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Complete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoides. Microbiol Resour Announc 2020; 9:9/27/e00644-20. [PMID: 32616649 PMCID: PMC7330251 DOI: 10.1128/mra.00644-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Starkeya sp. strain ORNL1 is an alphaproteobacterium isolated from the rhizosphere of an Eastern cottonwood tree. Starkeya spp. are physiologically versatile, using a wide range of nutritional and energetic resources and serving important ecological roles in carbon and sulfur cycling. The 6.3-Mb chromosome of Starkeya sp. strain ORNL1 was completely sequenced and will help in understanding nutrient cycles.
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2
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Marín P, Martirani‐Von Abercron SM, Urbina L, Pacheco‐Sánchez D, Castañeda‐Cataña MA, Retegi A, Eceiza A, Marqués S. Bacterial nanocellulose production from naphthalene. Microb Biotechnol 2019; 12:662-676. [PMID: 31087504 PMCID: PMC6559018 DOI: 10.1111/1751-7915.13399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 11/29/2022] Open
Abstract
Polycyclic aromatic compounds (PAHs) are toxic compounds that are released in the environment as a consequence of industrial activities. The restoration of PAH-polluted sites considers the use of bacteria capable of degrading aromatic compounds to carbon dioxide and water. Here we characterize a new Xanthobacteraceae strain, Starkeya sp. strain N1B, previously isolated during enrichment under microaerophilic conditions, which is capable of using naphthalene crystals as the sole carbon source. The strain produced a structured biofilm when grown on naphthalene crystals, which had the shape of a half-sphere organized over the crystal. Scanning electron microscopy (SEM) and GC-MS analysis indicated that the biofilm was essentially made of cellulose, composed of several micron-long nanofibrils of 60 nm diameter. A cellulosic biofilm was also formed when the cells grew with glucose as the carbon source. Fourier transformed infrared spectroscopy (FTIR) confirmed that the polymer was type I cellulose in both cases, although the crystallinity of the material greatly depended on the carbon source used for growth. Using genome mining and mutant analysis, we identified the genetic complements required for the transformation of naphthalene into cellulose, which seemed to have been successively acquired through horizontal gene transfer. The capacity to develop the biofilm around the crystal was found to be dispensable for growth when naphthalene was used as the carbon source, suggesting that the function of this structure is more intricate than initially thought. This is the first example of the use of toxic aromatic hydrocarbons as the carbon source for bacterial cellulose production. Application of this capacity would allow the remediation of a PAH into such a value-added polymer with multiple biotechnological usages.
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Affiliation(s)
- Patricia Marín
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Sophie Marie Martirani‐Von Abercron
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Leire Urbina
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Daniel Pacheco‐Sánchez
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Mayra Alejandra Castañeda‐Cataña
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Aloña Retegi
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Arantxa Eceiza
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Silvia Marqués
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
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3
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Tan YJC, Zhao C, Nasreen M, O'Rourke L, Dhouib R, Roberts L, Wan Y, Beatson SA, Kappler U. Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits. Front Microbiol 2019; 10:960. [PMID: 31139157 PMCID: PMC6527743 DOI: 10.3389/fmicb.2019.00960] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/16/2019] [Indexed: 11/15/2022] Open
Abstract
Although sulfite, a by-product of the degradation of many sulfur compounds, is highly reactive and can cause damage to DNA, proteins and lipids, comparatively little is known about the regulation of sulfite-oxidizing enzyme (SOEs) expression. Here we have investigated the regulation of SOE-encoding genes in two species of α-Proteobacteria, Sinorhizobium meliloti and Starkeya novella, that degrade organo- and inorganic sulfur compounds, respectively, and contain unrelated types of SOEs that show different expression patterns. Our work revealed that in both cases, the molecular signal that triggers SOE gene expression is sulfite, and strong up-regulation depends on the presence of a sulfite-responsive, cognate Extracytoplasmic function (ECF) sigma factor, making sulfite oxidation a bacterial stress response. An additional RpoE1-like ECF sigma factor was also involved in the regulation, but was activated by different molecular signals, taurine (Sm) and tetrathionate (Sn), respectively, targeted different gene promoters, and also differed in the magnitude of the response generated. We therefore propose that RpoE1 is a secondary, species-specific regulator of SOE gene expression rather than a general, conserved regulatory circuit. Sulfite produced by major dissimilatory processes appeared to be the trigger for SOE gene expression in both species, as we were unable to find evidence for an increase of SOE activity in stationary growth phase. The basic regulation of bacterial sulfite oxidation by cognate ECF sigma factors is likely to be applicable to three groups of alpha and beta-Proteobacteria in which we identified similar SOE operon structures.
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Affiliation(s)
- Yi Jie Chelsea Tan
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Chengzhi Zhao
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Marufa Nasreen
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Leo O'Rourke
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Rabeb Dhouib
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Leah Roberts
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ying Wan
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott A Beatson
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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Corel E, Méheust R, Watson AK, McInerney JO, Lopez P, Bapteste E. Bipartite Network Analysis of Gene Sharings in the Microbial World. Mol Biol Evol 2019; 35:899-913. [PMID: 29346651 PMCID: PMC5888944 DOI: 10.1093/molbev/msy001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.
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Affiliation(s)
- Eduardo Corel
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - Raphaël Méheust
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - Andrew K Watson
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - James O McInerney
- Chair in Evolutionary Biology, The University of Manchester, United Kingdom
| | - Philippe Lopez
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - Eric Bapteste
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
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Swiercz A, Frohmberg W, Kierzynka M, Wojciechowski P, Zurkowski P, Badura J, Laskowski A, Kasprzak M, Blazewicz J. GRASShopPER-An algorithm for de novo assembly based on GPU alignments. PLoS One 2018; 13:e0202355. [PMID: 30114279 PMCID: PMC6095601 DOI: 10.1371/journal.pone.0202355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022] Open
Abstract
Next generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes a great computational challenge in accurately reconstructing a genome sequence de novo using these short sequences. Here, we propose the GRASShopPER assembler, which follows an approach of overlap-layout-consensus. It uses an efficient GPU implementation for the sequence alignment during the graph construction stage and a greedy hyper-heuristic algorithm at the fork detection stage. A two-part fork detection method allows us to identify repeated fragments of a genome and to reconstruct them without misassemblies. The assemblies of data sets of bacteria Candidatus Microthrix, nematode Caenorhabditis elegans, and human chromosome 14 were evaluated with the golden standard tool QUAST. In comparison with other assemblers, GRASShopPER provided contigs that covered the largest part of the genomes and, at the same time, kept good values of other metrics, e.g., NG50 and misassembly rate.
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Affiliation(s)
- Aleksandra Swiercz
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
- * E-mail:
| | - Wojciech Frohmberg
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Michal Kierzynka
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - Pawel Wojciechowski
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Piotr Zurkowski
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Jan Badura
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Artur Laskowski
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Marta Kasprzak
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
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6
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Hausmann B, Pjevac P, Schreck K, Herbold CW, Daims H, Wagner M, Loy A. Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling. GENOME ANNOUNCEMENTS 2018; 6:e01524-17. [PMID: 29371357 PMCID: PMC5786683 DOI: 10.1128/genomea.01524-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022]
Abstract
The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation.
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Affiliation(s)
- Bela Hausmann
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Katharina Schreck
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Holger Daims
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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7
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Martirani-Von Abercron SM, Marín P, Solsona-Ferraz M, Castañeda-Cataña MA, Marqués S. Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity. Microb Biotechnol 2017; 10:1781-1796. [PMID: 28840968 PMCID: PMC5658598 DOI: 10.1111/1751-7915.12842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.
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Affiliation(s)
| | - Patricia Marín
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Marta Solsona-Ferraz
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Mayra-Alejandra Castañeda-Cataña
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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8
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Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). Stand Genomic Sci 2016; 11:38. [PMID: 27274784 PMCID: PMC4891895 DOI: 10.1186/s40793-016-0162-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 05/24/2016] [Indexed: 02/01/2023] Open
Abstract
Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1T is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1T is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
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9
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Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME JOURNAL 2014; 8:1440-51. [PMID: 24451205 DOI: 10.1038/ismej.2013.243] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/07/2013] [Accepted: 12/10/2013] [Indexed: 11/09/2022]
Abstract
Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.
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Affiliation(s)
- J Cameron Thrash
- 1] Department of Microbiology, Oregon State University, Corvallis, OR, USA [2] Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Ben Temperton
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Zachary C Landry
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Edward F DeLong
- 1] Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA [2] Center for Microbial Ecology: Research and Education, Honolulu, HI, USA
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10
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Kappler U, Nouwens AS. Metabolic adaptation and trophic strategies of soil bacteria-C1- metabolism and sulfur chemolithotrophy in Starkeya novella. Front Microbiol 2013; 4:304. [PMID: 24146664 PMCID: PMC3797975 DOI: 10.3389/fmicb.2013.00304] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/23/2013] [Indexed: 11/22/2022] Open
Abstract
The highly diverse and metabolically versatile microbial communities found in soil environments are major contributors to the global carbon, nitrogen, and sulfur cycles. We have used a combination of genome -based pathway analysis with proteomics and gene expression studies to investigate metabolic adaptation in a representative of these bacteria, Starkeya novella, which was originally isolated from agricultural soil. This bacterium was the first facultative sulfur chemolithoautotroph that was isolated and it is also able to grow with methanol and on over 39 substrates as a heterotroph. However, using glucose, fructose, methanol, thiosulfate as well as combinations of the carbon compounds with thiosulfate as growth substrates we have demonstrated here that contrary to the previous classification, S. novella is not a facultative sulfur chemolitho- and methylotroph, as the enzyme systems required for these two growth modes are always expressed at high levels. This is typical for key metabolic pathways. In addition enzymes for various pathways of carbon dioxide fixation were always expressed at high levels, even during heterotrophic growth on glucose or fructose, which suggests a role for these pathways beyond the generation of reduced carbon units for cell growth, possibly in redox balancing of metabolism. Our results then indicate that S. novella, a representative of the Xanthobacteraceae family of methylotrophic soil and freshwater dwelling bacteria, employs a mixotrophic growth strategy under all conditions tested here. As a result the contribution of this bacterium to either carbon sequestration or the release of climate active substances could vary very quickly, which has direct implications for the modeling of such processes if mixotrophy proves to be the main growth strategy for large populations of soil bacteria.
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Affiliation(s)
- Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
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11
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Göker M, Klenk HP. Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects. Stand Genomic Sci 2013; 8:360-74. [PMID: 23991265 PMCID: PMC3746418 DOI: 10.4056/sigs.3446951] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. Phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. Here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. The scoring itself, as well as pre- and post-processing of the data, is illustrated using two real-world examples in which the method has already been applied for selecting targets for genome sequencing. These projects are the JGI CSP Genomic Encyclopedia of Bacteria and Archaea phase I, targeting 1,000 type strains, and, on a smaller-scale, the phylogenomics of the Roseobacter clade. Potential artifacts of the method are discussed and compared to a selection approach based on the taxonomic classification.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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