated responses to multi-factor climate change. We assessed the bacterial community in vegetated soils in 2009, two years after the experiment was initiated, and bacterial and fungal community in vegetated and bare soils in 2011. The bacterial community structure was significantly changed by the treatments in vegetated soils. However, such changes in the bacterial community across the treatments were absent in the 2011 bare soils. These results suggest that the bacterial communities in vegetated soils were structured via plant community shifts in response to the abiotic manipulations. Co-variation between bacterial community structure and temperature sensitivities and stoichiometry of potential enzyme activities in the 2011 vegetated soils suggested a link between bacterial community structure and ecosystem function. This study emphasizes the importance of plant-soil-microbial interactions in mediating responses to future climate change.
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Affiliation(s)
- Akihiro Koyama
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Biology, Algoma University, Queen Street East, Sault Ste. Marie, Ontario P6A 2G4, Canada
| | - J Megan Steinweg
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Biology, Roanoke College, Salem, Virginia 24153, USA
| | - Michelle L Haddix
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Jeffrey S Dukes
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47907, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Matthew D Wallenstein
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado 80523, USA
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77
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Landesman WJ, Freedman ZB, Nelson DM. Seasonal, sub-seasonal and diurnal variation of soil bacterial community composition in a temperate deciduous forest. FEMS Microbiol Ecol 2019; 95:5281420. [PMID: 30629168 PMCID: PMC6353803 DOI: 10.1093/femsec/fiz002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/05/2019] [Indexed: 02/01/2023] Open
Abstract
The temporal dynamics of soil bacterial communities are understudied, but such understanding is critical to elucidating the drivers of community variation. The goal of this study was to characterize how soil bacterial communities vary across diurnal, sub-seasonal and seasonal time-scales in a 5.8 m2 plot and test the hypothesis that bacterial diversity varies on each of these scales. We used 16S rDNA gene amplicon sequencing to quantify the alpha and beta diversity of soil bacteria as well as the Net Relatedness Index and Nearest Taxon Indices to assess the degree of phylogenetic clustering, and the extent to which community shifts were driven by stochastic vs. deterministic limitation. We found that species richness was highest in winter, lowest in fall and that communities were compositionally distinct across seasons. There was no evidence of diurnal-scale shifts; the finest temporal scale over which community shifts were detected using our DNA-based analysis was between sampling dates separated by 6 weeks. Phylogenetic analyses suggested that seasonal-scale differences in community composition were the result of environmental filtering and homogeneous selection. Our findings provide insight into temporal variation of soil bacterial communities across the hourly to seasonal scales while minimizing the potential confounding effect of spatial variation.
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Affiliation(s)
- William J Landesman
- Biology Program, Green Mountain College, One Brennan Circle, Poultney, VT 05764
| | - Zachary B Freedman
- Division of Plant and Soil Sciences, West Virginia University, 370 Evansdale Drive, Morgantown, WV 26506
| | - David M Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD 21532
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78
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Short-Term Response of the Soil Microbial Abundances and Enzyme Activities to Experimental Warming in a Boreal Peatland in Northeast China. SUSTAINABILITY 2019. [DOI: 10.3390/su11030590] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Global warming is likely to influence the soil microorganisms and enzyme activity and alter the carbon and nitrogen balance of peatland ecosystems. To investigate the difference in sensitivities of carbon and nitrogen cycling microorganisms and enzyme activity to warming, we conducted three-year warming experiments in a boreal peatland. Our findings demonstrated that both mcrA and nirS gene abundance in shallow soil and deep soil exhibited insensitivity to warming, while shallow soil archaea 16S rRNA gene and amoA gene abundance in both shallow soil and deep soil increased under warming. Soil pmoA gene abundance of both layers, bacterial 16S rRNA gene abundance in shallow soil, and nirK gene abundance in deep soil decreased due to warming. The decreases of these gene abundances would be a result of losing labile substrates because of the competitive interactions between aboveground plants and underground soil microorganisms. Experimental warming inhibited β-glucosidase activity in two soil layers and invertase activity in deep soil, while it stimulated acid phosphatase activity in shallow soil. Both temperature and labile substrates regulate the responses of soil microbial abundances and enzyme activities to warming and affect the coupling relationships of carbon and nitrogen. This study provides a potential microbial mechanism controlling carbon and nitrogen cycling in peatland under climate warming.
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79
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Delgado-Baquerizo M, Eldridge DJ, Travers SK, Val J, Oliver I, Bissett A. Effects of climate legacies on above- and belowground community assembly. GLOBAL CHANGE BIOLOGY 2018; 24:4330-4339. [PMID: 29750385 DOI: 10.1111/gcb.14306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/05/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
The role of climatic legacies in regulating community assembly of above- and belowground species in terrestrial ecosystems remains largely unexplored and poorly understood. Here, we report on two separate regional and continental empirical studies, including >500 locations, aiming to identify the relative importance of climatic legacies (climatic anomaly over the last 20,000 years) compared to current climates in predicting the relative abundance of ecological clusters formed by species strongly co-occurring within two independent above- and belowground networks. Climatic legacies explained a significant portion of the variation in the current community assembly of terrestrial ecosystems (up to 15.4%) that could not be accounted for by current climate, soil properties, and management. Changes in the relative abundance of ecological clusters linked to climatic legacies (e.g., past temperature) showed the potential to indirectly alter other clusters, suggesting cascading effects. Our work illustrates the role of climatic legacies in regulating ecosystem community assembly and provides further insights into possible winner and loser community assemblies under global change scenarios.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado
- 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
- Office of Environment and Heritage, Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Samantha K Travers
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - James Val
- Office of Environment and Heritage, Buronga, NSW, Australia
| | - Ian Oliver
- Office of Environment and Heritage, Gosford, NSW, Australia
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80
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81
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Oliverio AM, Power JF, Washburne A, Cary SC, Stott MB, Fierer N. The ecology and diversity of microbial eukaryotes in geothermal springs. THE ISME JOURNAL 2018; 12:1918-1928. [PMID: 29662145 PMCID: PMC6052046 DOI: 10.1038/s41396-018-0104-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/18/2018] [Accepted: 03/05/2018] [Indexed: 11/09/2022]
Abstract
Decades of research into the Bacteria and Archaea living in geothermal spring ecosystems have yielded great insight into the diversity of life and organismal adaptations to extreme environmental conditions. Surprisingly, while microbial eukaryotes (protists) are also ubiquitous in many environments, their diversity across geothermal springs has mostly been ignored. We used high-throughput sequencing to illuminate the diversity and structure of microbial eukaryotic communities found in 160 geothermal springs with broad ranges in temperature and pH across the Taupō Volcanic Zone in New Zealand. Protistan communities were moderately predictable in composition and varied most strongly across gradients in pH and temperature. Moreover, this variation mirrored patterns observed for bacterial and archaeal communities across the same spring samples, highlighting that there are similar ecological constraints across the tree of life. While extreme pH values were associated with declining protist diversity, high temperature springs harbored substantial amounts of protist diversity. Although protists are often overlooked in geothermal springs and other extreme environments, our results indicate that such environments can host distinct and diverse protistan communities.
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Affiliation(s)
- Angela M Oliverio
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
| | - Jean F Power
- Extremophile Research Group, GNS Science, Private Bag 2000, Taupō, 3352, New Zealand
- Thermophile Research Unit, School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - S Craig Cary
- Thermophile Research Unit, School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Matthew B Stott
- Extremophile Research Group, GNS Science, Private Bag 2000, Taupō, 3352, New Zealand
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA.
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82
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Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa. ISME JOURNAL 2018; 12:2176-2186. [PMID: 29880909 DOI: 10.1038/s41396-018-0180-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 12/28/2022]
Abstract
The latitudinal diversity gradient is a pattern of biogeography observed broadly in plants and animals but largely undocumented in terrestrial microbial systems. Although patterns of microbial biogeography across broad taxonomic scales have been described in a range of contexts, the mechanisms that generate biogeographic patterns between closely related taxa remain incompletely characterized. Adaptive processes are a major driver of microbial biogeography, but there is less understanding of how microbial biogeography and diversification are shaped by dispersal limitation and drift. We recently described a latitudinal diversity gradient of species richness and intraspecific genetic diversity in Streptomyces by using a geographically explicit culture collection. Within this geographically explicit culture collection, we have identified Streptomyces sister-taxa whose geographic distribution is delimited by latitude. These sister-taxa differ in geographic distribution, genomic diversity, and ecological traits despite having nearly identical SSU rRNA gene sequences. Comparative genomic analysis reveals genomic differentiation of these sister-taxa consistent with restricted gene flow across latitude. Furthermore, we show phylogenetic conservatism of thermal traits between the sister-taxa suggesting that thermal trait adaptation limits dispersal and gene flow across climate regimes as defined by latitude. Such phylogenetic conservatism of thermal traits is commonly associated with latitudinal diversity gradients for plants and animals. These data provide further support for the hypothesis that the Streptomyces latitudinal diversity gradient was formed as a result of historical demographic processes defined by dispersal limitation and driven by paleoclimate dynamics.
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83
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Total C and N Pools and Fluxes Vary with Time, Soil Temperature, and Moisture Along an Elevation, Precipitation, and Vegetation Gradient in Southern Appalachian Forests. Ecosystems 2018. [DOI: 10.1007/s10021-018-0244-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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84
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Seasonal Effects on Microbial Community Structure and Nitrogen Dynamics in Temperate Forest Soil. FORESTS 2018. [DOI: 10.3390/f9030153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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85
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Ecoevolutionary Dynamics of Carbon Cycling in the Anthropocene. Trends Ecol Evol 2018; 33:213-225. [DOI: 10.1016/j.tree.2017.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 11/17/2022]
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86
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Delgado-Baquerizo M, Reith F, Dennis PG, Hamonts K, Powell JR, Young A, Singh BK, Bissett A. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology 2018; 99:583-596. [PMID: 29315530 DOI: 10.1002/ecy.2137] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/08/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA.,Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, Móstoles, 28933, Spain
| | - Frank Reith
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia, 5064, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Andrew Young
- National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, 2601, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, New South Wales, 2751, Australia
| | - Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania, 7000, Australia
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87
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Delgado-Baquerizo M, Bissett A, Eldridge DJ, Maestre FT, He JZ, Wang JT, Hamonts K, Liu YR, Singh BK, Fierer N. Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities. Nat Ecol Evol 2017; 1:1339-1347. [PMID: 29046544 DOI: 10.1038/s41559-017-0259-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/28/2017] [Indexed: 11/10/2022]
Abstract
The legacy impacts of past climates on the current distribution of soil microbial communities are largely unknown. Here, we use data from more than 1,000 sites from five separate global and regional datasets to identify the importance of palaeoclimatic conditions (Last Glacial Maximum and mid-Holocene) in shaping the current structure of soil bacterial communities in natural and agricultural soils. We show that palaeoclimate explains more of the variation in the richness and composition of bacterial communities than current climate. Moreover, palaeoclimate accounts for a unique fraction of this variation that cannot be predicted from geographical location, current climate, soil properties or plant diversity. Climatic legacies (temperature and precipitation anomalies from the present to ~20 kyr ago) probably shape soil bacterial communities both directly and indirectly through shifts in soil properties and plant communities. The ability to predict the distribution of soil bacteria from either palaeoclimate or current climate declines greatly in agricultural soils, highlighting the fact that anthropogenic activities have a strong influence on soil bacterial diversity. We illustrate how climatic legacies can help to explain the current distribution of soil bacteria in natural ecosystems and advocate that climatic legacies should be considered when predicting microbial responses to climate change.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA. .,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.
| | - Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania, 7000, Australia
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Calle Tulipán Sin Número, 28933, Móstoles, Spain
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Building L9, Locked Bag 1797, Penrith South, New South Wales, 2751, Australia
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
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