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Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun 2016; 7:10476. [PMID: 26814032 PMCID: PMC4737851 DOI: 10.1038/ncomms10476] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/07/2015] [Indexed: 01/01/2023] Open
Abstract
Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. The analysis of existing metagenomic data can lead to discovery of new microorganisms. Here, Eloe-Fadrosh et al. perform a large-scale analysis of global metagenomic data, followed by genome reconstruction and single-cell genomics, to describe a new bacterial phylum that inhabits geothermal springs.
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Affiliation(s)
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jessica Jarett
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada 89154, USA
| | - Anne E Dekas
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | | | - Allyson L Brady
- School of Geography &Earth Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Hailiang Dong
- Department of Geology and Environmental Earth Sciences, Miami University, Oxford, Ohio 45056, USA
| | - Brandon R Briggs
- Department of Biological Sciences, University of Alaska-Anchorage, Anchorage, Alaska 99508, USA
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Rex Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Amrita Pati
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Edward M Rubin
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
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252
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Davids M, Hugenholtz F, Martins dos Santos V, Smidt H, Kleerebezem M, Schaap PJ. Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline. PLoS One 2016; 11:e0146423. [PMID: 26756338 PMCID: PMC4710500 DOI: 10.1371/journal.pone.0146423] [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: 09/17/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Metatranscriptomic landscapes can provide insights in functional relationships within natural microbial communities. Analysis of complex metatranscriptome datasets of these communities poses a considerable bioinformatic challenge since they are non-restricted with a varying number of participating strains and species. For RNA-Seq data a standard approach is to align the generated reads to a set of closely related reference genomes. This only works well for microbial communities for which a near complete catalogue of reference genomes is available at a small evolutionary distance. In this study, we focus on the design of a validated de novo metatranscriptome assembly pipeline for single-end Illumina RNA-Seq data to obtain functional and taxonomic profiles of murine microbial communities. RESULTS The here developed de novo assembly metatranscriptome pipeline combined rRNA removal, IDBA-UD assembler, functional annotation and taxonomic classification. Different assemblers were tested and validated using RNA-Seq data from an in silico generated mock community and in vivo RNA-Seq data from a restricted microbial community taken from a mouse model colonized with Altered Schaedler Flora (ASF). Precision and recall of resulting gene expression, functional and taxonomic profiles were compared to those obtained with a standard alignment method. The validated pipeline was subsequently used to generate expression profiles from non-restricted cecal communities of four C57BL/6J mice fed on a high-fat high-protein diet spiked with an RNA-Seq data set from a well-characterized human sample. The spike in control was used to estimate precision and recall at assembly, functional and taxonomic level of non-restricted communities. CONCLUSIONS A generic de novo assembly pipeline for metatranscriptome data analysis was designed for microbial ecosystems, which can be applied for microbial metatranscriptome analysis in any chosen niche.
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Affiliation(s)
- Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, TI Food and Nutrition, Wageningen, The Netherlands
| | - Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, TI Food and Nutrition, Wageningen, The Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, TI Food and Nutrition, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, TI Food and Nutrition, Wageningen, The Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Wageningen University, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, TI Food and Nutrition, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, TI Food and Nutrition, Wageningen, The Netherlands
- * E-mail:
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253
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Yilmaz P, Yarza P, Rapp JZ, Glöckner FO. Expanding the World of Marine Bacterial and Archaeal Clades. Front Microbiol 2016; 6:1524. [PMID: 26779174 PMCID: PMC4705458 DOI: 10.3389/fmicb.2015.01524] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/18/2015] [Indexed: 12/18/2022] Open
Abstract
Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.
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Affiliation(s)
- Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | | | - Josephine Z Rapp
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen and the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Life Sciences and Chemistry, Jacobs UniversityBremen, Germany
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254
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Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol 2016; 6:1469. [PMID: 26779135 PMCID: PMC4704652 DOI: 10.3389/fmicb.2015.01469] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022] Open
Abstract
The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.
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Affiliation(s)
- Nurdyana Abdul Rahman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Advanced Water Management Center, The University of QueenslandBrisbane, QLD, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute Brisbane, QLD, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Genomics and Computational Biology, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
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255
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Ma L, Xia Y, Li B, Yang Y, Li LG, Tiedje JM, Zhang T. Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:420-7. [PMID: 26650334 DOI: 10.1021/acs.est.5b03522] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.
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Affiliation(s)
- Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Ying Yang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Li-Guan Li
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - James M Tiedje
- Department of Plant, Soil, and Microbial Sciences, Michigan State University , East Lansing, Michigan 48824, United States
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
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256
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Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F. Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea. Appl Environ Microbiol 2016; 82:1599-1612. [PMID: 26729711 PMCID: PMC4771326 DOI: 10.1128/aem.03381-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/11/2015] [Indexed: 11/20/2022] Open
Abstract
We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon " Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.
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Affiliation(s)
- Maliheh Mehrshad
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Rohit Ghai
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Seyed Abolhassan Shahzadeh Fazeli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
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257
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Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies. Appl Environ Microbiol 2016; 82:1613-1624. [PMID: 26729720 PMCID: PMC4771312 DOI: 10.1128/aem.03128-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022] Open
Abstract
Heterotrophic bacteria in the SAR11 and Roseobacter lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and Roseobacter genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger Roseobacter genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and Roseobacter. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic Alphaproteobacteria of the SAR11 and Roseobacter lineages.
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258
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Campanaro S, Treu L, Kougias PG, De Francisci D, Valle G, Angelidaki I. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:26. [PMID: 26839589 PMCID: PMC4736482 DOI: 10.1186/s13068-016-0441-1] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge. RESULTS In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway. CONCLUSION This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.
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Affiliation(s)
- Stefano Campanaro
- />Department of Biology, University of Padua, Via U. Bassi 58/b, 35131 Padua, Italy
| | - Laura Treu
- />Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Panagiotis G. Kougias
- />Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Davide De Francisci
- />Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Giorgio Valle
- />Department of Biology, University of Padua, Via U. Bassi 58/b, 35131 Padua, Italy
| | - Irini Angelidaki
- />Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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259
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Xia Y, Wang Y, Wang Y, Chin FYL, Zhang T. Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:111. [PMID: 27222666 PMCID: PMC4877987 DOI: 10.1186/s13068-016-0524-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/09/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND The Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; however, the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences. Our previous metatranscriptional analysis revealed this prevalent population that showed minimum involvement in the main pathways of cellulose hydrolysis and subsequent methanogenesis in the thermophilic cellulose fermentative consortium (TCF). RESULTS In further pursuit, five high-quality curated draft genomes (>98 % completeness) of this population, including two affiliated with the inaccessible lineage of SBR1031, were retrieved by sequence-based multi-dimensional coverage binning. Comparative genomic analyses revealed versatile genetic capabilities for carbohydrate-based fermentative lifestyle including key genes catalyzing cellulose hydrolysis in Anaerolinea phylotypes. However, the low transcriptional activities of carbohydrate-active genes (CAGs) excluded cellulolytic capability as the selective advantage for their prevalence in the community. Instead, a substantially active type VI pili (Tfp) assembly was observed. Expression of the tight adherence protein on the Tfp indicated its function for cellular attachment which was further testified to be more likely related to cell aggregation other than cellulose surface adhesion. Meanwhile, this Tfp structure was found not contributing to syntrophic methanogenesis. Members of the SBR1031 encoded key genes for acetogenic dehydrogenation that may allow ethanol to be used as a carbon source. CONCLUSION The common prevalence of Anaerolineae in anaerobic digesters should be originated from advantageous cellular adhesiveness enabled by Tfp assembly other than its potential as cellulose degrader or anaerobic syntrophs.
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Affiliation(s)
- Yu Xia
- />Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yubo Wang
- />Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yi Wang
- />Department of Computer Science, The University of Hong Kong, Hong Kong SAR, China
| | - Francis Y. L. Chin
- />Department of Computer Science, The University of Hong Kong, Hong Kong SAR, China
- />Department of Computing, Hang Seng Management College, Hong Kong SAR, China
| | - Tong Zhang
- />Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China
- />Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
- />Environmental Biotechnology Lab, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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260
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Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M. Complete nitrification by Nitrospira bacteria. Nature 2015; 528:504-9. [PMID: 26610024 PMCID: PMC5152751 DOI: 10.1038/nature16461] [Citation(s) in RCA: 1147] [Impact Index Per Article: 127.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/19/2015] [Indexed: 11/11/2022]
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
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Affiliation(s)
- Holger Daims
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Elena V. Lebedeva
- Winogradsky Institute of Microbiology, Research Center of
Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071
Moscow, Russia
| | - Petra Pjevac
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Ping Han
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marton Palatinszky
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Julia Vierheilig
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Alexandr Bulaev
- Winogradsky Institute of Microbiology, Research Center of
Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071
Moscow, Russia
| | - Rasmus H. Kirkegaard
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Metabolomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of
Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Bernd Bendinger
- DVGW-Forschungsstelle TUHH, Hamburg University of Technology, 21073
Hamburg, Germany
| | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
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261
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 488] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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262
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Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, Andersson AF. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol 2015; 16:279. [PMID: 26667648 PMCID: PMC4699468 DOI: 10.1186/s13059-015-0834-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/12/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. RESULTS We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. CONCLUSIONS We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.
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Affiliation(s)
- Luisa W Hugerth
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
| | - John Larsson
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Johannes Alneberg
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
| | - Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
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263
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Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:812-23. [PMID: 25953741 DOI: 10.1111/1758-2229.12297] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 04/13/2015] [Indexed: 05/07/2023]
Abstract
Bdellovibrio bacteriovorus are small Deltaproteobacteria that invade, kill and assimilate their prey. Metagenomic assembly analysis of the microbial mats of an arsenic rich, hot spring was performed to describe the genotypes of the predator Bdellovibrio and the ecogenetically adapted taxa Enterobacter. The microbial mats were enriched with Bdellovibrio (1.3%) and several Gram-negative bacteria including Bordetella (16%), Enterobacter (6.8%), Burkholderia (4.8%), Acinetobacter (2.3%) and Yersinia (1%). A high-quality (47 contigs, 25X coverage; 3.5 Mbp) draft genome of Bdellovibrio (strain ArHS; Arsenic Hot Spring) was reassembled, which lacked the marker gene Bd0108 associated with the usual method of prey interaction and invasion for this genus, while maintaining genes coding for the hydrolytic enzymes necessary for prey assimilation. By filtering microbial mat samples (< 0.45 μm) to enrich for small predatory cell sizes, we observed Bdellovibrio-like cells attached side-on to E. coli through electron microscopy. Furthermore, a draft pan-genome of the dominant potential host taxon, Enterobacter cloacae ArHS (4.8 Mb), along with three of its viral genotypes (n = 3; 42 kb, 49 kb and 50 kb), was assembled. These data were further used to analyse the population level evolutionary dynamics (taxonomical and functional) of reconstructed genotypes.
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Affiliation(s)
- Naseer Sangwan
- Department of Zoology, University of Delhi, Delhi, 110007, India
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Carey Lambert
- Institute of Genetics, School of Life Sciences, Nottingham University, Queen's Medical Centre, Nottingham, UK
| | - Anukriti Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - R Elizabeth Sockett
- Institute of Genetics, School of Life Sciences, Nottingham University, Queen's Medical Centre, Nottingham, UK
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
- Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India
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264
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Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I. Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. MICROBIOME 2015; 3:55. [PMID: 26617277 PMCID: PMC4663747 DOI: 10.1186/s40168-015-0121-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/30/2015] [Indexed: 05/27/2023]
Abstract
BACKGROUND The human gastrointestinal tract harbors a diverse microbial community, in which metabolic phenotypes play important roles for the human host. Recent developments in meta-omics attempt to unravel metabolic roles of microbes by linking genotypic and phenotypic characteristics. This connection, however, still remains poorly understood with respect to its evolutionary and ecological context. RESULTS We generated automatically refined draft genome-scale metabolic models of 301 representative intestinal microbes in silico. We applied a combination of unsupervised machine-learning and systems biology techniques to study individual and global differences in genomic content and inferred metabolic capabilities. Based on the global metabolic differences, we found that energy metabolism and membrane synthesis play important roles in delineating different taxonomic groups. Furthermore, we found an exponential relationship between phylogeny and the reaction composition, meaning that closely related microbes of the same genus can exhibit pronounced differences with respect to their metabolic capabilities while at the family level only marginal metabolic differences can be observed. This finding was further substantiated by the metabolic divergence within different genera. In particular, we could distinguish three sub-type clusters based on membrane and energy metabolism within the Lactobacilli as well as two clusters within the Bifidobacteria and Bacteroides. CONCLUSIONS We demonstrate that phenotypic differentiation within closely related species could be explained by their metabolic repertoire rather than their phylogenetic relationships. These results have important implications in our understanding of the ecological and evolutionary complexity of the human gastrointestinal microbiome.
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Affiliation(s)
- Eugen Bauer
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Cedric Christian Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Stefania Magnusdottir
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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265
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Yeoh YK, Sekiguchi Y, Parks DH, Hugenholtz P. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage. Mol Biol Evol 2015; 33:915-27. [PMID: 26615204 PMCID: PMC4776705 DOI: 10.1093/molbev/msv281] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0–1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms.
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Affiliation(s)
- Yun Kit Yeoh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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266
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Abstract
Nitrification is a two-step process where ammonia is considered to first be oxidized to nitrite by ammonia-oxidizing bacteria (AOB) and/or archaea (AOA), and subsequently to nitrate by nitrite-oxidizing bacteria (NOB). Described by Winogradsky already in 18901, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle2. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible and it was postulated that this process could occur under conditions selecting for species with lower growth-rates but higher growth-yields than canonical ammonia-oxidizing microorganisms3. Still, organisms catalysing this process have not yet been discovered. Here, we report the enrichment and initial characterization of two Nitrospira species that encode all enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding on the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.
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267
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Ju F, Zhang T. Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12628-40. [PMID: 26451629 DOI: 10.1021/acs.est.5b03719] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong , Hong Kong SRA, China
| | - Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong , Hong Kong SRA, China
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268
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Abstract
Environmental studies are primarily done by culturing isolated microorganisms or by amplifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing sample heterogeneity using single-cell genomics, metaomic studies can be simplified.
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Affiliation(s)
- Rimantas Kodzius
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia.
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia.
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269
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Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll. Sci Rep 2015; 5:15383. [PMID: 26481089 PMCID: PMC4611231 DOI: 10.1038/srep15383] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/24/2015] [Indexed: 11/09/2022] Open
Abstract
Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.
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270
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Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 2015; 3:e1319. [PMID: 26500826 PMCID: PMC4614810 DOI: 10.7717/peerj.1319] [Citation(s) in RCA: 1030] [Impact Index Per Article: 114.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022] Open
Abstract
Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
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Affiliation(s)
- A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States ; Department of Medicine, The University of Chicago , Chicago, IL , United States
| | - Özcan C Esen
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Christopher Quince
- Warwick Medical School, University of Warwick , Coventry , United Kingdom
| | - Joseph H Vineis
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Hilary G Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Mitchell L Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Tom O Delmont
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
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271
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Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. Ocean plankton. Structure and function of the global ocean microbiome. Science 2015; 348:1261359. [PMID: 25999513 DOI: 10.1126/science.1261359] [Citation(s) in RCA: 1449] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
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Affiliation(s)
- Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Karine Labadie
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Bardya Djahanschiri
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel R Mende
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Adriana Alberti
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France
| | - Stefan Engelen
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Florian Kokoszka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France
| | - Cyrille Lepoivre
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Julie Poulain
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Hugo Sarmento
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Céline Dimier
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Jean Weissenbach
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Patrick Wincker
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.
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272
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Hiras J, Wu YW, Eichorst SA, Simmons BA, Singer SW. Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. ISME JOURNAL 2015; 10:833-45. [PMID: 26325358 DOI: 10.1038/ismej.2015.158] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 07/22/2015] [Accepted: 07/28/2015] [Indexed: 01/29/2023]
Abstract
Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.
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Affiliation(s)
- Jennifer Hiras
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephanie A Eichorst
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Sandia National Laboratories, Biofuels and Biomaterials Science and Technology Department, Livermore, CA, USA
| | - Steven W Singer
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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273
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Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li Y, Cai L, Wong YH, Zhang G, Zhou G, Zhang X, Bajic VB, Al-Suwailem A, Qian PY. Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. Environ Microbiol 2015; 17:4089-104. [DOI: 10.1111/1462-2920.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Weipeng Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yong Wang
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
| | - Salim Bougouffa
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Renmao Tian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Huiluo Cao
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yongxin Li
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Lin Cai
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yue Him Wong
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Gen Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Guowei Zhou
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Xixiang Zhang
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Abdulaziz Al-Suwailem
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
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274
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From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci 2015; 72:4287-308. [PMID: 26254872 PMCID: PMC4611022 DOI: 10.1007/s00018-015-2004-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 12/30/2022]
Abstract
Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.
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275
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Lindholm L, Ariöz C, Jawurek M, Liebau J, Mäler L, Wieslander Å, von Ballmoos C, Barth A. Effect of lipid bilayer properties on the photocycle of green proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:698-708. [DOI: 10.1016/j.bbabio.2015.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/20/2023]
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276
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Saito MA, Dorsk A, Post AF, McIlvin MR, Rappé MS, DiTullio GR, Moran DM. Needles in the blue sea: sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome. Proteomics 2015; 15:3521-31. [PMID: 26097212 DOI: 10.1002/pmic.201400630] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/17/2015] [Accepted: 06/09/2015] [Indexed: 11/06/2022]
Abstract
Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8 ± 1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13 ± 15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ∼4 × 10(7) , 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples.
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Affiliation(s)
- Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Alexander Dorsk
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Anton F Post
- Coastal Resources Center, URI Graduate School of Oceanography, Narragansett, RI, USA
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, HI, USA
| | | | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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277
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Abstract
SUMMARY Members of the Roseobacter clade are equipped with a tremendous diversity of metabolic capabilities, which in part explains their success in so many different marine habitats. Ideas on how this diversity evolved and is maintained are reviewed, focusing on recent evolutionary studies exploring the timing and mechanisms of Roseobacter ecological diversification.
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278
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Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015. [PMID: 25977477 DOI: 10.1101/gr.186072.114.42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
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Affiliation(s)
- Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Michael Imelfort
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Connor T Skennerton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia; Advanced Water Management Centre, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
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279
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Luo H, Thompson LR, Stingl U, Hughes AL. Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages. Mol Biol Evol 2015; 32:2738-48. [DOI: 10.1093/molbev/msv149] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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280
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Langlois R, Großkopf T, Mills M, Takeda S, LaRoche J. Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype. PLoS One 2015; 10:e0128912. [PMID: 26103055 PMCID: PMC4477881 DOI: 10.1371/journal.pone.0128912] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/01/2015] [Indexed: 01/15/2023] Open
Abstract
Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however γ-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH γ-proteobacterial sequences available in public databases and qPCR data of a γ-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic γ-proteobacteria. One phylotype in particular, Gamma A, was described in several traditional and quantitative PCR studies. Though several γ-proteobacterial nifH sequences have been described as laboratory contaminants, Gamma A is part of a large cluster of sequences isolated from marine environments and distantly related to the clade of contaminants. Using a TaqMan probe and primer set, Gamma A nifH DNA abundance and expression were analyzed in nearly 1000 samples collected during 15 cruises to the Atlantic and Pacific Oceans. The data showed that Gamma A is an active, cosmopolitan diazotroph found throughout oxygenated, oligotrophic waters reaching maximum abundances of 8 x 104 nifH DNA copies l-1 and 5 x 105 nifH transcript copies l-1. Gamma A nifH transcript abundances were on average 3 fold higher than nifH DNA abundances. The widespread distribution and activity of Gamma A indicate that it has potential to be a globally important N2 fixing organism.
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Affiliation(s)
- Rebecca Langlois
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
- * E-mail:
| | | | - Matthew Mills
- Environmental Earth System Science, Stanford University, Stanford, California, United States of America
| | | | - Julie LaRoche
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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281
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Gasc C, Ribière C, Parisot N, Beugnot R, Defois C, Petit-Biderre C, Boucher D, Peyretaillade E, Peyret P. Capturing prokaryotic dark matter genomes. Res Microbiol 2015; 166:814-30. [PMID: 26100932 DOI: 10.1016/j.resmic.2015.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022]
Abstract
Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.
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Affiliation(s)
- Cyrielle Gasc
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Céline Ribière
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Nicolas Parisot
- Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, Villeurbanne, France.
| | - Réjane Beugnot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Clémence Defois
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Corinne Petit-Biderre
- Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171 Aubière, France.
| | - Delphine Boucher
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Eric Peyretaillade
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
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282
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Bergen B, Herlemann DPR, Jürgens K. Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling. Front Microbiol 2015; 6:621. [PMID: 26150812 PMCID: PMC4471433 DOI: 10.3389/fmicb.2015.00621] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Upwelling areas are shaped by enhanced primary production in surface waters, accompanied by a well-investigated planktonic succession. Although bacteria play an important role in biogeochemical cycles of upwelling systems, little is known about bacterial community composition and its development during upwelling events. The aim of this study was to investigate the succession of bacterial assemblages in aging upwelled water of the Benguela upwelling from coastal to offshore sites. Water from the upper mixed layer at 12 stations was sampled along two transects from the origin of the upwelling to a distance of 220 km. 16S rRNA gene amplicon sequencing was then used in a bacterial diversity analysis and major bacterial taxa were quantified by catalyzed reporter deposition-fluorescence in situ hybridization. Additionally, bacterial cell numbers and bacterial production were assessed. Community statistical analysis revealed a reproducible zonation along the two transects, with four clusters of significantly different microbial assemblages. Clustering was mainly driven by phytoplankton composition and abundance. Similar to the temporal succession that occurs during phytoplankton blooms in temperate coastal waters, operational taxonomic units (OTUs) affiliated with Bacteroidetes and Gammaproteobacteria were dominant during algal blooming whereas "Pelagibacterales" were highly abundant in regions with low algal abundance. The most dominant heterotrophic OTU (9% of all reads) was affiliated with "Pelagibacterales" and showed a strong negative correlation with phytoplankton. By contrast, the second most abundant heterotrophic OTU (6% of all reads) was affiliated with the phylum Verrucomicrobia and correlated positively with phytoplankton. Together with the close relation of bacterial production and phytoplankton abundance, our results showed that bacterial community dynamics is strongly driven by the development and composition of the phytoplankton community.
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Affiliation(s)
- Benjamin Bergen
- Leibniz Institute for Baltic Sea Research Warnemünde Rostock, Germany
| | | | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde Rostock, Germany
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283
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Characterization of an Unconventional Rhodopsin from the Freshwater Actinobacterium Rhodoluna lacicola. J Bacteriol 2015; 197:2704-12. [PMID: 26055118 DOI: 10.1128/jb.00386-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Rhodopsin-encoding microorganisms are common in many environments. However, knowing that rhodopsin genes are present provides little insight into how the host cells utilize light. The genome of the freshwater actinobacterium Rhodoluna lacicola encodes a rhodopsin of the uncharacterized actinorhodopsin family. We hypothesized that actinorhodopsin was a light-activated proton pump and confirmed this by heterologously expressing R. lacicola actinorhodopsin in retinal-producing Escherichia coli. However, cultures of R. lacicola did not pump protons, even though actinorhodopsin mRNA and protein were both detected. Proton pumping in R. lacicola was induced by providing exogenous retinal, suggesting that the cells lacked the retinal cofactor. We used high-performance liquid chromatography (HPLC) and oxidation of accessory pigments to confirm that R. lacicola does not synthesize retinal. These results suggest that in some organisms, the actinorhodopsin gene is constitutively expressed, but rhodopsin-based light capture may require cofactors obtained from the environment. IMPORTANCE Up to 70% of microbial genomes in some environments are predicted to encode rhodopsins. Because most microbial rhodopsins are light-activated proton pumps, the prevalence of this gene suggests that in some environments, most microorganisms respond to or utilize light energy. Actinorhodopsins were discovered in an analysis of freshwater metagenomic data and subsequently identified in freshwater actinobacterial cultures. We hypothesized that actinorhodopsin from the freshwater actinobacterium Rhodoluna lacicola was a light-activated proton pump and confirmed this by expressing actinorhodopsin in retinal-producing Escherichia coli. Proton pumping in R. lacicola was induced only after both light and retinal were provided, suggesting that the cells lacked the retinal cofactor. These results indicate that photoheterotrophy in this organism and others may require cofactors obtained from the environment.
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284
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Luo H, Moran MA. How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends Microbiol 2015; 23:577-84. [PMID: 26051014 DOI: 10.1016/j.tim.2015.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 05/04/2015] [Accepted: 05/11/2015] [Indexed: 12/16/2022]
Abstract
Heterotrophic bacteria in pelagic marine environments are frequently categorized into two canonical ecological groups: patch-associated and free-living. This framework provides a conceptual basis for understanding bacterial utilization of oceanic organic matter. Some patch-associated bacteria are ecologically linked with eukaryotic phytoplankton, and this observation fits with predicted coincidence of their genome expansion with marine phytoplankton diversification. By contrast, free-living bacteria in today's oceans typically live singly with streamlined metabolic and regulatory functions that allow them to grow in nutrient-poor seawater. Recent analyses of marine Alphaproteobacteria suggest that some free-living bacterioplankton lineages evolved from patch-associated ancestors up to several hundred million years ago. While evolutionary analyses agree with the hypothesis that natural selection has maintained these distinct ecological strategies and genomic traits in present-day populations, they do not rule out a major role for genetic drift in driving ancient ecological switches. These two evolutionary forces may have acted on ocean bacteria at different geological time scales and under different geochemical constraints, with possible implications for future adaptations to a changing ocean. New evolutionary models and genomic data are leading to a more comprehensive understanding of marine bacterioplankton evolutionary history.
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Affiliation(s)
- Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.
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285
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Lindh MV, Lefébure R, Degerman R, Lundin D, Andersson A, Pinhassi J. Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment. AMBIO 2015; 44 Suppl 3:402-12. [PMID: 26022323 PMCID: PMC4447689 DOI: 10.1007/s13280-015-0659-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Predicted increases in runoff of terrestrial dissolved organic matter (DOM) and sea surface temperatures implicate substantial changes in energy fluxes of coastal marine ecosystems. Despite marine bacteria being critical drivers of marine carbon cycling, knowledge of compositional responses within bacterioplankton communities to such disturbances is strongly limited. Using 16S rRNA gene pyrosequencing, we examined bacterioplankton population dynamics in Baltic Sea mesocosms with treatments combining terrestrial DOM enrichment and increased temperature. Among the 200 most abundant taxa, 62 % either increased or decreased in relative abundance under changed environmental conditions. For example, SAR11 and SAR86 populations proliferated in combined increased terrestrial DOM/temperature mesocosms, while the hgcI and CL500-29 clades (Actinobacteria) decreased in the same mesocosms. Bacteroidetes increased in both control mesocosms and in the combined increased terrestrial DOM/temperature mesocosms. These results indicate considerable and differential responses among distinct bacterial populations to combined climate change effects, emphasizing the potential of such effects to induce shifts in ecosystem function and carbon cycling in the future Baltic Sea.
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Affiliation(s)
- Markus V. Lindh
- />Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 391 82 Kalmar, Sweden
| | - Robert Lefébure
- />Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
- />Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH UK
| | - Rickard Degerman
- />Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
| | - Daniel Lundin
- />Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 391 82 Kalmar, Sweden
| | - Agneta Andersson
- />Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
| | - Jarone Pinhassi
- />Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 391 82 Kalmar, Sweden
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286
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Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043-55. [PMID: 25977477 PMCID: PMC4484387 DOI: 10.1101/gr.186072.114] [Citation(s) in RCA: 6210] [Impact Index Per Article: 690.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/13/2015] [Indexed: 02/07/2023]
Abstract
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
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Affiliation(s)
- Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Michael Imelfort
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Connor T Skennerton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia; Advanced Water Management Centre, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia
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287
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Labonté JM, Field EK, Lau M, Chivian D, Van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front Microbiol 2015; 6:349. [PMID: 25954269 PMCID: PMC4406082 DOI: 10.3389/fmicb.2015.00349] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/08/2015] [Indexed: 12/12/2022] Open
Abstract
A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.
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Affiliation(s)
| | - Erin K Field
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Maggie Lau
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | - Dylan Chivian
- Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Esta Van Heerden
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware Newark, DE, USA
| | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology Socorro, NM, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University Princeton, NJ, USA
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288
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Sharma A, Sangwan N, Negi V, Kohli P, Khurana JP, Rao DLN, Lal R. Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite. BMC Genomics 2015; 16:313. [PMID: 25898829 PMCID: PMC4405911 DOI: 10.1186/s12864-015-1488-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
Background Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient. Results Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1488-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anukriti Sharma
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Naseer Sangwan
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Vivek Negi
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Puneet Kohli
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
| | - Desiraju Lakshmi Narsimha Rao
- All India Network Project on Soil Biodiversity and Biofertilizers, Indian Institute of Soil Science, Bhopal, 462038, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
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289
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Spring S, Scheuner C, Göker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281. [PMID: 25914684 PMCID: PMC4391266 DOI: 10.3389/fmicb.2015.00281] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/21/2015] [Indexed: 11/13/2022] Open
Abstract
In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Carmen Scheuner
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; School of Biology, Newcastle University Newcastle upon Tyne, UK
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290
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Alonso-Sáez L, Díaz-Pérez L, Morán XAG. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton. Environ Microbiol 2015; 17:3766-80. [DOI: 10.1111/1462-2920.12801] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Laura Alonso-Sáez
- Instituto Español de Oceanografía; Centro Oceanográfico de Xixón; 33212 Xixón Spain
- AZTI; Marine Research Division; 48395 Sukarrieta Spain
| | - Laura Díaz-Pérez
- Instituto Español de Oceanografía; Centro Oceanográfico de Xixón; 33212 Xixón Spain
| | - Xosé Anxelu G. Morán
- Instituto Español de Oceanografía; Centro Oceanográfico de Xixón; 33212 Xixón Spain
- Red Sea Research Center; King Abdullah University of Science and Technology; 23955-6900 Thuwal Saudi Arabia
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291
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Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle. Proc Natl Acad Sci U S A 2015; 112:4251-6. [PMID: 25831533 DOI: 10.1073/pnas.1422332112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual "inflation" of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.
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292
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Luo H. The use of evolutionary approaches to understand single cell genomes. Front Microbiol 2015; 6:174. [PMID: 25806025 PMCID: PMC4354383 DOI: 10.3389/fmicb.2015.00191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/20/2015] [Indexed: 11/13/2022] Open
Abstract
The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.
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Affiliation(s)
- Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, China
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293
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Rodriguez-R LM, Overholt WA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. ISME JOURNAL 2015; 9:1928-40. [PMID: 25689026 DOI: 10.1038/ismej.2015.5] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/16/2014] [Accepted: 12/23/2014] [Indexed: 12/30/2022]
Abstract
Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.
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Affiliation(s)
| | - Will A Overholt
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Christopher Hagan
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA, USA [2] School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA, USA [2] School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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294
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Yang C, Li Y, Zhou B, Zhou Y, Zheng W, Tian Y, Van Nostrand JD, Wu L, He Z, Zhou J, Zheng T. Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China. Sci Rep 2015; 5:8476. [PMID: 25684124 PMCID: PMC4329561 DOI: 10.1038/srep08476] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/22/2015] [Indexed: 11/12/2022] Open
Abstract
Although phytoplankton are the major source of marine dissolved organic matter (DOM), their blooms are a global problem that can greatly affect marine ecological systems, especially free-living bacteria, which are the primary DOM degraders. In this study, we analyzed free-living bacterial communities from Xiamen sea during an Akashiwo sanguine bloom using Illumina MiSeq sequencing of 16S rRNA gene amplicons. The bloom was probably stimulated by low salinity and ended after abatement of eutrophication pollution. A total of 658,446 sequence reads and 11,807 OTUs were obtained in both bloom and control samples with Alpha-proteobacteria and Gamma-proteobacteria being the predominant classes detected. The bloom decreased bacterial diversity, increased species evenness, and significantly changed the bacterial community structure. Bacterial communities within the bloom were more homogeneous than those within the control area. The bacteria stimulated by this bloom included the SAR86 and SAR116 clades and the AEGEAN-169 marine group, but a few were suppressed. In addition, many bacteria known to be associated with phytoplankton were detected only in the bloom samples. This study revealed the great influence of an A. sanguinea bloom on free-living bacterial communities, and provided new insights into the relationship between bacteria and A. sanguinea in marine ecosystems.
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Affiliation(s)
- Caiyun Yang
- State Key Laboratory for Marine Environmental Science, and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Yi Li
- State Key Laboratory for Marine Environmental Science, and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Benjamin Zhou
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Yanyan Zhou
- State Key Laboratory for Marine Environmental Science, and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Wei Zheng
- State Key Laboratory for Marine Environmental Science, and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Yun Tian
- State Key Laboratory for Marine Environmental Science, and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 730722, USA
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 730722, USA
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 730722, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 730722, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tianling Zheng
- State Key Laboratory for Marine Environmental Science, and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
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295
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El-Swais H, Dunn KA, Bielawski JP, Li WKW, Walsh DA. Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton. Environ Microbiol 2015; 17:3642-61. [DOI: 10.1111/1462-2920.12629] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Heba El-Swais
- Department of Biology; Concordia University; 7141 Sherbrooke St West Montreal QC H4B 1R6 Canada
| | - Katherine A. Dunn
- Department of Biology; Dalhousie University; 1355 Oxford St Halifax NS B3H 4R2 Canada
| | - Joseph P. Bielawski
- Department of Biology; Dalhousie University; 1355 Oxford St Halifax NS B3H 4R2 Canada
| | - William K. W. Li
- Department of Fisheries and Oceans; Bedford Institute of Oceanography; Dartmouth NS B2Y 4A2 Canada
| | - David A. Walsh
- Department of Biology; Concordia University; 7141 Sherbrooke St West Montreal QC H4B 1R6 Canada
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296
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Lindh MV, Sjöstedt J, Andersson AF, Baltar F, Hugerth LW, Lundin D, Muthusamy S, Legrand C, Pinhassi J. Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling. Environ Microbiol 2015; 17:2459-76. [PMID: 25403576 DOI: 10.1111/1462-2920.12720] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/11/2014] [Accepted: 11/11/2014] [Indexed: 01/08/2023]
Abstract
Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1) . Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.
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Affiliation(s)
- Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, KTH Royal Institute of Technology, School of Biotechnology, Stockholm, SE-10691, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden.,Department of Marine Sciences, University of Otago, PO Box 56, Dunedin, NZ-9054, New Zealand
| | - Luisa W Hugerth
- Science for Life Laboratory, KTH Royal Institute of Technology, School of Biotechnology, Stockholm, SE-10691, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Saraladevi Muthusamy
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
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297
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Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW, Hugenholtz P. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ 2015; 3:e740. [PMID: 25650158 PMCID: PMC4312070 DOI: 10.7717/peerj.740] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/05/2015] [Indexed: 01/22/2023] Open
Abstract
Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking) in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking.
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Affiliation(s)
- Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki , Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki , Japan
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia
| | - Toshihiro Yamauchi
- Administrative Management Department, Kubota Kasui Corporation , Minato-ku, Tokyo , Japan
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia ; Advanced Water Management Centre, The University of Queensland , St. Lucia, Queensland , Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia ; Institute for Molecular Bioscience, The University of Queensland , St. Lucia, Queensland , Australia
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298
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Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean. Proc Natl Acad Sci U S A 2015; 112:1173-8. [PMID: 25587132 DOI: 10.1073/pnas.1416223112] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.
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299
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Statistical research on the bioactivity of new marine natural products discovered during the 28 years from 1985 to 2012. Mar Drugs 2015; 13:202-21. [PMID: 25574736 PMCID: PMC4306932 DOI: 10.3390/md13010202] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/22/2014] [Indexed: 01/08/2023] Open
Abstract
Every year, hundreds of new compounds are discovered from the metabolites of marine organisms. Finding new and useful compounds is one of the crucial drivers for this field of research. Here we describe the statistics of bioactive compounds discovered from marine organisms from 1985 to 2012. This work is based on our database, which contains information on more than 15,000 chemical substances including 4196 bioactive marine natural products. We performed a comprehensive statistical analysis to understand the characteristics of the novel bioactive compounds and detail temporal trends, chemical structures, species distribution, and research progress. We hope this meta-analysis will provide useful information for research into the bioactivity of marine natural products and drug development.
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300
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Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, Coronado S, der Maaten LV, Vlassis N, Wilmes P. VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. MICROBIOME 2015; 3:1. [PMID: 25621171 PMCID: PMC4305225 DOI: 10.1186/s40168-014-0066-1] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge. RESULTS We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented. CONCLUSIONS VizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.
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Affiliation(s)
- Cedric C Laczny
- />Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, 4362 Luxembourg
| | - Tomasz Sternal
- />Institute of Computing Science, Poznan University of Technology, Poznan, 60-965 Poland
| | - Valentin Plugaru
- />Computer Science and Communications Research Unit, University of Luxembourg, Luxembourg, 1359 Luxembourg
| | - Piotr Gawron
- />Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, 4362 Luxembourg
| | - Arash Atashpendar
- />Computer Science and Communications Research Unit, University of Luxembourg, Luxembourg, 1359 Luxembourg
| | - Houry Hera Margossian
- />Computer Science and Communications Research Unit, University of Luxembourg, Luxembourg, 1359 Luxembourg
| | - Sergio Coronado
- />Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, 4362 Luxembourg
| | - Laurens van der Maaten
- />Pattern Recognition and Bioinformatics Group, Delft University of Technology, CD Delft, 2628 Netherlands
| | | | - Paul Wilmes
- />Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, 4362 Luxembourg
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