551
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Nazir R, Mazurier S, Yang P, Lemanceau P, van Elsas JD. The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent. Front Microbiol 2017; 8:38. [PMID: 28197129 PMCID: PMC5282467 DOI: 10.3389/fmicb.2017.00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 12/14/2022] Open
Abstract
Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS). Starting with a brief description of the versatility of the T3SS as an interaction system with diverse eukaryotic hosts, we subsequently examine the recent advances made in our understanding of its contribution to interactions with soil fungi. The analysis used data sets ranging from circumstantial evidence to gene-knockout-based experimental data. The initial finding that the abundance of T3SSs in microbiomes is often enhanced in fungal-affected habitats like the mycosphere and the mycorrhizosphere is now substantiated with in-depth knowledge of the specific systems involved. Different fungal–interactive bacteria, in positive or negative associations with partner fungi, harbor and express T3SSs, with different ecological outcomes. In some particular cases, bacterial T3SSs have been shown to modulate the physiology of its fungal partner, affecting its ecological characteristics and consequently shaping its own habitat. Overall, the analyses of the collective data set revealed that diverse T3SSs have assumed diverse roles in the interactions of bacteria with host fungi, as driven by ecological and evolutionary niche requirements.
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Affiliation(s)
- Rashid Nazir
- Department of Environmental Sciences, COMSATS Institute of Information TechnologyAbbottabad, Pakistan; Department of Soil Environmental Science, Research Centre for Eco-environmental Sciences - Chinese Academy of SciencesBeijing, China
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Pu Yang
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
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552
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McHugh AJ, Feehily C, Hill C, Cotter PD. Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products. Front Microbiol 2017; 8:109. [PMID: 28197144 PMCID: PMC5281614 DOI: 10.3389/fmicb.2017.00109] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/16/2017] [Indexed: 01/28/2023] Open
Abstract
With the abolition of milk quotas in the European Union in 2015, several member states including Ireland, Luxembourg, and Belgium have seen year on year bi-monthly milk deliveries to dairies increase by up to 35%. Milk production has also increased outside of Europe in the past number of years. Unsurprisingly, there has been a corresponding increased focus on the production of dried milk products for improved shelf life. These powders are used in a wide variety of products, including confectionery, infant formula, sports dietary supplements and supplements for health recovery. To ensure quality and safety standards in the dairy sector, strict controls are in place with respect to the acceptable quantity and species of microorganisms present in these products. A particular emphasis on spore-forming bacteria is necessary due to their inherent ability to survive extreme processing conditions. Traditional microbiological detection methods used in industry have limitations in terms of time, efficiency, accuracy, and sensitivity. The following review will explore the common spore-forming bacterial contaminants of milk powders, will review the guidelines with respect to the acceptable limits of these microorganisms and will provide an insight into recent advances in methods for detecting these microbes. The various advantages and limitations with respect to the application of these diagnostics approaches for dairy food will be provided. It is anticipated that the optimization and application of these methods in appropriate ways can ensure that the enhanced pressures associated with increased production will not result in any lessening of safety and quality standards.
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Affiliation(s)
- Aoife J McHugh
- Food Bioscience Department, Teagasc Food Research CentreCork, Ireland; School of Microbiology, University College CorkCork, Ireland
| | - Conor Feehily
- Food Bioscience Department, Teagasc Food Research CentreCork, Ireland; APC Microbiome InstituteCork, Ireland
| | - Colin Hill
- School of Microbiology, University College CorkCork, Ireland; APC Microbiome InstituteCork, Ireland
| | - Paul D Cotter
- Food Bioscience Department, Teagasc Food Research CentreCork, Ireland; APC Microbiome InstituteCork, Ireland
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553
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Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil. Sci Rep 2017; 7:40189. [PMID: 28071697 PMCID: PMC5223211 DOI: 10.1038/srep40189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/01/2016] [Indexed: 11/23/2022] Open
Abstract
Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.
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554
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Johnson RM, Ramond JB, Gunnigle E, Seely M, Cowan DA. Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters. Extremophiles 2017; 21:381-392. [PMID: 28058513 DOI: 10.1007/s00792-016-0911-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/19/2016] [Indexed: 01/31/2023]
Abstract
The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R 2 = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R 2 ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.
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Affiliation(s)
- Riegardt M Johnson
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
| | - Eoin Gunnigle
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Mary Seely
- Gobabeb Research and Training Centre, Walvis Bay, Namibia
- School of Animal, Plant and Environmental Sciences (AP&ES), University of the Witwatersrand, Johannesburg, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
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555
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Zhang X, Johnston ER, Li L, Konstantinidis KT, Han X. Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe. ISME JOURNAL 2016; 11:885-895. [PMID: 27996978 DOI: 10.1038/ismej.2016.180] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 10/20/2016] [Accepted: 10/28/2016] [Indexed: 02/01/2023]
Abstract
Identifying soil microbial feedbacks to increasing temperatures and moisture alterations is critical for predicting how terrestrial ecosystems will respond to climate change. We performed a 5-year field experiment manipulating warming, watering and their combination in a semiarid temperate steppe in northern China. Warming stimulated the abundance of genes responsible for degrading recalcitrant soil organic matter (SOM) and reduced SOM content by 13%. Watering, and warming plus watering also increased the abundance of recalcitrant SOM catabolism pathways, but concurrently promoted plant growth and increased labile SOM content, which somewhat offset SOM loss. The treatments also increased microbial biomass, community complexity and metabolic potential for nitrogen and sulfur assimilation. Both microbial and plant community composition shifted with the treatment conditions, and the sample-to-sample compositional variations of the two communities (pairwise β-diversity distances) were significantly correlated. In particular, microbial community composition was substantially correlated with the dominant plant species (~0.54 Spearman correlation coefficient), much more than with measured soil indices, affirming a tight coupling between both biological communities. Collectively, our study revealed the direction and underlying mechanisms of microbial feedbacks to warming and suggested that semiarid regions of northern steppes could act as a net carbon source under increased temperatures, unless precipitation increases concurrently.
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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.,School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric R Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Linghao Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Konstantinos T Konstantinidis
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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556
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Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek AT, Orlando L, Barrett JH, Star B. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol Ecol Resour 2016; 17:742-751. [DOI: 10.1111/1755-0998.12623] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/29/2016] [Accepted: 10/21/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Sanne Boessenkool
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066 Blindern N-0316 Oslo Norway
| | - Kristian Hanghøj
- Centre for Geogenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- Laboratoire AMIS; CNRS UMR 5288; Université de Toulouse, University Paul Sabatier (UPS); Toulouse France
| | - Heidi M. Nistelberger
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066 Blindern N-0316 Oslo Norway
| | - Clio Der Sarkissian
- Centre for Geogenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Agata T. Gondek
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066 Blindern N-0316 Oslo Norway
| | - Ludovic Orlando
- Centre for Geogenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- Laboratoire AMIS; CNRS UMR 5288; Université de Toulouse, University Paul Sabatier (UPS); Toulouse France
| | - James H. Barrett
- McDonald Institute for Archaeological Research; University of Cambridge; Downing Street Cambridge CB2 3ER UK
| | - Bastiaan Star
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066 Blindern N-0316 Oslo Norway
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557
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Oh SY, Fong JJ, Park MS, Lim YW. Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil. PLoS One 2016; 11:e0168573. [PMID: 27977803 PMCID: PMC5158061 DOI: 10.1371/journal.pone.0168573] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/03/2016] [Indexed: 02/01/2023] Open
Abstract
Tricholoma matsutake, the pine mushroom, is a valuable forest product with high economic value in Asia, and plays an important ecological role as an ectomycorrhizal fungus. Around the host tree, T. matsutake hyphae generate a distinctive soil aggregating environment called a fairy ring, where fruiting bodies form. Because T. matsutake hyphae dominate the soil near the fairy ring, this species has the potential to influence the microbial community. To explore the influence of T. matsutake on the microbial communities, we compared the microbial community and predicted bacterial function between two different soil types-T. matsutake dominant and T. matsutake minor. DNA sequence analyses showed that fungal and bacterial diversity were lower in the T. matsutake dominant soil compared to T. matsutake minor soil. Some microbial taxa were significantly more common in the T. matsutake dominant soil across geographic locations, many of which were previously identified as mycophillic or mycorrhiza helper bacteria. Between the two soil types, the predicted bacterial functional profiles (using PICRUSt) had significantly distinct KEGG modules. Modules for amino acid uptake, carbohydrate metabolism, and the type III secretion system were higher in the T. matsutake dominant soil than in the T. matsutake minor soil. Overall, similar microbial diversity, community structure, and bacterial functional profiles of the T. matsutake dominant soil across geographic locations suggest that T. matsutake may generate a dominance effect.
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Affiliation(s)
- Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jonathan J. Fong
- Science Unit, Lingnan University, Tuen Mun, New Territories, Hong Kong
| | - Myung Soo Park
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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558
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Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, Flater J, Tiedje JM, Hofmockel KS, Gelder B, Howe A. Strategies to improve reference databases for soil microbiomes. ISME JOURNAL 2016; 11:829-834. [PMID: 27935589 PMCID: PMC5364351 DOI: 10.1038/ismej.2016.168] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/10/2016] [Accepted: 10/21/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | | | - Erick Cardenas
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aaron Garoutte
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Ryan Williams
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Jared Flater
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Kirsten S Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Brian Gelder
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
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559
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Yan B, Li J, Xiao N, Qi Y, Fu G, Liu G, Qiao M. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing. Sci Rep 2016; 6:38811. [PMID: 27934957 PMCID: PMC5146926 DOI: 10.1038/srep38811] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/14/2016] [Indexed: 11/25/2022] Open
Abstract
Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.
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Affiliation(s)
- Bing Yan
- College of Water Sciences, Beijing Normal University, Beijing, China.,Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Junsheng Li
- Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Nengwen Xiao
- Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yue Qi
- College of Water Sciences, Beijing Normal University, Beijing, China.,Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Gang Fu
- College of Water Sciences, Beijing Normal University, Beijing, China.,Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Gaohui Liu
- Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Mengping Qiao
- School of Environment and Natural Resources, Renmin University of China, Beijing, China
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560
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A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. PLoS Comput Biol 2016; 12:e1005224. [PMID: 27918579 PMCID: PMC5137872 DOI: 10.1371/journal.pcbi.1005224] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/28/2016] [Indexed: 11/20/2022] Open
Abstract
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra. This approach is often limited because protein coding genes predicted from metagenomes are incomplete and fragmental. In this paper, we present a graph-centric approach to improving metagenome-guided peptide and protein identification in metaproteomics. Our method exploits the de Bruijn graph structure reported by metagenome assembly algorithms to generate a comprehensive database of protein sequences encoded in the community. We tested our method using several public metaproteomic datasets with matched metagenomic and metatranscriptomic sequencing data acquired from complex microbial communities in a biological wastewater treatment plant. The results showed that many more peptides and proteins can be identified when assembly graphs were utilized, improving the characterization of the proteins expressed in the microbial communities. The additional proteins we identified contribute to the characterization of important pathways such as those involved in degradation of chemical hazards. Our tools are released as open-source software on github at https://github.com/COL-IU/Graph2Pro. In recent years, meta-omic (including metatranscriptomic and metaproteomic) techniques have been adopted as complementary approaches to metagenomic sequencing to study functional characteristics and dynamics of microbial communities, aiming at a holistic understanding of a community to respond to the changes in the environment. Currently, metaproteomic data are largely analyzed using the bioinformatics tools originally designed in bottom-up proteomics. In particular, recent metaproteomic studies employed a metagenome-guided approach, in which complete or fragmental protein-coding genes were first predicted from metagenomic sequences (i.e., contigs or scaffolds), acquired from the matched community samples, and predicted protein sequences were then used in peptide identification. A key challenge of this approach is that the protein coding genes predicted from assembled metagenomic contigs can be incomplete and fragmented due to the complexity of metagenomic samples and the short reads length in metagenomic sequencing. To address this issue, in this paper, we present a graph-centric approach that exploits the de bruijn graph structure reported by metagenome assembly algorithms to improve metagenome-guided peptide and protein identification in metaproteomics. We show that our method can identify much more peptides and proteins, improving the characterization of the proteins expressed in the microbial communities.
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561
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Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M. High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 2016; 1:15. [PMID: 28812567 DOI: 10.1038/s41559-016-0015] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 01/08/2023]
Abstract
Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Institute of Applied Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada
| | - Saulo M S Jacques
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.,Programa de Pós-Graduação em Ecologia e Evolugão, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, 20550-013, Brazil
| | - Aliny P F Pires
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Juliana S Leal
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-971, Brazil
| | - Diane S Srivastava
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Vinicius F Farjalla
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada
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562
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Saghaï A, Zivanovic Y, Moreira D, Benzerara K, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient. Environ Microbiol 2016; 18:4990-5004. [PMID: 27422734 PMCID: PMC5477898 DOI: 10.1111/1462-2920.13456] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022]
Abstract
Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.
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Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Yvan Zivanovic
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Sud Orsay, Université Paris-Saclay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Marie Ragon
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico
| | | | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
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563
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Berlemont R, Martiny AC. Glycoside Hydrolases across Environmental Microbial Communities. PLoS Comput Biol 2016; 12:e1005300. [PMID: 27992426 PMCID: PMC5218504 DOI: 10.1371/journal.pcbi.1005300] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 01/06/2017] [Accepted: 12/11/2016] [Indexed: 11/25/2022] Open
Abstract
Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.
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Affiliation(s)
- Renaud Berlemont
- Dept. of Biological Sciences, California State University, Long Beach, California, United States of America
| | - Adam C. Martiny
- Dept. of Earth System Science, University of California, Irvine, California, United States of America
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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564
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Yuan J, Zhao M, Li R, Huang Q, Rensing C, Raza W, Shen Q. Antibacterial Compounds-Macrolactin Alters the Soil Bacterial Community and Abundance of the Gene Encoding PKS. Front Microbiol 2016; 7:1904. [PMID: 27965639 PMCID: PMC5126139 DOI: 10.3389/fmicb.2016.01904] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/15/2016] [Indexed: 12/24/2022] Open
Abstract
Macrolactin produced by many soil microbes has been shown to be an efficient antibacterial agent against many bacterial pathogens. However, studies examining the effect of macrolactin on both the soil bacterial community and the intrinsic bacterial species that harbor genes responsible for the production of this antibiotic have not been conducted so far. In this study, a mixture of macrolactin was isolated from the liquid culture of Bacillus amyloliquefaciens NJN-6, and applied to the soil once a week for four weeks. 16S rRNA Illumina MiSeq sequencing showed that continuous application of macrolactin reduced the α-diversity of the soil bacterial community and thereby changed the relative abundance of microbes at both the phylum and genus level. The relative abundance of Proteobacteria and Firmicutes was significantly increased along with a significant decrease in the relative abundance of Acidobacteria. However, the application of macrolactins had an insignificant effect on the total numbers of bacteria. Further, the native gene responsible for the production of macrolactin, the gene encoding polyketide synthase was reduced in copy number after the application of macrolactin. The results of this study suggested that a bactericide from a microbial source could decrease the diversity of the soil bacterial community and change the bacterial community structure. Moreover, the populations of the intrinsic bacterial species which harbor genes responsible for macrolactin production were inhibited when the external source antibiotic was applied.
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Affiliation(s)
- Jun Yuan
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization - College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Mengli Zhao
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization - College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization - College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization - College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China; J. Craig Venter InstituteLa Jolla, CA, USA
| | - Waseem Raza
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization - College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization and Jiangsu Collaborative Innovation Center for Organic Solid Waste Utilization - College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
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565
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Adair KL, Douglas AE. Making a microbiome: the many determinants of host-associated microbial community composition. Curr Opin Microbiol 2016; 35:23-29. [PMID: 27907842 DOI: 10.1016/j.mib.2016.11.002] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/07/2016] [Accepted: 11/14/2016] [Indexed: 02/07/2023]
Abstract
The composition of many host-associated microbial communities is characterized by seemingly contradictory features: strong selection for specific taxa by the host, but substantial variability among hosts and over time within one host. Recent advances have revealed that both deterministic and stochastic processes operating across multiple spatial scales shape the composition of host-associated microbial communities. Although most research has focused on deterministic processes within individual hosts, the microbiota within each host is increasingly recognized to contribute to a wider metacommunity maintained by transmission between individual hosts and dispersal between host-associated and free-living microbial communities. By applying a community ecology perspective encompassing the microbial metacommunity, the many determinants of host-associated microbial community composition can be identified, guiding the directions of future research.
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Affiliation(s)
- Karen L Adair
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca 14853, NY, USA.
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566
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Jonsson V, Österlund T, Nerman O, Kristiansson E. Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes. J Comput Biol 2016; 24:311-326. [PMID: 27892712 DOI: 10.1089/cmb.2016.0180] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metagenomics is the study of microorganisms in environmental and clinical samples using high-throughput sequencing of random fragments of their DNA. Since metagenomics does not require any prior culturing of isolates, entire microbial communities can be studied directly in their natural state. In metagenomics, the abundance of genes is quantified by sorting and counting the DNA fragments. The resulting count data are high-dimensional and affected by high levels of technical and biological noise that make the statistical analysis challenging. In this article, we introduce an hierarchical overdispersed Poisson model to explore the variability in metagenomic data. By analyzing three comprehensive data sets, we show that the gene-specific variability varies substantially between genes and is dependent on biological function. We also assess the power of identifying differentially abundant genes and show that incorrect assumptions about the gene-specific variability can lead to unacceptable high rates of false positives. Finally, we evaluate shrinkage approaches to improve the variance estimation and show that the prior choice significantly affects the statistical power. The results presented in this study further elucidate the complex variance structure of metagenomic data and provide suggestions for accurate and reliable identification of differentially abundant genes.
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Affiliation(s)
- Viktor Jonsson
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Olle Nerman
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden
| | - Erik Kristiansson
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
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567
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Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil. PLoS One 2016; 11:e0166578. [PMID: 27855202 PMCID: PMC5113961 DOI: 10.1371/journal.pone.0166578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/31/2016] [Indexed: 01/30/2023] Open
Abstract
Despite the central role of soil microbial communities in global carbon (C) cycling, little is known about soil microbial community structure and even less about their metabolic pathways. Efforts to characterize soil communities often focus on identifying differences in gene content across environmental gradients, but an alternative question is what genes are similar in soils. These genes may indicate critical species or potential functions that are required in all soils. Here we identified the "core" set of C cycling sequences widely present in multiple soil metagenomes from a fertilized prairie (FP). Of 226,887 sequences associated with known enzymes involved in the synthesis, metabolism, and transport of carbohydrates, 843 were identified to be consistently prevalent across four replicate soil metagenomes. This core metagenome was functionally and taxonomically diverse, representing five enzyme classes and 99 enzyme families within the CAZy database. Though it only comprised 0.4% of all CAZy-associated genes identified in FP metagenomes, the core was found to be comprised of functions similar to those within cumulative soils. The FP CAZy-associated core sequences were present in multiple publicly available soil metagenomes and most similar to soils sharing geographic proximity. In soil ecosystems, where high diversity remains a key challenge for metagenomic investigations, these core genes represent a subset of critical functions necessary for carbohydrate metabolism, which can be targeted to evaluate important C fluxes in these and other similar soils.
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568
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Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta. Sci Rep 2016; 6:36550. [PMID: 27824160 PMCID: PMC5099912 DOI: 10.1038/srep36550] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.
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569
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Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 2016; 4:e2687. [PMID: 27843720 PMCID: PMC5103831 DOI: 10.7717/peerj.2687] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 01/03/2023] Open
Abstract
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
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Affiliation(s)
- Cristina N Butterfield
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Peter F Andeer
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Susan Spaulding
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Andrea Singh
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Kenwyn B Suttle
- Department of Ecology and Evolutionary Biology, University of California , Santa Cruz , CA , United States
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | | | - Trent Northen
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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570
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Keiblinger KM, Fuchs S, Zechmeister-Boltenstern S, Riedel K. Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. FEMS Microbiol Ecol 2016; 92:fiw180. [PMID: 27549116 PMCID: PMC5026301 DOI: 10.1093/femsec/fiw180] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 08/18/2016] [Indexed: 11/14/2022] Open
Abstract
The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters.
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Affiliation(s)
- Katharina M Keiblinger
- Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Strasse 82, 1190 Vienna, Austria
| | - Stephan Fuchs
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17489 Greifswald, Germany
| | - Sophie Zechmeister-Boltenstern
- Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Strasse 82, 1190 Vienna, Austria
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17489 Greifswald, Germany
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571
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Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’. Nat Microbiol 2016; 2:16198. [DOI: 10.1038/nmicrobiol.2016.198] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/09/2016] [Indexed: 02/06/2023]
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572
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Kim HM, Lee MJ, Jung JY, Hwang CY, Kim M, Ro HM, Chun J, Lee YK. Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra. J Microbiol 2016; 54:713-723. [DOI: 10.1007/s12275-016-6294-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/29/2016] [Accepted: 09/20/2016] [Indexed: 01/14/2023]
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573
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Wei STS, Lacap-Bugler DC, Lau MCY, Caruso T, Rao S, de Los Rios A, Archer SK, Chiu JMY, Higgins C, Van Nostrand JD, Zhou J, Hopkins DW, Pointing SB. Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1642. [PMID: 27812351 PMCID: PMC5071352 DOI: 10.3389/fmicb.2016.01642] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/03/2016] [Indexed: 12/04/2022] Open
Abstract
The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.
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Affiliation(s)
- Sean T S Wei
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Donnabella C Lacap-Bugler
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | - Tancredi Caruso
- School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland
| | - Subramanya Rao
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, China
| | - Asunción de Los Rios
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales Madrid, Spain
| | - Stephen K Archer
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Jill M Y Chiu
- Department of Biology, Hong Kong Baptist University Hong Kong, China
| | - Colleen Higgins
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - David W Hopkins
- School of Agriculture, Food and Environment, The Royal Agricultural University Gloucestershire, UK
| | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of TechnologyAuckland, New Zealand; Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
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574
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Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res 2016; 26:1612-1625. [PMID: 27803195 PMCID: PMC5088602 DOI: 10.1101/gr.201863.115] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 09/08/2016] [Indexed: 01/19/2023]
Abstract
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution.
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Affiliation(s)
- Stephen Nayfach
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | | | - Nandita Garud
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Katherine S Pollard
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Institute for Human Genetics, Institute for Computational Health Sciences, and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94158, USA
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575
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Smith CR, Blair PL, Boyd C, Cody B, Hazel A, Hedrick A, Kathuria H, Khurana P, Kramer B, Muterspaw K, Peck C, Sells E, Skinner J, Tegeler C, Wolfe Z. Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem. Ecol Evol 2016; 6:8075-8084. [PMID: 27878079 PMCID: PMC5108259 DOI: 10.1002/ece3.2553] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022] Open
Abstract
The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.
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Affiliation(s)
- Chris R Smith
- Department of Biology Earlham College Richmond IN USA
| | - Peter L Blair
- Department of Biology Earlham College Richmond IN USA
| | - Charlie Boyd
- Department of Biology Earlham College Richmond IN USA
| | - Brianne Cody
- Department of Biology Earlham College Richmond IN USA
| | - Alexander Hazel
- Department of Biology Earlham College Richmond IN USA; Present address: Department of Entomology University of Illinois Urbana Champaign IL USA
| | | | - Hitesh Kathuria
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Parul Khurana
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Brent Kramer
- Department of Biology Earlham College Richmond IN USA
| | | | - Charles Peck
- Department of Computer Science Earlham College Richmond IN USA
| | - Emily Sells
- Department of Biology Earlham College Richmond IN USA
| | - Jessica Skinner
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Cara Tegeler
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Zoe Wolfe
- Department of Biology Earlham College Richmond IN USA
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576
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Niu J, Deng J, Xiao Y, He Z, Zhang X, Van Nostrand JD, Liang Y, Deng Y, Liu X, Yin H. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system. Sci Rep 2016; 6:34744. [PMID: 27698381 PMCID: PMC5048113 DOI: 10.1038/srep34744] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/20/2016] [Indexed: 11/16/2022] Open
Abstract
Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.
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Affiliation(s)
- Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Jie Deng
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhili He
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
| | - Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - J. D. Van Nostrand
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100081, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
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577
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Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir. mSystems 2016; 1:mSystems00052-16. [PMID: 27822552 PMCID: PMC5080400 DOI: 10.1128/msystems.00052-16] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 09/06/2016] [Indexed: 02/07/2023] Open
Abstract
Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. Author Video: An author video summary of this article is available.
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578
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Fernandez AL, Sheaffer CC, Wyse DL, Staley C, Gould TJ, Sadowsky MJ. Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 566-567:949-959. [PMID: 27288977 DOI: 10.1016/j.scitotenv.2016.05.073] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 06/06/2023]
Abstract
Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions.
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Affiliation(s)
- Adria L Fernandez
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, United States
| | - Craig C Sheaffer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, United States
| | - Donald L Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, United States
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
| | - Trevor J Gould
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN 55455, United States
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN 55108, United States.
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579
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Associations between an Invasive Plant (Taeniatherum caput-medusae, Medusahead) and Soil Microbial Communities. PLoS One 2016; 11:e0163930. [PMID: 27685330 PMCID: PMC5042559 DOI: 10.1371/journal.pone.0163930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/16/2016] [Indexed: 11/19/2022] Open
Abstract
Understanding plant-microbe relationships can be important for developing management strategies for invasive plants, particularly when these relationships interact with underlying variables, such as habitat type and seedbank density, to mediate control efforts. In a field study located in California, USA, we investigated how soil microbial communities differ across the invasion front of Taeniatherum caput-medusae (medusahead), an annual grass that has rapidly invaded most of the western USA. Plots were installed in habitats where medusahead invasion is typically successful (open grassland) and typically not successful (oak woodland). Medusahead was seeded into plots at a range of densities (from 0-50,000 seeds/m2) to simulate different levels of invasion. We found that bacterial and fungal soil community composition were significantly different between oak woodland and open grassland habitats. Specifically, ectomycorrhizal fungi were more abundant in oak woodlands while arbuscular mycorrhizal fungi and plant pathogens were more abundant in open grasslands. We did not find a direct effect of medusahead density on soil microbial communities across the simulated invasion front two seasons after medusahead were seeded into plots. Our results suggest that future medusahead management initiatives might consider plant-microbe interactions.
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580
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Armstrong A, Valverde A, Ramond JB, Makhalanyane TP, Jansson JK, Hopkins DW, Aspray TJ, Seely M, Trindade MI, Cowan DA. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input. Sci Rep 2016; 6:34434. [PMID: 27680878 PMCID: PMC5041089 DOI: 10.1038/srep34434] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/14/2016] [Indexed: 02/01/2023] Open
Abstract
The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.
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Affiliation(s)
- Alacia Armstrong
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Angel Valverde
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David W Hopkins
- The Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS, UK
| | - Thomas J Aspray
- School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Mary Seely
- Gobabeb Training and Research Centre (GTRC), Walvis Bay, Namibia.,Animal, Plant and Environmental Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Marla I Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM). University of the Western Cape, Bellville 7535, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
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581
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Shelton JL, Akob DM, McIntosh JC, Fierer N, Spear JR, Warwick PD, McCray JE. Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient. Front Microbiol 2016; 7:1535. [PMID: 27733847 PMCID: PMC5039232 DOI: 10.3389/fmicb.2016.01535] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/13/2016] [Indexed: 11/24/2022] Open
Abstract
Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.
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Affiliation(s)
- Jenna L Shelton
- Eastern Energy Resources Science Center, U.S. Geological Survey Reston, VA, USA
| | - Denise M Akob
- National Research Program-Eastern Branch, U.S. Geological Survey Reston, VA, USA
| | - Jennifer C McIntosh
- Eastern Energy Resources Science Center, U.S. Geological SurveyReston, VA, USA; Department of Hydrology and Atmospheric Sciences, University of ArizonaTucson, AZ, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA; Cooperative Institute for Research in Environmental Science, University of ColoradoBoulder, CO, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines Golden, CO, USA
| | - Peter D Warwick
- Eastern Energy Resources Science Center, U.S. Geological Survey Reston, VA, USA
| | - John E McCray
- Department of Civil and Environmental Engineering, Colorado School of MinesGolden, CO, USA; Hydrologic Science and Engineering Program, Colorado School of MinesGolden, CO, USA
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582
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Verdon J, Coutos-Thevenot P, Rodier MH, Landon C, Depayras S, Noel C, La Camera S, Moumen B, Greve P, Bouchon D, Berjeaud JM, Braquart-Varnier C. Armadillidin H, a Glycine-Rich Peptide from the Terrestrial Crustacean Armadillidium vulgare, Displays an Unexpected Wide Antimicrobial Spectrum with Membranolytic Activity. Front Microbiol 2016; 7:1484. [PMID: 27713732 PMCID: PMC5031766 DOI: 10.3389/fmicb.2016.01484] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/06/2016] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial peptides (AMPs) are key components of innate immunity and are widespread in nature, from bacteria to vertebrate animals. In crustaceans, there are currently 15 distinct AMP families published so far in the literature, mainly isolated from members of the Decapoda order. Up to now, armadillidin is the sole non-decapod AMP isolated from the haemocytes of Armadillidium vulgare, a crustacean isopod. Its first description demonstrated that armadillidin is a linear glycine-rich (47%) cationic peptide with an antimicrobial activity directed toward Bacillus megaterium. In the present work, we report identification of armadillidin Q, a variant of armadillidin H (earlier known as armadillidin), from crude haemocyte extracts of A. vulgare using LC-MS approach. We demonstrated that both armadillidins displayed broad spectrum antimicrobial activity against several Gram-positive and Gram-negative bacteria, fungi, but were totally inactive against yeasts. Membrane permeabilization assays, only performed with armadillidin H, showed that the peptide is membrane active against bacterial and fungal strains leading to deep changes in cell morphology. This damaging activity visualized by electronic microscopy correlates with a rapid decrease of cell viability leading to highly blebbed cells. In contrast, armadillidin H does not reveal cytotoxicity toward human erythrocytes. Furthermore, no secondary structure could be defined in this study [by circular dichroism (CD) and nuclear magnetic resonance (NMR)] even in a membrane mimicking environment. Therefore, armadillidins represent interesting candidates to gain insight into the biology of glycine-rich AMPs.
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Affiliation(s)
- Julien Verdon
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Pierre Coutos-Thevenot
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Marie-Helene Rodier
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Celine Landon
- Centre de Biophysique Moléculaire, CNRS UPR4301 Orléans, France
| | - Segolene Depayras
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Cyril Noel
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Sylvain La Camera
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Pierre Greve
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Jean-Marc Berjeaud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
| | - Christine Braquart-Varnier
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers Poitiers, France
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583
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Abdul Majid S, Graw MF, Chatziefthimiou AD, Nguyen H, Richer R, Louge M, Sultan AA, Schloss P, Hay AG. Microbial Characterization of Qatari Barchan Sand Dunes. PLoS One 2016; 11:e0161836. [PMID: 27655399 PMCID: PMC5031452 DOI: 10.1371/journal.pone.0161836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/13/2016] [Indexed: 01/17/2023] Open
Abstract
This study represents the first characterization of sand microbiota in migrating barchan sand dunes. Bacterial communities were studied through direct counts and cultivation, as well as 16S rRNA gene and metagenomic sequence analysis to gain an understanding of microbial abundance, diversity, and potential metabolic capabilities. Direct on-grain cell counts gave an average of 5.3 ± 0.4 x 105 cells g-1 of sand. Cultured isolates (N = 64) selected for 16S rRNA gene sequencing belonged to the phyla Actinobacteria (58%), Firmicutes (27%) and Proteobacteria (15%). Deep-sequencing of 16S rRNA gene amplicons from 18 dunes demonstrated a high relative abundance of Proteobacteria, particularly enteric bacteria, and a dune-specific-pattern of bacterial community composition that correlated with dune size. Shotgun metagenome sequences of two representative dunes were analyzed and found to have similar relative bacterial abundance, though the relative abundances of eukaryotic, viral and enterobacterial sequences were greater in sand from the dune closer to a camel-pen. Functional analysis revealed patterns similar to those observed in desert soils; however, the increased relative abundance of genes encoding sporulation and dormancy are consistent with the dune microbiome being well-adapted to the exceptionally hyper-arid Qatari desert.
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Affiliation(s)
- Sara Abdul Majid
- Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar
| | - Michael F. Graw
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | | | - Hanh Nguyen
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Renee Richer
- Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar
| | - Michel Louge
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, United States of America
| | - Ali A. Sultan
- Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar
| | - Patrick Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
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584
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Xiao Y, Liu X, Liang Y, Niu J, Zhang X, Ma L, Hao X, Gu Y, Yin H. Insights into functional genes and taxonomical/phylogenetic diversity of microbial communities in biological heap leaching system and their correlation with functions. Appl Microbiol Biotechnol 2016; 100:9745-9756. [DOI: 10.1007/s00253-016-7819-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 01/17/2023]
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585
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Le PT, Makhalanyane TP, Guerrero LD, Vikram S, Van de Peer Y, Cowan DA. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts. Genome Biol Evol 2016; 8:2737-47. [PMID: 27503299 PMCID: PMC5630931 DOI: 10.1093/gbe/evw189] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.
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Affiliation(s)
- Phuong Thi Le
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Leandro D Guerrero
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, Ghent Belgium
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
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586
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587
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Ji Y, Angel R, Klose M, Claus P, Marotta H, Pinho L, Enrich-Prast A, Conrad R. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol 2016; 18:5082-5100. [PMID: 27507000 DOI: 10.1111/1462-2920.13491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/06/2016] [Indexed: 11/28/2022]
Abstract
Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.
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Affiliation(s)
- Yang Ji
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Humberto Marotta
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil
| | - Luana Pinho
- Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil
| | - Alex Enrich-Prast
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Environmental Change, Linköping University, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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588
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Walter JM, Tschoeke DA, Meirelles PM, de Oliveira L, Leomil L, Tenório M, Valle R, Salomon PS, Thompson CC, Thompson FL. Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil). PLoS One 2016; 11:e0161168. [PMID: 27548380 PMCID: PMC4993507 DOI: 10.1371/journal.pone.0161168] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/01/2016] [Indexed: 12/25/2022] Open
Abstract
Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms.
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Affiliation(s)
- Juline M Walter
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Pedro M Meirelles
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Louisi de Oliveira
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciana Leomil
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Márcio Tenório
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rogério Valle
- COPPE-Production Engineering Program, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo S Salomon
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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589
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Aslam SN, Dumbrell AJ, Sabir JS, Mutwakil MHZ, Baeshen MMN, Abo-Aba SEM, Clark DR, Yates SA, Baeshen NA, Underwood GJC, McGenity TJ. Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota. Environ Microbiol 2016; 18:5048-5062. [PMID: 27459511 DOI: 10.1111/1462-2920.13474] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Although desert soils support functionally important microbial communities that affect plant growth and influence many biogeochemical processes, the impact of future changes in precipitation patterns on the microbiota and their activities is largely unknown. We performed in-situ experiments to investigate the effect of simulated rainfall on bacterial communities associated with the widespread perennial shrub, Rhazya stricta in Arabian desert soils. The bacterial community composition was distinct between three different soil compartments: surface biological crust, root-attached, and the broader rhizosphere. Simulated rainfall had no significant effect on the overall bacterial community composition, but some population-level responses were observed, especially in soil crusts where Betaproteobacteria, Sphingobacteria, and Bacilli became more abundant. Bacterial biomass in the nutrient-rich crust increased three-fold one week after watering, whereas it did not change in the rhizosphere, despite its much higher water retention. These findings indicate that between rainfall events, desert-soil microbial communities enter into stasis, with limited species turnover, and reactivate rapidly and relatively uniformly when water becomes available. However, microbiota in the crust, which was relatively enriched in nutrients and organic matter, were primarily water-limited, compared with the rhizosphere microbiota that were co-limited by nutrients and water.
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Affiliation(s)
- Shazia N Aslam
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Alex J Dumbrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Jamal S Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed H Z Mutwakil
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed M N Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Salah E M Abo-Aba
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Dave R Clark
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Steven A Yates
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Graham J C Underwood
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
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590
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Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type. Appl Environ Microbiol 2016; 82:5186-96. [PMID: 27316957 DOI: 10.1128/aem.00916-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols. IMPORTANCE This work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.
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591
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Abstract
ABSTRACT
Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.
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592
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de la Cuesta-Zuluaga J, Escobar JS. Considerations For Optimizing Microbiome Analysis Using a Marker Gene. Front Nutr 2016; 3:26. [PMID: 27551678 PMCID: PMC4976105 DOI: 10.3389/fnut.2016.00026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/26/2016] [Indexed: 12/22/2022] Open
Abstract
Next-generation sequencing technologies have found a widespread use in the study of host–microbe interactions due to the increase in their throughput and their ever-decreasing costs. The analysis of human-associated microbial communities using a marker gene, particularly the 16S rRNA, has been greatly benefited from these technologies – the human gut microbiome research being a remarkable example of such analysis that has greatly expanded our understanding of microbe-mediated human health and disease, metabolism, and food absorption. 16S studies go through a series of in vitro and in silico steps that can greatly influence their outcomes. However, the lack of a standardized workflow has led to uncertainties regarding the transparency and reproducibility of gut microbiome studies. We, here, discuss the most common challenges in the archetypical 16S rRNA workflow, including the extraction of total DNA, its use as template in PCR with primers that amplify specific hypervariable regions of the gene, amplicon sequencing, the denoising and removal of low-quality reads, the detection and removal of chimeric sequences, the clustering of high-quality sequences into operational taxonomic units, and their taxonomic classification. We recommend the essential technical information that should be conveyed in publications for reproducibility of results and encourage non-experts to include procedures and available tools that mitigate most of the problems encountered in microbiome analysis.
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Affiliation(s)
| | - Juan S Escobar
- Vidarium - Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa , Medellín , Colombia
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593
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Babujia LC, Silva AP, Nakatani AS, Cantão ME, Vasconcelos ATR, Visentainer JV, Hungria M. Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome. Transgenic Res 2016; 25:425-40. [PMID: 26873023 DOI: 10.1007/s11248-016-9938-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/04/2016] [Indexed: 01/21/2023]
Abstract
The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.
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Affiliation(s)
- Letícia Carlos Babujia
- Department of Chemistry, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil
| | | | | | | | | | - Jesuí Vergilio Visentainer
- Department of Chemistry, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil
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594
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Shen C, Shi Y, Ni Y, Deng Y, Van Nostrand JD, He Z, Zhou J, Chu H. Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain. Front Microbiol 2016; 7:1184. [PMID: 27524983 PMCID: PMC4965465 DOI: 10.3389/fmicb.2016.01184] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022] Open
Abstract
The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.
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Affiliation(s)
- Congcong Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; University of the Chinese Academy of SciencesBeijing, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; State Key Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
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595
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Xia Z, Bai E, Wang Q, Gao D, Zhou J, Jiang P, Wu J. Biogeographic Distribution Patterns of Bacteria in Typical Chinese Forest Soils. Front Microbiol 2016; 7:1106. [PMID: 27468285 PMCID: PMC4942481 DOI: 10.3389/fmicb.2016.01106] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/01/2016] [Indexed: 11/13/2022] Open
Abstract
Microbes are widely distributed in soils and play a very important role in nutrient cycling and ecosystem services. To understand the biogeographic distribution of forest soil bacteria, we collected 115 soil samples in typical forest ecosystems across eastern China to investigate their bacterial community compositions using Illumina MiSeq high throughput sequencing based on 16S rRNA. We obtained 4,667,656 sequences totally and more than 70% of these sequences were classified into five dominant groups, i.e., Actinobacteria, Acidobacteria, Alphaproteobacteria, Verrucomicrobia, and Planctomycetes (relative abundance >5%). The bacterial diversity showed a parabola shape along latitude and the maximum diversity appeared at latitudes between 33.50°N and 40°N, an area characterized by warm-temperate zones and moderate temperature, neutral soil pH and high substrate availability (soil C and N) from dominant deciduous broad-leaved forests. Pairwise dissimilarity matrix in bacterial community composition showed that bacterial community structure had regional similarity and the latitude of 30°N could be used as the dividing line between southern and northern forest soils. Soil properties and climate conditions (MAT and MAP) greatly accounted for the differences in the soil bacterial structure. Among all soil parameters determined, soil pH predominantly affected the diversity and composition of the bacterial community, and soil pH = 5 probably could be used as a threshold below which soil bacterial diversity might decline and soil bacterial community structure might change significantly. Moreover, soil exchangeable cations, especially Ca(2+) (ECa(2+)) and some other soil variables were also closely related to bacterial community structure. The selected environmental variables (21.11%) explained more of the bacterial community variation than geographic distance (15.88%), indicating that the edaphic properties and environmental factors played a more important role than geographic dispersal limitation in determining the bacterial community structure in Chinese forest soils.
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Affiliation(s)
| | - Edith Bai
- Institute of Applied Ecology, Chinese Academy of SciencesShenyang, China
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596
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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597
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Cao P, Wang JT, Hu HW, Zheng YM, Ge Y, Shen JP, He JZ. Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils. MICROBIAL ECOLOGY 2016; 72:221-230. [PMID: 27072664 DOI: 10.1007/s00248-016-0762-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/28/2016] [Indexed: 05/12/2023]
Abstract
Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.
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Affiliation(s)
- Peng Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yuan-Ming Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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598
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Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient. Sci Rep 2016; 6:28819. [PMID: 27357005 PMCID: PMC4928066 DOI: 10.1038/srep28819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 04/05/2016] [Indexed: 11/21/2022] Open
Abstract
Microorganisms play key roles in ecosystem processes and biogeochemical cycling, however, the relationship between soil microbial taxa diversity and their function in natural ecosystems is largely unknown. To determine how soil bacteria community and function are linked from the local to regional scale, we studied soil bacteria community composition, potential function and environmental conditions in natural and mature broadleaf forests along a latitudinal gradient in China, using the Illumina 16S rRNA sequencing and GeoChip technologies. The results showed strong biogeographic endemism pattern in soil bacteria were existed, and the spatial distance and climatic variables were the key controlling factors for this pattern. Therefore, dispersal limitation and environmental selection may represent two key processes in generating and maintaining the soil bacterial biogeographic pattern. By contrast, the soil bacterial potential function is highly convergent along the latitudinal gradient and there were highly differing bacterial community compositions, and the soil chemistry may include the main factors active in shaping the soil bacterial potential function. Therefore, the soil bacterial potential function may be affected by local gradients in resource availability, and predicting soil bacterial potential function requires knowledge of abiotic and biotic environmental factors.
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599
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Weigold P, El-Hadidi M, Ruecker A, Huson DH, Scholten T, Jochmann M, Kappler A, Behrens S. A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil. Sci Rep 2016; 6:28958. [PMID: 27353292 PMCID: PMC4926216 DOI: 10.1038/srep28958] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/13/2016] [Indexed: 11/16/2022] Open
Abstract
In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas. We detected a so far unknown diversity of genes encoding for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases as well as metabolic and cometabolic dehalogenases. Genes for non-heme, no-metal chloroperoxidases and haloalkane dehalogenases were the most abundant halogenase and dehalogenase genes, respectively. The high diversity and abundance of (de)halogenating enzymes suggests a strong microbial contribution to natural halogen cycling. This was also confirmed in microcosm experiments in which we quantified the biotic formation of chloroform and bromoform. Knowledge on microorganisms and genes that catalyze (de)halogenation reactions is critical because they are highly relevant to industrial biotechnologies and bioremediation applications.
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Affiliation(s)
- Pascal Weigold
- Geomicrobiology, Center for Applied Geosciences, University of
Tuebingen, Germany
| | - Mohamed El-Hadidi
- Algorithms in Bioinformatics, Center for Bioinformatics,
University of Tuebingen, Germany
| | - Alexander Ruecker
- Geomicrobiology, Center for Applied Geosciences, University of
Tuebingen, Germany
| | - Daniel H. Huson
- Algorithms in Bioinformatics, Center for Bioinformatics,
University of Tuebingen, Germany
| | - Thomas Scholten
- Soil Science and Geomorphology, Geography, University of
Tuebingen, Germany
| | - Maik Jochmann
- Instrumental Analytical Chemistry, Faculty of Chemistry,
University of Duisburg-Essen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of
Tuebingen, Germany
| | - Sebastian Behrens
- Department of Civil, Environmental, and Geo- Engineering,
University of Minnesota, MN, USA
- BioTechnology Institute, University of Minnesota,
MN, USA
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600
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Salvetti E, Campanaro S, Campedelli I, Fracchetti F, Gobbi A, Tornielli GB, Torriani S, Felis GE. Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. Front Microbiol 2016; 7:937. [PMID: 27445999 PMCID: PMC4917526 DOI: 10.3389/fmicb.2016.00937] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
Vitis vinifera L. cv. Corvina grape forms the basis for the production of unique wines, such as Amarone, whose distinctive sensory features are strongly linked to the post-harvest grape withering process. Indeed, this process increases sugar concentration and changes must characteristics. While microorganisms involved in must fermentation have been widely investigated, few data are available on the microbiota of withered grapes. Thus, in this paper, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortium associated with Corvina berries at the end of the withering process performed in two different conditions ("traditional withering," TW or "accelerated withering," AW), and to unveil whether changes of drying parameters could have an impact on microbial diversity. Samples of healthy undamaged berries were collected and washed, to recover microorganisms from the surface and avoid contamination with grapevine genetic material. Isolated DNA was sequenced and the data obtained were analyzed with several bioinformatics methods. The eukaryotic community was mainly composed by members of the phylum Ascomycota, including Eurotiomycetes, Sordariomycetes, and Dothideomycetes. Moreover, the distribution of the genera Aspergillus and Penicillium (class Eurotiomycetes) varied between the withered berry samples. Instead, Botryotinia, Saccharomyces, and other wine technologically useful microorganisms were relatively scarce in both samples. For prokaryotes, 25 phyla were identified, nine of which were common to both conditions. Environmental bacteria belonging to the class Gammaproteobacteria were dominant and, in particular, the TW sample was characterized by members of the family Pseudomonadaceae, while members of the family Enterobacteriaceae dominated the AW sample, in addition to Sphyngobacteria and Clostridia. Finally, the binning procedure discovered 15 putative genomes which dominated the microbial community of the two samples, and included representatives of genera Erwinia, Pantoea, Pseudomonas, Clostridium, Paenibacillus, and of orders Lactobacillales and Actinomycetales. These results provide insights into the microbial consortium of Corvina withered berries and reveal relevant variations attributable to post-harvest withering conditions, underling how WMS could open novel perspectives in the knowledge and management of the withering process of Corvina, with an impact on the winemaking of important Italian wines.
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Affiliation(s)
- Elisa Salvetti
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | | | | | - Alex Gobbi
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Sandra Torriani
- Department of Biotechnology, University of VeronaVerona, Italy
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