201
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Mascarenhas R, Ruziska FM, Moreira EF, Campos AB, Loiola M, Reis K, Trindade-Silva AE, Barbosa FAS, Salles L, Menezes R, Veiga R, Coutinho FH, Dutilh BE, Guimarães PR, Assis APA, Ara A, Miranda JGV, Andrade RFS, Vilela B, Meirelles PM. Integrating Computational Methods to Investigate the Macroecology of Microbiomes. Front Genet 2020; 10:1344. [PMID: 32010196 PMCID: PMC6979972 DOI: 10.3389/fgene.2019.01344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 12/09/2019] [Indexed: 12/15/2022] Open
Abstract
Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as “everything is everywhere, but the environment selects”) as well as applied ecological problems, such as those posed by human induced global environmental changes.
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Affiliation(s)
| | - Flávia M Ruziska
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | | | - Amanda B Campos
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Miguel Loiola
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Kaike Reis
- Chemical Engineering Department, Polytechnic School of Federal University of Bahia, Salvador, Brazil
| | - Amaro E Trindade-Silva
- Institute of Biology, Federal University of Bahia, Salvador, Brazil.,Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Lucas Salles
- Institute of Geology, Federal University of Bahia, Salvador, Brazil
| | - Rafael Menezes
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil.,Institute of Physics, Federal University of Bahia, Salvador, Brazil
| | - Rafael Veiga
- Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Brazil
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paulo R Guimarães
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Butantã, Brazil
| | - Ana Paula A Assis
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Butantã, Brazil
| | - Anderson Ara
- Institute of Mathematics, Federal University of Bahia, Salvador, Brazil
| | - José G V Miranda
- Institute of Physics, Federal University of Bahia, Salvador, Brazil
| | - Roberto F S Andrade
- Institute of Physics, Federal University of Bahia, Salvador, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Brazil
| | - Bruno Vilela
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Pedro Milet Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Brazil.,Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
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202
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Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes. Nat Commun 2020; 11:116. [PMID: 31913270 PMCID: PMC6949233 DOI: 10.1038/s41467-019-13966-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 12/10/2019] [Indexed: 01/01/2023] Open
Abstract
Soil bacterial diversity varies across biomes with potential impacts on soil ecological functioning. Here, we incorporate key factors that affect soil bacterial abundance and diversity across spatial scales into a mechanistic modeling framework considering soil type, carbon inputs and climate towards predicting soil bacterial diversity. The soil aqueous-phase content and connectivity exert strong influence on bacterial diversity for each soil type and rainfall pattern. Biome-specific carbon inputs deduced from net primary productivity provide constraints on soil bacterial abundance independent from diversity. The proposed heuristic model captures observed global trends of bacterial diversity in good agreement with predictions by an individual-based mechanistic model. Bacterial diversity is highest at intermediate water contents where the aqueous phase forms numerous disconnected habitats and soil carrying capacity determines level of occupancy. The framework delineates global soil bacterial diversity hotspots; located mainly in climatic transition zones that are sensitive to potential climate and land use changes.
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203
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Liu L, Zhu K, Wurzburger N, Zhang J. Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales. Ecosphere 2020. [DOI: 10.1002/ecs2.2999] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Lan Liu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station & Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Department of Environmental Studies University of California Santa Cruz California 95064 USA
- Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 China
| | - Kai Zhu
- Department of Environmental Studies University of California Santa Cruz California 95064 USA
| | - Nina Wurzburger
- Odum School of Ecology University of Georgia Athens Georgia 30602 USA
| | - Jian Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station & Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 China
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204
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Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments. ISME JOURNAL 2020; 14:931-944. [PMID: 31896789 PMCID: PMC7082341 DOI: 10.1038/s41396-019-0574-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/25/2019] [Accepted: 12/16/2019] [Indexed: 11/11/2022]
Abstract
Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.
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205
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Favero VO, Carvalho RH, Motta VM, Leite ABC, Coelho MRR, Xavier GR, Rumjanek NG, Urquiaga S. Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean ( Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products. FRONTIERS IN PLANT SCIENCE 2020; 11:602645. [PMID: 33510747 PMCID: PMC7835340 DOI: 10.3389/fpls.2020.602645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/14/2020] [Indexed: 05/07/2023]
Abstract
The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.
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Affiliation(s)
| | | | | | | | | | | | - Norma Gouvêa Rumjanek
- Embrapa Agrobiology, Seropédica, Rio de Janeiro, Brazil
- *Correspondence: Norma Gouvêa Rumjanek,
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206
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Wang P, Li S, Yang X, Zhou J, Shu W, Jiang L. Mechanisms of soil bacterial and fungal community assembly differ among and within islands. Environ Microbiol 2019; 22:1559-1571. [DOI: 10.1111/1462-2920.14864] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, School of Life Sciences Sun Yat‐sen University Guangzhou 510275 People's Republic of China
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Shao‐Peng Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Institute of Eco‐Chongming (IEC) Shanghai 200062 China
| | - Xian Yang
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman OK 73019 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing 100084 People's Republic of China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University Guangzhou 510631 People's Republic of China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
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207
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Liu JL, Yao J, Duran R, Mihucz VG, Hudson-Edwards KA. Bacterial shifts during in-situ mineralization bio-treatment to non-ferrous metal(loid) tailings. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113165. [PMID: 31546074 DOI: 10.1016/j.envpol.2019.113165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Nonferrous mine tailings have caused serious problems of co-contamination with metal(loid)s. It is still a global challenge to cost-effectively manage and mitigate the effect of the mining wastes. We conducted an in-situ bio-treatment of non-ferrous metal(loid) tailings using a microbial consortium of sulfate reducing bacteria (SRB). During the bio-treatment, the transformation of metal(loid)s (such as Cu, Fe, Mn, Pb, Sb, and Zn) into oxidizable and residual fractions in the subsurface tended to be higher than that observed in the surface. As well the mineral compositions changed becoming more complex, indicating that the sulfur reducing process of bio-treatment shaped the bio-transformation of metal(loid)s. The added SRB genera, especially Desulfotomaculum genus, colonized the tailings suggesting the coalescence of SRB consortia with indigenous communities of tailings. Such observation provides new insights for understanding the functional microbial community coalescence applied to bio-treatment. PICRUSt analysis revealed presence of genes involved in sulfate reduction, both assimilatory and dissimilatory. The potential for the utilization of both inorganic and organic sulfur compounds as S source, as well as the presence of sulfite oxidation genes indicated that SRB play an important role in the transformation of metal(loid)s. We advocate that the management of microorganisms involved in S-cycle is of paramount importance for the in situ bio-treatment of tailings, which provide new insights for the implementation of bio-treatments for mitigating the effect of tailings.
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Affiliation(s)
- Jian-Li Liu
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China.
| | - Robert Duran
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour/E2S UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Victor G Mihucz
- Sino-Hungarian Joint Research Laboratory for Environmental Sciences and Health, ELTE-Eötvös Loránd University, H-1117, Budapest, Pázmány Péter stny. 1/A, Hungary
| | - Karen A Hudson-Edwards
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn, Cornwall, TR10 9DF, UK
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208
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Yeh CF, Soininen J, Teittinen A, Wang J. Elevational patterns and hierarchical determinants of biodiversity across microbial taxonomic scales. Mol Ecol 2019; 28:86-99. [PMID: 30427089 DOI: 10.1111/mec.14935] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 10/22/2018] [Accepted: 11/02/2018] [Indexed: 01/06/2023]
Abstract
Microbial biogeography is gaining increasing attention due to recent molecular methodological advance. However, the diversity patterns and their environmental determinants across taxonomic scales are still poorly studied. By sampling along an extensive elevational gradient in subarctic ponds of Finland and Norway, we examined the diversity patterns of aquatic bacteria and fungi from whole community to individual taxa across taxonomic coverage and taxonomic resolutions. We further quantified cross-phylum congruence in multiple biodiversity metrics and evaluated the relative importance of climate, catchment and local pond variables as the hierarchical drivers of biodiversity across taxonomic scales. Bacterial community showed significantly decreasing elevational patterns in species richness and evenness, and U-shaped patterns in local contribution to beta diversity (LCBD). Conversely, no significant species richness and evenness patterns were found for fungal community. Elevational patterns in species richness and LCBD, but not in evenness, were congruent across bacterial phyla. When narrowing down the taxonomic scope towards higher resolutions, bacterial diversity showed weaker and more complex elevational patterns. Taxonomic downscaling also indicated a notable change in the relative importance of biodiversity determinants with stronger local environmental filtering, but decreased importance of climatic variables. This suggested that niche conservatism of temperature preference was phylogenetically deeper than that of water chemistry variables. Our results provide novel perspectives for microbial biogeography and highlight the importance of taxonomic scale dependency and hierarchical drivers when modelling biodiversity and species distribution responses to future climatic scenarios.
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Affiliation(s)
- Chih-Fu Yeh
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Anette Teittinen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Jianjun Wang
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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209
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Plant Taxonomic Diversity Better Explains Soil Fungal and Bacterial Diversity than Functional Diversity in Restored Forest Ecosystems. PLANTS 2019; 8:plants8110479. [PMID: 31698841 PMCID: PMC6918236 DOI: 10.3390/plants8110479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022]
Abstract
Plant attributes have direct and indirect effects on soil microbes via plant inputs and plant-mediated soil changes. However, whether plant taxonomic and functional diversities can explain the soil microbial diversity of restored forest ecosystems remains elusive. Here, we tested the linkage between plant attributes and soil microbial communities in four restored forests (Acacia species, Eucalyptus species, mixed coniferous species, mixed native species). The trait-based approaches were applied for plant properties and high-throughput Illumina sequencing was applied for fungal and bacterial diversity. The total number of soil microbial operational taxonomic units (OTUs) varied among the four forests. The highest richness of fungal OTUs was found in the Acacia forest. However, bacterial OTUs were highest in the Eucalyptus forest. Species richness was positively and significantly related to fungal and bacterial richness. Plant taxonomic diversity (species richness and species diversity) explained more of the soil microbial diversity than the functional diversity and soil properties. Prediction of fungal richness was better than that of bacterial richness. In addition, root traits explained more variation than the leaf traits. Overall, plant taxonomic diversity played a more important role than plant functional diversity and soil properties in shaping the soil microbial diversity of the four forests.
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210
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Jiao S, Lu Y. Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems. Environ Microbiol 2019; 22:1052-1065. [DOI: 10.1111/1462-2920.14815] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Shuo Jiao
- College of Urban and Environmental SciencesPeking University Beijing 100871 P. R. China
| | - Yahai Lu
- College of Urban and Environmental SciencesPeking University Beijing 100871 P. R. China
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211
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Sheng Y, Cong W, Yang L, Liu Q, Zhang Y. Forest Soil Fungal Community Elevational Distribution Pattern and Their Ecological Assembly Processes. Front Microbiol 2019; 10:2226. [PMID: 31636612 PMCID: PMC6787267 DOI: 10.3389/fmicb.2019.02226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Soil fungi play vital roles in natural ecosystems, however, their community distribution patterns along different environmental gradients and ecological assembly processes remain unclear. In this study, Illumina MiSeq sequencing was used to investigate the soil fungal community structures of five different forest types along an elevational gradient, and a framework based on a null model was adopted to quantify the relative contribution of deterministic and stochastic ecological assembly processes. The results showed that the majority of soil fungal OTUs were derived from Zygomycota, Basidiomycota, and Ascomycota. Soil fungal community structure differed significantly among the five sites (P < 0.01), and the fungal α-diversity decreased as elevation increased (P < 0.01). The null model showed that the relative contribution of stochastic processes (37.78-73.33%) was higher than that of deterministic processes (26.67-62.22%) within the same forest type, while that of deterministic processes (35.00-93.00%) was higher than stochastic processes (7.00-65.00%) between forest types. These results suggest that forest soil fungal diversity decreased significantly with increasing elevation, and that deterministic processes may be key factors influencing soil fungal community assemblies among forest types. The results of this study provide new insight into soil fungal distribution patterns and community assembly processes in natural forest ecosystems.
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Affiliation(s)
- Yuyu Sheng
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Wei Cong
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Linsen Yang
- Shennongjia National Park Administration, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, China
| | - Qiang Liu
- Shennongjia National Park Administration, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, China
| | - Yuguang Zhang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
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212
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Grossman JJ, Butterfield AJ, Cavender-Bares J, Hobbie SE, Reich PB, Gutknecht J, Kennedy PG. Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment. FEMS Microbiol Ecol 2019; 95:5553462. [PMID: 31437281 DOI: 10.1093/femsec/fiz134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/21/2019] [Indexed: 11/13/2022] Open
Abstract
While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.
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Affiliation(s)
- Jake J Grossman
- Arnold Arboretum, Harvard University, 1300 Centre St., Boston, MA 02131, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota -- Twin Cities, 1475 Gortner Ave., St. Paul, MN, 55108, USA
| | - Allen J Butterfield
- Department of Chemical Engeineering, University of Minnesota -- Duluth, 1303 Ordean Ct., Duluth, MN 55812, USA
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution, and Behavior, University of Minnesota -- Twin Cities, 1475 Gortner Ave., St. Paul, MN, 55108, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota -- Twin Cities, 1475 Gortner Ave., St. Paul, MN, 55108, USA
| | - Peter B Reich
- Department of Forest Resources, University of Minnesota -- Twin Cities, 1530 Cleveland Ave. N., St. Paul, MN 55108, USA.,Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith 2751, NSW, Australia
| | - Jessica Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota --Twin Cities, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota -- Twin Cities, 1475 Gortner Ave., St. Paul, MN 55108, USA
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213
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Zhang X, Johnston ER, Wang Y, Yu Q, Tian D, Wang Z, Zhang Y, Gong D, Luo C, Liu W, Yang J, Han X. Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes. mSystems 2019; 4:e00374-19. [PMID: 31575666 PMCID: PMC6774018 DOI: 10.1128/msystems.00374-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/13/2019] [Indexed: 11/20/2022] Open
Abstract
It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.
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Affiliation(s)
- Ximei Zhang
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eric R Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Yaosheng Wang
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Yu
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dashuan Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Zhiping Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yanqing Zhang
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daozhi Gong
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun Luo
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd., Shanghai, China
| | - Wei Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Junjie Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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214
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Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands. mSystems 2019; 4:4/5/e00566-19. [PMID: 31575667 PMCID: PMC6774019 DOI: 10.1128/msystems.00566-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil, while the subsoil is assumed to have microbial diversity patterns similar to those of the topsoil. Here we compared patterns and drivers of microbial alpha and beta diversity in and between topsoils (0 to 10 cm) and subsoils (30 to 50 cm) of temperate grasslands in Inner Mongolia of China, covering an ∼1,500-km transect along an aridity gradient. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity remains constant or increases with increasing aridity in topsoil and decreases in subsoil, archaeal diversity decreases in topsoil and remains constant in subsoil. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation and contemporary climate but is most strongly influenced by the factor historical temperature anomaly since the Last Glacial Maximum (LGM) and by soil pH in the subsoil. Moreover, the biogeographic patterns of topsoil-subsoil community dissimilarities vary for different microbial groups and are overall most strongly influenced by soil fertility differences between depths for bacteria and by contemporary climate for archaea. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the spatial variation of bacterial diversity. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth.IMPORTANCE Exploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from an ∼1,500-km temperate grassland transect, we find divergent patterns of microbial diversity and its determinants in the topsoil versus the subsoil. Furthermore, we find important and direct legacy effects of historical climate change on the microbial diversity of subsoil yet indirect effects on topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with various climate histories.
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215
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Effects of Two Trichoderma Strains on Plant Growth, Rhizosphere Soil Nutrients, and Fungal Community of Pinus sylvestris var. mongolica Annual Seedlings. FORESTS 2019. [DOI: 10.3390/f10090758] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Trichoderma spp. are proposed as major plant growth-promoting fungi that widely exist in the natural environment. These strains have the abilities of rapid growth and reproduction and efficient transformation of soil nutrients. Moreover, they can change the plant rhizosphere soil environment and promote plant growth. Pinus sylvestris var. mongolica has the characteristics of strong drought resistance and fast growth and plays an important role in ecological construction and environmental restoration. The effects on the growth of annual seedlings, root structure, rhizosphere soil nutrients, enzyme activity, and fungal community structure of P. sylvestris var. mongolica were studied after inoculation with Trichoderma harzianum E15 and Trichoderma virens ZT05, separately. The results showed that after inoculation with T. harzianum E15 and T. virens ZT05, seedling biomass, root structure index, soil nutrients, and soil enzyme activity were significantly increased compared with the control (p < 0.05). There were significant differences in the effects of T. harzianum E15 and T. virens ZT05 inoculation on the growth and rhizosphere soil nutrient of P. sylvestris var. mongolica (p < 0.05). For the E15 treatment, the seedling height, ground diameter, and total biomass of seedlings were higher than that those of the ZT05 treatment, and the rhizosphere soil nutrient content and enzyme activity of the ZT05 treatment were higher than that of the E15 treatment. The results of alpha and beta diversity analyses showed that the fungi community structure of rhizosphere soil was significantly different (p < 0.05) among the three treatments (inoculated with T. harzianum E15, T. virens ZT05, and not inoculated with Trichoderma). Overall, Trichoderma inoculation was correlated with the change of rhizosphere soil nutrient content.
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216
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Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists' warning to humanity: microorganisms and climate change. Nat Rev Microbiol 2019; 17:569-586. [PMID: 31213707 PMCID: PMC7136171 DOI: 10.1038/s41579-019-0222-5] [Citation(s) in RCA: 673] [Impact Index Per Article: 134.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 11/27/2022]
Abstract
In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Baylis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Antje Boetius
- Alfred Wegener Institute, Helmholtz Center for Marine and Polar Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Aimée T Classen
- Rubenstein School of Environment and Natural Resources, and The Gund Institute for Environment, University of Vermont, Burlington, VT, USA
| | | | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Christine M Foreman
- Center for Biofilm Engineering, and Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - David A Hutchins
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science & Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - David S Reay
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Virginia I Rich
- Microbiology Department, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Department of Microbiology, and Department of Civil, Environmental and Geodetic Engineering, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Scott C Weaver
- Department of Microbiology and Immunology, and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
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217
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Zeng Q, An S, Liu Y, Wang H, Wang Y. Biogeography and the driving factors affecting forest soil bacteria in an arid area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 680:124-131. [PMID: 31100663 DOI: 10.1016/j.scitotenv.2019.04.184] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 05/24/2023]
Abstract
Bacteria are one of the most abundant and diverse groups and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large-scale biogeography patterns across longitude (east-west transect), and the processes that determine these patterns lags significantly behind that of macro-organisms. Here, we used 16S rRNA gene sequencing to evaluate the geographic distributions of bacterial diversity and their driving factors across different longitude sites along an 800-km east-west transect in the Loess Plateau. Twenty-four phyla were detected across all soil samples and the most sequence-abundant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Chloroflexi and Gemmatimonadetes (average relative abundance >5%). Soil bacterial α-diversity, expressed by the richness of soil bacterial communities and Shannon diversity, differed among climates (MAP) but showed strong correlations with MAP (r=-0.537 and r=-0.42, respectively; p<0.05 in both bacterial diversity indices). Variation partition analysis demonstrated that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 62% of the community variation. Soil properties contributed more to bacterial community variation than the combined geographic distance (historical contingencies) and climate factors. Among all environmental factors, soil pH exhibited a dominant role in structuring bacterial communities in this arid area. Our findings provide new evidence of bacterial biogeography patterns in an arid area (MAP ranged from 473mm to 547mm). Additionally, the results indicated a close linkage among soil bacterial community, climate and edaphic variables, which is critical for predicting promoting sustainable ecosystem services in the Loess Plateau.
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Affiliation(s)
- Quanchao Zeng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China.
| | - Yang Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - Honglei Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - Ying Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
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218
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Crowther TW, van den Hoogen J, Wan J, Mayes MA, Keiser AD, Mo L, Averill C, Maynard DS. The global soil community and its influence on biogeochemistry. Science 2019; 365:365/6455/eaav0550. [DOI: 10.1126/science.aav0550] [Citation(s) in RCA: 316] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022]
Abstract
Soil organisms represent the most biologically diverse community on land and govern the turnover of the largest organic matter pool in the terrestrial biosphere. The highly complex nature of these communities at local scales has traditionally obscured efforts to identify unifying patterns in global soil biodiversity and biogeochemistry. As a result, environmental covariates have generally been used as a proxy to represent the variation in soil community activity in global biogeochemical models. Yet over the past decade, broad-scale studies have begun to see past this local heterogeneity to identify unifying patterns in the biomass, diversity, and composition of certain soil groups across the globe. These unifying patterns provide new insights into the fundamental distribution and dynamics of organic matter on land.
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219
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A hierarchy of environmental covariates control the global biogeography of soil bacterial richness. Sci Rep 2019; 9:12129. [PMID: 31431661 PMCID: PMC6702155 DOI: 10.1038/s41598-019-48571-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/08/2019] [Indexed: 02/01/2023] Open
Abstract
Soil bacterial communities are central to ecosystem functioning and services, yet spatial variations in their composition and diversity across biomes and climatic regions remain largely unknown. We employ multivariate general additive modeling of recent global soil bacterial datasets to elucidate dependencies of bacterial richness on key soil and climatic attributes. Although results support the well-known association between bacterial richness and soil pH, a hierarchy of novel covariates offers surprising new insights. Defining climatic soil water content explains both, the extent and connectivity of aqueous micro-habitats for bacterial diversity and soil pH, thus providing a better causal attribution. Results show that globally rare and abundant soil bacterial phylotypes exhibit different levels of dependency on environmental attributes. Surprisingly, the strong sensitivity of rare bacteria to certain environmental conditions improves their predictability relative to more abundant phylotypes that are often indifferent to variations in environmental drivers.
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220
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Buzzard V, Michaletz ST, Deng Y, He Z, Ning D, Shen L, Tu Q, Van Nostrand JD, Voordeckers JW, Wang J, Weiser MD, Kaspari M, Waide RB, Zhou J, Enquist BJ. Continental scale structuring of forest and soil diversity via functional traits. Nat Ecol Evol 2019; 3:1298-1308. [DOI: 10.1038/s41559-019-0954-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 06/25/2019] [Indexed: 11/09/2022]
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221
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Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon. ISME JOURNAL 2019; 13:2901-2915. [PMID: 31384013 DOI: 10.1038/s41396-019-0485-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 04/17/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.
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222
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Jiang Y, Huang H, Ma T, Ru J, Blank S, Kurmayer R, Deng L. Temperature Response of Planktonic Microbiota in Remote Alpine Lakes. Front Microbiol 2019; 10:1714. [PMID: 31417513 PMCID: PMC6685043 DOI: 10.3389/fmicb.2019.01714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/11/2019] [Indexed: 02/01/2023] Open
Abstract
Alpine lakes are considered pristine freshwater ecosystems and sensitive to direct and indirect changes in water temperature as induced by climate change. The bacterial plankton constitutes a key component in the water column and bacterial metabolic activity has direct consequences for water quality. In order to understand bacterial response to global temperature rise in five alpine lakes located in the Austrian Alps (1700-2188 m a.S.L.) water temperature was compared within a decadal period. Depth-integrated samples were characterized in community composition by 16S rDNA deep-amplicon sequencing early [56 ± 16 (SD) days after ice break up] and later (88 ± 16 days) in the growing season. Within the 10 years period, temperature rise was observed through reduced ice cover duration and increased average water temperature. During the early growing season, the average water temperature recorded between circulation in spring until sampling date (WAS), and the day of autumn circulation, as well as chemical composition including dissolved organic carbon influenced bacterial community composition. In contrast, only nutrients (such as nitrate) were found influential later in the growing season. Metabolic theory of ecology (MTE) was applied to explain the dependence of taxonomic richness on WAS in mathematical terms. The calculated activation energy exceeded the frequently reported prediction emphasizing the role of WAS during early growing season. Accordingly, the relative abundance of predicted metabolism related genes increased with WAS. Thus, the dominant influence of temperature after ice break up could be explained by overall climate change effects, such as a more intense warming in spring and an overall higher amplitude of temperature variation.
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Affiliation(s)
- Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Haiying Huang
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Tianli Ma
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Stephan Blank
- Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | - Rainer Kurmayer
- Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
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223
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Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus. Int J Oral Sci 2019; 11:13. [PMID: 31263096 PMCID: PMC6802619 DOI: 10.1038/s41368-019-0045-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/19/2018] [Accepted: 01/16/2019] [Indexed: 02/07/2023] Open
Abstract
The biodiversity of the mycobiome, an important component of the oral microbial community, and the roles of fungal–bacterial and fungal–immune system interactions in the pathogenesis of oral lichen planus (OLP) remain largely uncharacterized. In this study, we sequenced the salivary mycobiome and bacteriome associated with OLP. First, we described the dysbiosis of the microbiome in OLP patients, which exhibits lower levels of fungi and higher levels of bacteria. Significantly higher abundances of the fungi Candida and Aspergillus in patients with reticular OLP and of Alternaria and Sclerotiniaceae_unidentified in patients with erosive OLP were observed compared to the healthy controls. Aspergillus was identified as an “OLP-associated” fungus because of its detection at a higher frequency than in the healthy controls. Second, the co-occurrence patterns of the salivary mycobiome–bacteriome demonstrated negative associations between specific fungal and bacterial taxa identified in the healthy controls, which diminished in the reticular OLP group and even became positive in the erosive OLP group. Moreover, the oral cavities of OLP patients were colonized by dysbiotic oral flora with lower ecological network complexity and decreased fungal–Firmicutes and increased fungal–Bacteroidetes sub-networks. Third, several keystone fungal genera (Bovista, Erysiphe, Psathyrella, etc.) demonstrated significant correlations with clinical scores and IL-17 levels. Thus, we established that fungal dysbiosis is associated with the aggravation of OLP. Fungal dysbiosis could alter the salivary bacteriome or may reflect a direct effect of host immunity, which participates in OLP pathogenesis. Imbalance in the oral fungal community could lead to the development of oral lichen planus (OLP), a chronic inflammatory disease that affects the mucous membranes in the mouth. The exact cause of OLP is uncertain, which is a major obstacle to therapeutic development. Using salivary samples, a team headed by Xuedong Zhou at Sichuan University in China investigated the composition and diversity of the fungal community in OLP patients and healthy individuals. The authors found that the oral fungal community was less diverse and that there were higher levels of bacteria in OLP patients. The team concluded that fungal community imbalance could affect the bacterial community in the saliva and the host immunity in the mucous membrane, thereby constituting a direct or indirect cause of the development of OLP.
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224
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Fan YY, Li BB, Yang ZC, Cheng YY, Liu DF, Yu HQ. Mediation of functional gene and bacterial community profiles in the sediments of eutrophic Chaohu Lake by total nitrogen and season. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:233-240. [PMID: 30999200 DOI: 10.1016/j.envpol.2019.04.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/24/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
Microbes in sediments contribute to nutrient release and play an important role in lake eutrophication. However, information about the profiles of functional genes and bacterial communities and the most important environmental factor affecting them in the sediments of eutrophic lake remains unrevealed. In this work, the real-time fluorescent quantitative polymerase chain reaction (qPCR) assay and 16S ribosomal RNA gene next generation sequencing analysis were used to explore the profiles of functional genes and bacterial communities in the sediments of Chaohu Lake. The selected 18 functional genes involved in C, N and P cycles were detected in most of samples. Seasonal variation and sediment variables were found to affect the profiles of functional genes and bacterial communities, and total nitrogen was the dominant environmental factor to drive the formation of bacterial community structure. Proteobacteria and Firmicutes were observed to be the two dominant phyla in the sediments with relative abundance ranging from 10.8% to 36.0% and 7.7%-46.7%, respectively. Three bacterial phyla, i.e., Actinobacteria, Proteobacteria, and Spirochaetes, were found to be significantly positively correlated with the C, N and P-cycle related functional genes. Bacterial community structure was the most important driver to shape the profiles of functional genes. Seasonal variation also influenced the co-occurrence patterns between functional genes and bacterial taxa as revealed by network analysis. The findings from this work facilitate a better understanding about the C, N, and P cycles in the sediments of eutrophic lakes.
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Affiliation(s)
- Yang-Yang Fan
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Bing-Bing Li
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Zong-Chuang Yang
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China
| | - Yuan-Yuan Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China.
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225
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Liu JL, Yao J, Lu C, Li H, Li ZF, Duran R, Sunahara G, Mihucz VG. Microbial activity and biodiversity responding to contamination of metal(loid) in heterogeneous nonferrous mining and smelting areas. CHEMOSPHERE 2019; 226:659-667. [PMID: 30959450 DOI: 10.1016/j.chemosphere.2019.03.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 02/28/2019] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
The combined contamination of nonferrous metal(loid) mining and smelting areas is a global issue, in need of urgent management. To our knowledge, this is the first report of microbial activities by microcalorimetry in specific nonferrous metal(loid) tailings with oligonutrition and high contents of toxic metal(loid)s. Dynamics of bacterial diversity were also characterized. Here we show that tailings had low microbial activities (Pmax = 64.1-331 μW g-1), which were accelerated by the presence of dipotassium phosphate (Pmax = 346-856 μW g-1), as measured by microcalorimetry. Frequent detection of S- and metal-resistant related genera and differences of Thiobacillus and Acidithiobacillus abundances indicated that the tailings were in an early stage of acidification. It has been further confirmed by the presence of a weak acid environment and secondary sulfur associated minerals, such as Sb2S3, FeAsS, FeS2, and CuFeS2. During the acidification process, phosphate, metal(loid)s, and microbial activity were correlated to the bacterial communities. It is suggested that the bacterial communities have metabolic capacities with a high potential for the use in management processes of multi-contaminated nonferrous metalliferous tailings.
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Affiliation(s)
- Jian-Li Liu
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China.
| | - Chao Lu
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China
| | - Hao Li
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China
| | - Zi-Fu Li
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Robert Duran
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China; Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China; Department of Natural Resource Sciences, McGill University, 21111, Lakeshore Drive, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Victor G Mihucz
- Sino-Hungarian Joint Research Laboratory for Environmental Sciences and Health, ELTE -Eötvös Loránd University, H-1117, Budapest, Pázmány Péter stny. 1/A, Hungary
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226
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Sheng Y, Cong J, Lu H, Yang L, Liu Q, Li D, Zhang Y. Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents. Microbiologyopen 2019; 8:e874. [PMID: 31215766 PMCID: PMC6813455 DOI: 10.1002/mbo3.874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 11/06/2022] Open
Abstract
Evergreen broad-leaved (EBF) and deciduous broad-leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.
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Affiliation(s)
- Yuyu Sheng
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Jing Cong
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Hui Lu
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Linsen Yang
- Shennongjia National Park, Shennongjia, Hubei Province, China
| | - Qiang Liu
- Shennongjia National Park, Shennongjia, Hubei Province, China
| | - Diqiang Li
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Yuguang Zhang
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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227
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Muletz-Wolz CR, Fleischer RC, Lips KR. Fungal disease and temperature alter skin microbiome structure in an experimental salamander system. Mol Ecol 2019; 28:2917-2931. [PMID: 31066947 DOI: 10.1111/mec.15122] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/27/2019] [Accepted: 04/25/2019] [Indexed: 12/29/2022]
Abstract
Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17 and 21°C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified operational taxonomic units (OTUs) taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and the abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. After exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research reveals complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species.
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Affiliation(s)
- Carly R Muletz-Wolz
- Department of Biology, University of Maryland, College Park, Maryland.,Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland
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228
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Truong C, Gabbarini LA, Corrales A, Mujic AB, Escobar JM, Moretto A, Smith ME. Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia. THE NEW PHYTOLOGIST 2019; 222:1936-1950. [PMID: 30689219 DOI: 10.1111/nph.15714] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
The biological and functional diversity of ectomycorrhizal (ECM) associations remain largely unknown in South America. In Patagonia, the ECM tree Nothofagus pumilio forms monospecific forests along mountain slopes without confounding effects of vegetation on plant-fungi interactions. To determine how fungal diversity and function are linked to elevation, we characterized fungal communities, edaphic variables, and eight extracellular enzyme activities along six elevation transects in Tierra del Fuego (Argentina and Chile). We also tested whether pairing ITS1 rDNA Illumina sequences generated taxonomic biases related to sequence length. Fungal community shifts across elevations were mediated primarily by soil pH with the most species-rich fungal families occurring mostly within a narrow pH range. By contrast, enzyme activities were minimally influenced by elevation but correlated with soil factors, especially total soil carbon. The activity of leucine aminopeptidase was positively correlated with ECM fungal richness and abundance, and acid phosphatase was correlated with nonECM fungal abundance. Several fungal lineages were undetected when using exclusively paired or unpaired forward ITS1 sequences, and these taxonomic biases need reconsideration for future studies. Our results suggest that soil fungi in N. pumilio forests are functionally similar across elevations and that these diverse communities help to maintain nutrient mobilization across the elevation gradient.
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Affiliation(s)
- Camille Truong
- Instituto de Biología, Universidad Nacional Autónoma de México, CP, 04510, Ciudad de México, México
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Luciano A Gabbarini
- Programa Interacciones Biológicas, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, B1876BX, Argentina
| | - Adriana Corrales
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, DC, 111221, Colombia
| | - Alija B Mujic
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, California State University at Fresno, Fresno, CA, 93740, USA
| | - Julio M Escobar
- Centro Austral de Investigaciones Científicas (CONICET), Ushuaia, V9410BFD, Tierra del Fuego, Argentina
| | - Alicia Moretto
- Centro Austral de Investigaciones Científicas (CONICET), Ushuaia, V9410BFD, Tierra del Fuego, Argentina
- Universidad Nacional de Tierra del Fuego, Ushuaia, V9410BFD, Tierra del Fuego, Argentina
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
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229
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Multi-driver and multi-scale assessment of vine community structure and composition across a complex tropical environmental matrix. PLoS One 2019; 14:e0215274. [PMID: 31075096 PMCID: PMC6510454 DOI: 10.1371/journal.pone.0215274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/31/2019] [Indexed: 11/19/2022] Open
Abstract
Ecological communities are structured by multiple processes operating at multiple scales yet understanding the scale-dependency of these processes remains an open challenge. This might be particularly true for parasites, for which biotic rather than abiotic processes may play a primary role in structuring communities. Focusing on vines, a group of structural parasites that gain access to the canopy using different climbing mechanisms, we examined the influence of abiotic factors in tandem with host-parasite and parasite-parasite interactions in the assembly of tropical vine communities. Two synthetic variables, namely Climate1 and landscape Variety, were consistently important in explaining variation in species richness and diversity, as well as species composition, but their importance varied with scale. Whereas Climate1 summarizes the largest variability among climatic variables, landscape Variety expresses landscape heterogeneity within a neighborhood. Significant patterns of species co-occurrences suggest that vine-vine interactions also contribute to vine community assembly. Our results may be critical to understand vine proliferation and help design management strategies for their control.
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230
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Qin H, Wang S, Feng K, He Z, Virta MPJ, Hou W, Dong H, Deng Y. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. MICROBIOME 2019; 7:71. [PMID: 31054577 PMCID: PMC6500586 DOI: 10.1186/s40168-019-0688-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 05/07/2023]
Abstract
Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.
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Affiliation(s)
- Huayu Qin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhili He
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Marko P J Virta
- Department of Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, United States
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China.
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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231
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Hu A, Nie Y, Yu G, Han C, He J, He N, Liu S, Deng J, Shen W, Zhang G. Diurnal Temperature Variation and Plants Drive Latitudinal Patterns in Seasonal Dynamics of Soil Microbial Community. Front Microbiol 2019; 10:674. [PMID: 31001239 PMCID: PMC6454054 DOI: 10.3389/fmicb.2019.00674] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
Seasonality, an exogenous driver, motivates the biological and ecological temporal dynamics of animal and plant communities. Underexplored microbial temporal endogenous dynamics hinders the prediction of microbial response to climate change. To elucidate temporal dynamics of microbial communities, temporal turnover rates, phylogenetic relatedness, and species interactions were integrated to compare those of a series of forest ecosystems along latitudinal gradients. The seasonal turnover rhythm of microbial communities, estimated by the slope (w value) of similarity-time decay relationship, was spatially structured across the latitudinal gradient, which may be caused by a mixture of both diurnal temperature variation and seasonal patterns of plants. Statistical analyses revealed that diurnal temperature variation instead of average temperature imposed a positive and considerable effect alone and also jointly with plants. Due to higher diurnal temperature variation with more climatic niches, microbial communities might evolutionarily adapt into more dispersed phylogenetic assembly based on the standardized effect size of MNTD metric, and ecologically form higher community resistance and resiliency with stronger network interactions among species. Archaea and the bacterial groups of Chloroflexi, Alphaproteobacteria, and Deltaproteobacteria were sensitive to diurnal temperature variation with greater turnover rates at higher latitudes, indicating that greater diurnal temperature fluctuation imposes stronger selective pressure on thermal specialists, because bacteria and archaea, single-celled organisms, have extreme short generation period compared to animal and plant. Our findings thus illustrate that the dynamics of microbial community and species interactions are crucial to assess ecosystem stability to climate variations in an increased climatic variability era.
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Affiliation(s)
- Ang Hu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Yanxia Nie
- Center for Ecology and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Conghai Han
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Jinhong He
- Center for Ecology and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Shirong Liu
- Key Laboratory of Forest Ecology and Environment, Chinese Academy of Forestry, Beijing, China
| | - Jie Deng
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Weijun Shen
- Center for Ecology and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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232
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Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Qiu G, Liu X, Luo Y, Tiedje JM, Yang Y, Zhou J. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nat Ecol Evol 2019; 3:612-619. [PMID: 30911147 DOI: 10.1038/s41559-019-0848-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 02/05/2019] [Indexed: 12/24/2022]
Abstract
Determining the temporal scaling of biodiversity, typically described as species-time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (-50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39-0.64) than those of plants and animals (w = 0.21-0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world.
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Affiliation(s)
- Xue Guo
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xishu Zhou
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Water Management Research Unit, SJVASC, USDA-ARS, Parlier, CA, USA
| | - Mengting Yuan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jiajie Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhou Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhenxin Li
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Bin Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Qun Gao
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Linwei Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Weiling Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ying Fu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Guanzhou Qiu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.,Department of Earth System Science, Tsinghua University, Beijing, China
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA. .,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA. .,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. .,School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA. .,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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233
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Liao B, Yan X, Zhang J, Chen M, Li Y, Huang J, Lei M, He H, Wang J. Microbial community composition in alpine lake sediments from the Hengduan Mountains. Microbiologyopen 2019; 8:e00832. [PMID: 30848090 PMCID: PMC6741133 DOI: 10.1002/mbo3.832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 11/18/2022] Open
Abstract
Microbial communities in sediments play an important role in alpine lake ecosystems. However, the microbial diversity and community composition of alpine lake sediments from the Hengduan Mountains remain largely unknown. Therefore, based on the Illumina MiSeq platform, high‐throughput sequencing analysis of the 16S rRNA gene was performed on 15 alpine lake sediments collected at different locations in the Hengduan Mountains. The abundance‐based coverage estimate (ACE), Chao1, and Shannon indices indicated that the microbial abundance and diversity of these sediments were high. There are some differences in the composition of microbial communities among sediments. However, in general, Proteobacteria accounted for the largest proportion of all sediments (22.3%–67.6%) and was the dominant phylum. Followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes. In addition, the operational taxonomic unit (OTU) interactions network had modular structures and suggested more cooperation than competition in the microbial community. Besides, we also found that temperature has a significant contribution to the sample–environment relationship. This study revealed the diversity and composition of microbial communities in alpine lake sediments from the Hengduan Mountains, and describe the correlation between microbial community structure and different environmental variables.
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Affiliation(s)
- Binqiang Liao
- School of Life Science Central South University, Changsha, China
| | - Xiaoxin Yan
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Xuzhou, China
| | - Jiang Zhang
- School of Life Science Central South University, Changsha, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, China
| | - Yanling Li
- Key Laboratory of Plateau Lake Ecology and Environment Change, Institute of Plateau Lake Ecology and Pollution Management, School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Jiafeng Huang
- School of Life Science Central South University, Changsha, China
| | - Ming Lei
- School of Life Science Central South University, Changsha, China
| | - Hailun He
- School of Life Science Central South University, Changsha, China
| | - Jun Wang
- School of Life Science Central South University, Changsha, China.,Sanway Gene Technology Inc., Changsha, China
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234
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Abstract
With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions. Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.
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235
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Hao X, Jiao S, Lu Y. Geographical pattern of methanogenesis in paddy and wetland soils across eastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:281-290. [PMID: 30243161 DOI: 10.1016/j.scitotenv.2018.09.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/08/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Large variation of CH4 emissions from paddy and wetland ecosystems exists across different geographical locations in China. To obtain mechanistic understanding of this variation, we investigated the dynamics of methanogenesis over the course of glucose degradation in fourteen paddy field soils and five wetland soils collected from different regions of China. The results revealed that the maximal rate (2-3 mM per day) and the total amount (25-30 mM) of CH4 produced were similar across soil samples. The lag phase of methanogenesis, however, differed substantially with the shortest lag phase of 4 days in a paddy soil from north China and the longest of 32 days in a soil from south China, and this difference reflected a general geographical trend among all soils tested. Nitrate was reduced completely within 4 days in all soils. The reduction of Fe(III) and sulfate was completed after 21 days and 29 days, respectively. The depletion time of Fe(III) and sulfate were positively correlated with the lag phase of methanogenesis. Competition for common substrates between methanogens and iron and sulfate reducers, however, does not explain this coincidence because a slow production of CH4 was detected at the very beginning. It appears that the geographical variations in methanogenesis and the reduction of ferric iron and sulfate are related to the variation in soil pH but not to temperature, soil organic C and nutrient conditions in paddy and wetland soils across eastern China.
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Affiliation(s)
- Xin Hao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China.
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236
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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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237
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Heděnec P, Angel R, Lin Q, Rui J, Li X. Increased methane concentration alters soil prokaryotic community structure along an artificial pH gradient. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1421-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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238
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239
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Muñoz-Martín MÁ, Becerra-Absalón I, Perona E, Fernández-Valbuena L, Garcia-Pichel F, Mateo P. Cyanobacterial biocrust diversity in Mediterranean ecosystems along a latitudinal and climatic gradient. THE NEW PHYTOLOGIST 2019; 221:123-141. [PMID: 30047599 DOI: 10.1111/nph.15355] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria are a key biotic component as primary producers in biocrusts, topsoil communities that have important roles in the functioning of drylands. Yet, major knowledge gaps exist regarding the composition of biocrust cyanobacterial diversity and distribution in Mediterranean ecosystems. We describe cyanobacterial diversity in Mediterranean semiarid soil crusts along an aridity gradient by using next-generation sequencing and bioinformatics analyses, and detect clear shifts along it in cyanobacterial dominance. Statistical analyses show that temperature and precipitation were major parameters determining cyanobacterial composition, suggesting the presence of differentiated climatic niches for distinct cyanobacteria. The responses to temperature of a set of cultivated, pedigreed strains representative of the field populations lend direct support to that contention, with psychrotolerant vs thermotolerant physiology being strain dependent, and consistent with their dominance along the natural gradient. Our results suggest a possible replacement, as global warming proceeds, of cool-adapted by warm-adapted nitrogen-fixing cyanobacteria (such as Scytonema) and a switch in the dominance of Microcoleus vaginatus by thermotolerant, novel phylotypes of bundle-forming cyanobacteria. These differential sensitivities of cyanobacteria to rising temperatures and decreasing precipitation, their ubiquity, and their low generation time point to their potential as bioindicators of global change.
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Affiliation(s)
- M Ángeles Muñoz-Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Itzel Becerra-Absalón
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología Comparada, Facultad de Ciencia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elvira Perona
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lara Fernández-Valbuena
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Pilar Mateo
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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240
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Ruhl IA, Grasby SE, Haupt ES, Dunfield PF. Analysis of microbial communities in natural halite springs reveals a domain-dependent relationship of species diversity to osmotic stress. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:695-703. [PMID: 30246403 DOI: 10.1111/1758-2229.12695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Microbial species diversity may peak at certain optimal environmental conditions and decrease toward more extreme conditions. Indeed, bell-shaped relationships of species diversity against pH and temperature have been demonstrated, but diversity patterns across other environmental conditions are less well reported. In this study, we investigated the impact of salinity on the diversity of microorganisms from all three domains in a large set of natural springs with salinities ranging from freshwater to halite saturated. Habitat salinity was found to be linearly and inversely related to diversity of all three domains. The relationship was strongest in the bacteria, where salinity explained up to 44% of the variation in different diversity metrics (OTUs, Shannon index, and Phylogenetic Diversity). However, the relationship was weaker for Eukarya and Archaea. The known salt-in strategist Archaea of the Halobacteriaceae even showed the opposite trend, with increasing diversity at higher salinity. We propose that high energetic requirements constrain species diversity at high salinity but that the diversity of taxa with energetically less expensive osmotolerance strategies is less affected. Declining diversity with increasing osmotic stress may be a general rule for microbes as well as plants and animals, but the strength of this relationship varies greatly across microbial taxa.
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Affiliation(s)
- Ilona A Ruhl
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Stephen E Grasby
- Geological Survey of Canada, Natural Resources Canada, 3303 33rd St. NW, Calgary, AB, T2L 2A7, Canada
| | - Evan S Haupt
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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241
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Passy SI, Larson CA, Jamoneau A, Budnick W, Heino J, Leboucher T, Tison-Rosebery J, Soininen J. Biogeographical Patterns of Species Richness and Abundance Distribution in Stream Diatoms Are Driven by Climate and Water Chemistry. Am Nat 2018; 192:605-617. [DOI: 10.1086/699830] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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242
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Nottingham AT, Fierer N, Turner BL, Whitaker J, Ostle NJ, McNamara NP, Bardgett RD, Leff JW, Salinas N, Silman MR, Kruuk LEB, Meir P. Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes. Ecology 2018; 99:2455-2466. [PMID: 30076592 PMCID: PMC6850070 DOI: 10.1002/ecy.2482] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 06/11/2018] [Accepted: 07/05/2018] [Indexed: 01/13/2023]
Abstract
More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change.
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Affiliation(s)
- Andrew T. Nottingham
- School of GeosciencesUniversity of EdinburghCrew Building, Kings BuildingsEdinburghEH9 3FFUnited Kingdom
- Smithsonian Tropical Research Institute0843‐03092BalboaAnconPanama
| | - Noah Fierer
- Department of Ecology and Evolutionary BiologyCooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulderColoradoUSA
| | | | - Jeanette Whitaker
- Centre for Ecology & HydrologyLancaster Environment CentreLancasterLA1 4APUnited Kingdom
| | - Nick J. Ostle
- Lancaster Environment CentreLancaster UniversityLibrary AvenueLancasterLA1 4YQUnited Kingdom
| | - Niall P. McNamara
- Centre for Ecology & HydrologyLancaster Environment CentreLancasterLA1 4APUnited Kingdom
| | - Richard D. Bardgett
- School of Earth and Environmental SciencesThe University of ManchesterMichael Smith Building, Oxford RoadManchesterM13 9PTUnited Kingdom
| | - Jonathan W. Leff
- Department of Ecology and Evolutionary BiologyCooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulderColoradoUSA
| | - Norma Salinas
- Seccion QuímicaPontificia Universidad Católica del PeruAv. Universitaria 1801, San MiguelLima32Peru
| | - Miles R. Silman
- Department of BiologyWake Forest UniversityWinston‐SalemNC27109USA
| | - Loeske E. B. Kruuk
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Patrick Meir
- School of GeosciencesUniversity of EdinburghCrew Building, Kings BuildingsEdinburghEH9 3FFUnited Kingdom
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital Territory2601Australia
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243
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Hendershot JN, Read QD, Henning JA, Sanders NJ, Classen AT. Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales. Ecology 2018; 98:1757-1763. [PMID: 28380683 DOI: 10.1002/ecy.1829] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 01/31/2023]
Abstract
Macroecology seeks to understand broad-scale patterns in the diversity and abundance of organisms, but macroecologists typically study aboveground macroorganisms. Belowground organisms regulate numerous ecosystem functions, yet we lack understanding of what drives their diversity. Here, we examine the controls on belowground diversity along latitudinal and elevational gradients. We performed a global meta-analysis of 325 soil communities across 20 studies conducted along temperature and soil pH gradients. Belowground taxa, whether bacterial or fungal, observed along a given gradient of temperature or soil pH were equally likely to show a linear increase, linear decrease, humped pattern, trough-shaped pattern, or no pattern in diversity along the gradient. Land-use intensity weakly affected the diversity-temperature relationship, but no other factor did so. Our study highlights disparities among diversity patterns of soil microbial communities. Belowground diversity may be controlled by the associated climatic and historical contexts of particular gradients, by factors not typically measured in community-level studies, or by processes operating at scales that do not match the temporal and spatial scales under study. Because these organisms are responsible for a suite of key processes, understanding the drivers of their distribution and diversity is fundamental to understanding the functioning of ecosystems.
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Affiliation(s)
- John Nicholas Hendershot
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996, USA.,The Rocky Mountain Biological Laboratory, P.O. Box 519, Crested Butte, Colorado, 81224, USA
| | - Quentin D Read
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996, USA.,The Rocky Mountain Biological Laboratory, P.O. Box 519, Crested Butte, Colorado, 81224, USA
| | - Jeremiah A Henning
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996, USA.,The Rocky Mountain Biological Laboratory, P.O. Box 519, Crested Butte, Colorado, 81224, USA
| | - Nathan J Sanders
- The Rocky Mountain Biological Laboratory, P.O. Box 519, Crested Butte, Colorado, 81224, USA.,Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, 05405, USA.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, Copenhagen, 2100, Denmark
| | - Aimée T Classen
- The Rocky Mountain Biological Laboratory, P.O. Box 519, Crested Butte, Colorado, 81224, USA.,Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, 05405, USA.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, Copenhagen, 2100, Denmark
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244
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Li HY, Wang H, Wang HT, Xin PY, Xu XH, Ma Y, Liu WP, Teng CY, Jiang CL, Lou LP, Arnold W, Cralle L, Zhu YG, Chu JF, Gilbert JA, Zhang ZJ. The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. MICROBIOME 2018; 6:187. [PMID: 30340631 PMCID: PMC6195703 DOI: 10.1186/s40168-018-0561-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/20/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition. RESULTS We report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales, Thermoleophilia, Geobacter, Spirochaeta, Gaiella, and Defluviicoccus. DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis. CONCLUSIONS Our study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.
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Affiliation(s)
- Hong-Yi Li
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Hang Wang
- National Plateau Wetlands Research Center, Southwest Forestry University, 300 Bailongsi, Kunming, 650224 China
| | - Hai-Tiao Wang
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Pei-Yong Xin
- National Center of Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Xin-Hua Xu
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Yun Ma
- College of Biological and Environmental Engineering, Zhejiang University of Technology, 18 Chaowang Ave, Hangzhou, 310014 China
| | - Wei-Ping Liu
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Chang-Yun Teng
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108 China
| | - Cheng-Liang Jiang
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108 China
| | - Li-Ping Lou
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Wyatt Arnold
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Lauren Cralle
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Ave, Xiamen, 361021 China
| | - Jin-Fang Chu
- National Center of Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Jack A Gilbert
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Zhi-Jian Zhang
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108 China
- China Academy of West Region Development, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
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245
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Wang X, Wang C, Wang P, Chen J, Miao L, Feng T, Yuan Q, Liu S. How bacterioplankton community can go with cascade damming in the highly regulated Lancang-Mekong River Basin. Mol Ecol 2018; 27:4444-4458. [PMID: 30225945 DOI: 10.1111/mec.14870] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 12/20/2022]
Abstract
Rivers make vital contributions to the transport of water, sediment and nutrients from terrestrial to marine ecosystems. However, many large rivers worldwide are suffering from dam regulation. Increasing attention has been paid to bacterioplankton communities since they are highly responsive to river alterations and may influence biogeochemical processes. Here, a comprehensive study was conducted in the highly regulated Lancang-Mekong River Basin to address the question of how bacterioplankton communities respond to cascade damming. The results showed that dam constructions increased nutrient concentrations and threatened water quality in cascade reservoirs. Bacterioplankton cell abundance was reduced by damming, and α-diversity was inhibited in cascade reservoirs. Fortunately, however, river ecosystems were resilient after the remarkable disturbance caused by damming. Moreover, bacterioplankton community composition was significantly altered by cascade dams, including a shift in the dominant phylum from r-strategists to k-strategists. Meanwhile, according to GeoChip analysis, the functional composition of bacterioplankton was less affected than taxonomic composition. In addition, geographic and environmental features both followed a distance-decay relationship with community and functional composition, but the local environment condition was the dominant driver in the Lancang River. Therefore, the impoundments of cascade dams had significant impacts on bacterioplankton communities and more attention should be paid to the potential ecological consequences of river regulation.
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Affiliation(s)
- Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Tao Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
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246
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Zhang X, Johnston ER, Barberán A, Ren Y, Wang Z, Han X. Effect of intermediate disturbance on soil microbial functional diversity depends on the amount of effective resources. Environ Microbiol 2018; 20:3862-3875. [PMID: 30209865 DOI: 10.1111/1462-2920.14407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/28/2018] [Accepted: 09/06/2018] [Indexed: 11/30/2022]
Abstract
Many anthropogenic environmental changes are leading to a rapid decline in soil microbial functional diversity. However, ecological mechanisms that can serve to counteract/resist the diversity loss remain largely underexplored. In particular, although intermediate disturbance and increased amount of effective resources can promote the diversity of higher organisms, the potential role of these factors, and their combination, in maintaining microbial functional diversity is poorly studied. We conducted a 5-year experiment in a Eurasian steppe, manipulating mowing, nitrogen addition, phosphorus addition and their combinations. Nitrogen addition decreased soil pH by ~0.6 and bacterial abundance by ~19.5%, causing a disturbance effect. Phosphorus addition significantly decreased the effective amount of soil carbon-, nitrogen-, phosphorus- and water-relevant resources. Across all nitrogen-addition treatments subject to intermediate disturbance, there was a significant positive correlation between soil effective resource amount and microbial gene richness (r > 0.6, p < 0.01), which was elevated, in part, due to the increased fungal abundance. In contrast, significant correlations between gene richness and resource amount were not found under low-disturbance conditions. Overall, gene richness was greatest under conditions of both intermediate disturbance and ample effective resources, suggesting that the two factors could be manipulated in combination for the maintenance of microbial functional diversity.
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Affiliation(s)
- Ximei Zhang
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Eric R Johnston
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Albert Barberán
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Yi Ren
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, 201318, China
| | - Zhiping Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xingguo Han
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Chen Y, Jiang Y, Huang H, Mou L, Ru J, Zhao J, Xiao S. Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1400-1412. [PMID: 29801233 DOI: 10.1016/j.scitotenv.2018.05.109] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 05/13/2023]
Abstract
The world is facing a hard battle against soil pollution such as heavy metals. Metagenome sequencing, 16S rRNA sequencing, and quantitative polymerase chain reaction (qPCR) were used to examine microbial adaptation mechanism to contaminated sediments under natural conditions. Results showed that sediment from a tributary of the Yellow River, which was named Dongdagou River (DDG) supported less bacterial biomass and owned lower richness than sediment from Maqu (MQ), an uncontaminated site in the upper reaches of the Yellow River. Additionally, microbiome structures in these two sites were different. Metagenome sequencing and functional gene annotations revealed that sediment from DDG contains a larger number of genes related to DNA recombination, DNA damage repair, and heavy-metal resistance. KEGG pathway analysis indicated that the sediment of DDG contains a greater number of enzymes associated with heavy-metal resistance and reduction. Additionally, the bacterial phyla Proteobacteria, Bacteroidetes, and Firmicutes, which harbored a larger suite of metal-resistance genes, were found to be the core functional phyla in the contaminated sediments. Furthermore, sediment in DDG owned higher viral abundance, indicating virus-mediated heavy-metal resistance gene transfer might be an adaptation mechanism. In conclusion, microbiome of sediment from DDG has evolved into an integrated system resistant to long-term heavy-metal pollution.
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Affiliation(s)
- Yong Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, PR China
| | - Yiming Jiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, PR China; Institute of Virology (VIRO), Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | - Haiying Huang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, PR China; Institute of Virology (VIRO), Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Lichao Mou
- Signal Processing in Earth Observation (SiPEO), Technische Universität München, 80333 Munich, Germany; Remote Sensing Technology Institute (IMF), German Aerospace Center (DLR), 82234 Wessling, Germany
| | - Jinlong Ru
- Department of Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
| | - Jianhua Zhao
- Shanghai Majorbio Bio-pharm Technology Co., Ltd., Building 3, Lane 3399, Kangxin Road, International Medical Zone, Pudong New Area, Shanghai, PR China
| | - Shan Xiao
- Shanghai Majorbio Bio-pharm Technology Co., Ltd., Building 3, Lane 3399, Kangxin Road, International Medical Zone, Pudong New Area, Shanghai, PR China
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248
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Li S, Luo Z, Ji G. Seasonal function succession and biogeographic zonation of assimilatory and dissimilatory nitrate-reducing bacterioplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1518-1525. [PMID: 29801245 DOI: 10.1016/j.scitotenv.2018.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
The dominance of different nitrate-reducing pathways determines nitrogen cycling patterns. Denitrification (DNF) has been widely studied, but assimilatory nitrate reduction (ANR) and dissimilatory nitrate reduction to ammonium (DNRA) have received much less attention. Their ecological patterns and responsible microbes are poorly understood. Here, we studied the structure and function succession of the three functional groups in the middle route of the South-to-North Water Diversion Project, which is a 1230 km canal spanning 8 degrees of latitude. The results reflected a nitrogen-removing pattern dominated by DNF in the summer and a nitrogen-retaining pattern dominated by ANR and DNRA in the winter. Stenotrophomonas, a typical denitrifier, was the keystone species in the summer and contributed to N2O production. Clostridium, a genus able to conduct ANR and DNRA, was the keystone species in the winter. Notably, a significant zonation pattern was discovered. According to the community structure, the system could be separated into two biogeographic zones, and the Yellow River (about latitude 35°N) is an important cut-off line. This bacterial biogeography followed different water characteristics and ecological processes. ANR was found to be an important process and seasonally transformed its habitat from the northern zone to the southern zone. DNRA bacteria were acclimated to the northern zone and favored at this region in both seasons. The generation of N2O, a strong greenhouse gas, also exhibited this zonation pattern. This is the first study to consider assimilatory and dissimilatory nitrate reducers together at a molecular level, and provides new insights into the underlying patterns of a nitrate-reducing bacterioplankton community.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Zhongxin Luo
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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249
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Shade A, Dunn RR, Blowes SA, Keil P, Bohannan BJ, Herrmann M, Küsel K, Lennon JT, Sanders NJ, Storch D, Chase J. Macroecology to Unite All Life, Large and Small. Trends Ecol Evol 2018; 33:731-744. [DOI: 10.1016/j.tree.2018.08.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 12/13/2022]
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250
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Wang B, Adachi Y, Sugiyama S. Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil. PLoS One 2018; 13:e0204085. [PMID: 30248134 PMCID: PMC6152964 DOI: 10.1371/journal.pone.0204085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/04/2018] [Indexed: 01/22/2023] Open
Abstract
Soil productivity is strongly influenced by the activities of microbial communities. However, it is not well understood how community structure, including its richness, mass, and composition, influences soil functions. We investigated the relationships between soil productivity and microbial communities in unfertilized arable soils extending over 1000 km in eastern Japan. Soil properties, including C turnover rate, N mineralization rate, microbial C, and various soil chemical properties, were measured. Soil bacterial and fungal communities were analyzed by Illumina's MiSeq using 16S rRNA and ITS regions. In addition, root microbial communities from maize grown in each soil were also investigated. Soil bacterial communities shared many operational taxonomic units (OTUs) among farms. An ordination plot based on correspondence analysis revealed convergent distribution of soil bacterial communities across the farms, which seemed to be a result of similar agricultural management practices. Although fungal communities showed lower richness and a lower proportion of shared OTUs than bacterial communities, community structure between the farms tended to be convergent. On the other hand, root communities had lower richness and a higher abundance of specific taxa than the soil communities. Two soil functions, decomposition activity and soil productivity, were extracted by principal component analysis (PCA) based on eight soil properties. Soil productivity correlated with N mineralization rate, P2O5, and maize growth, but not with decomposition activity, which is characterized by C turnover rate, soil organic C, and microbial mass. Soil productivity showed a significant association with community composition, but not with richness and mass of soil microbial communities. Soil productivity also correlated with the abundance of several specific taxa, both in bacteria and fungi. Root communities did not show any clear correlations with soil productivity. These results demonstrate that community composition and abundance of soil microbial communities play important roles in determining soil productivity.
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Affiliation(s)
- Boxi Wang
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan
| | - Yoichi Adachi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Shuichi Sugiyama
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- * E-mail:
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