1
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Hiser C, Montgomery BL, Ferguson-Miller S. TSPO protein binding partners in bacteria, animals, and plants. J Bioenerg Biomembr 2021; 53:463-487. [PMID: 34191248 PMCID: PMC8243069 DOI: 10.1007/s10863-021-09905-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/12/2021] [Indexed: 12/11/2022]
Abstract
The ancient membrane protein TSPO is phylogenetically widespread from archaea and bacteria to insects, vertebrates, plants, and fungi. TSPO’s primary amino acid sequence is only modestly conserved between diverse species, although its five transmembrane helical structure appears mainly conserved. Its cellular location and orientation in membranes have been reported to vary between species and tissues, with implications for potential diverse binding partners and function. Most TSPO functions relate to stress-induced changes in metabolism, but in many cases it is unclear how TSPO itself functions—whether as a receptor, a sensor, a transporter, or a translocator. Much evidence suggests that TSPO acts indirectly by association with various protein binding partners or with endogenous or exogenous ligands. In this review, we focus on proteins that have most commonly been invoked as TSPO binding partners. We suggest that TSPO was originally a bacterial receptor/stress sensor associated with porphyrin binding as its most ancestral function and that it later developed additional stress-related roles in eukaryotes as its ability to bind new partners evolved.
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Affiliation(s)
- Carrie Hiser
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
| | - Beronda L Montgomery
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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2
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Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. MICROBIOME 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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3
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Xue CX, Zhang H, Lin HY, Sun Y, Luo D, Huang Y, Zhang XH, Luo H. Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages. Environ Microbiol 2020; 22:3234-3247. [PMID: 32390223 DOI: 10.1111/1462-2920.15065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022]
Abstract
Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - He-Yu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Danli Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
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4
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Hameed A, Lai WA, Shahina M, Stothard P, Young LS, Lin SY, Sridhar KR, Young CC. Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria. FEMS Microbiol Ecol 2020; 96:5710931. [PMID: 31960903 DOI: 10.1093/femsec/fiaa011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.
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Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 1427 College Plaza, Edmonton, Alberta, Canada
| | - Li-Sen Young
- Tetanti AgriBiotech Inc. No. 1, Gongyequ 10th Rd., Xitun Dist., Taichung 40755, Taiwan
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | | | - Chiu-Chung Young
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
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5
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Smith MW, Herfort L, Rivers AR, Simon HM. Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary. Front Microbiol 2019; 10:2475. [PMID: 31749780 PMCID: PMC6848030 DOI: 10.3389/fmicb.2019.02475] [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: 06/04/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
In fast-flowing, river-dominated estuaries, “hotspots” of microbial biogeochemical cycling can be found within areas of extended water retention. Lateral bays located off of the North and South channels of the Columbia River estuary are proposed to be such hotspots. Previous metagenomic studies on water samples indicated that these regions function both as sources and sinks of biogenic particles, with potential to impact organic matter fluxes in the estuary. To extend this work, we analyzed 11 sediment metagenomes from three disparate bays: the freshwater Cathlamet Bay, and the brackish Youngs Bay and more saline Baker Bay located nearer the mouth to the south and north of the main channel, respectively. Samples were collected from upper layers of sediments in August of 2011 and 2013 for DNA extraction and metagenome sequencing. All metagenomes were dominated by bacterial sequences, although diatom sequences as high as 26% of the total annotated sequences were observed in the higher salinity samples. Unsupervised 2D hierarchical clustering analysis resulted in the eleven metagenome samples clustered into four groups by microbial taxonomic composition, with Bacteroides, diatom, and phage levels driving most of the grouping. Results of functional gene clustering further indicated that diatom bloom degradation stage (early vs. late) was an important factor. While the Flavobacteriia and Cytophagia classes were well represented in metagenomes containing abundant diatoms, taxa from the Bacteroidia class, along with certain members of the Sphingobacteriia class, were particularly abundant in metagenomes representing later stages of diatom decomposition. In contrast, the sediment metagenomes with low relative abundance of diatom and Bacteroidetes sequences appeared to have a metabolic potential biased toward microbial growth under nutrient limitation. While differences in water salinity clearly also influenced the microbial community composition and metabolic potential, our results highlight a central role for allochthonous labile organic matter (i.e., diatom detritus), in shaping bacterial taxonomic and functional properties in the Columbia River estuary lateral bay sediments. These results suggest that in fast-flowing, river-dominated estuaries, sediment microbial communities in areas of extended water retention, such as the lateral bays, may contribute disproportionately to estuarine organic matter degradation and recycling.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States
| | - Lydie Herfort
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, United States
| | - Adam R Rivers
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Holly M Simon
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, United States
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6
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Liu J, Xue CX, Sun H, Zheng Y, Meng Z, Zhang XH. Carbohydrate catabolic capability of a Flavobacteriia bacterium isolated from hadal water. Syst Appl Microbiol 2019; 42:263-274. [DOI: 10.1016/j.syapm.2019.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/17/2018] [Accepted: 01/15/2019] [Indexed: 11/26/2022]
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7
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Zhang W, Li J, Wang C, Zhou X, Gao Y, Jia Z. Stable-isotope probing of bacterial community for dissolved inorganic carbon utilization in Microcystis aeruginosa-dominated eutrophic water. J Environ Sci (China) 2019; 79:264-272. [PMID: 30784450 DOI: 10.1016/j.jes.2018.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Dissolved inorganic carbon (DIC) is an important source of carbon in aquatic ecosystems, especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indirect utilization of DIC has been widely overlooked in eutrophic freshwater. To identify the functional bacteria that can actively utilize DIC in eutrophic freshwater during cyanobacterial bloom, stable-isotope probing (SIP) experiments were conducted on eutrophic river water with or without inoculation with cyanobacteria (Microcystis aeruginosa). Our 16S rRNA sequencing results revealed the significance of Betaproteobacteria, with similar relative abundance as Alphaproteobacteria, in the active assimilation of H13CO3- into their DNA directly or indirectly, which include autotrophic genera Betaproteobacterial ammonia-oxidizing bacteria. Other bacterial groups containing autotrophic members, e.g. Planctomycetes and Nitrospira, also presented higher abundance among free-living bacteria in water without cyanobacteria. Microcystis aggregates showed a preference for some specific bacterial members that may utilize H13CO3- metabolized by Microcystis as organic matter, e.g. Bacteroidetes (Cytophagales, Sphingobacteriales), and microcystin-degrading bacteria Betaproteobacteria (Paucibacter/Burkholderiaceae). This study provides some valuable information regarding the functional bacteria that can actively utilize DIC in eutrophic freshwater.
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Affiliation(s)
- Weiguo Zhang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Nanjing 210014, China; China Ministry of Agriculture Key Laboratory at Yangtze River Plain for Agricultural Environment, Nanjing 210014, China.
| | - Jiangye Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Chengcheng Wang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xue Zhou
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China
| | - Yan Gao
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Nanjing 210014, China; China Ministry of Agriculture Key Laboratory at Yangtze River Plain for Agricultural Environment, Nanjing 210014, China.
| | - Zhongjun Jia
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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8
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Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA. " Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities. Front Microbiol 2019; 9:3159. [PMID: 30687241 PMCID: PMC6338057 DOI: 10.3389/fmicb.2018.03159] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Nathaniel W Fortney
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Joval N Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Natural Sciences, University of St. La Salle, Bacolod, Philippines
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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9
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Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. ISME JOURNAL 2018; 12:1329-1343. [PMID: 29410487 PMCID: PMC5932025 DOI: 10.1038/s41396-018-0058-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/17/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Proteorhodopsin (PR) is a light-driven proton pump that is found in diverse bacteria and archaea species, and is widespread in marine microbial ecosystems. To date, many studies have suggested the advantage of PR for microorganisms in sunlit environments. The ecophysiological significance of PR is still not fully understood however, including the drivers of PR gene gain, retention, and loss in different marine microbial species. To explore this question we sequenced 21 marine Flavobacteriia genomes of polyphyletic origin, which encompassed both PR-possessing as well as PR-lacking strains. Here, we show that the possession or alternatively the lack of PR genes reflects one of two fundamental adaptive strategies in marine bacteria. Specifically, while PR-possessing bacteria utilize light energy ("solar-panel strategy"), PR-lacking bacteria exclusively possess UV-screening pigment synthesis genes to avoid UV damage and would adapt to microaerobic environment ("parasol strategy"), which also helps explain why PR-possessing bacteria have smaller genomes than those of PR-lacking bacteria. Collectively, our results highlight the different strategies of dealing with light, DNA repair, and oxygen availability that relate to the presence or absence of PR phototrophy.
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10
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Hameed A, Shahina M, Huang HC, Lai WA, Lin SY, Stothard P, Young CC. Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1 T, a flavobacterium isolated from coastal surface seawater. Mar Genomics 2018; 37:21-25. [PMID: 33250121 DOI: 10.1016/j.margen.2017.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 11/24/2022]
Abstract
Here we present the complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a flavobacterium isolated from coastal surface seawater. A 3.3Mb genome revealed remarkable specialization of this bacterium particularly in the degradation of sulfated polysaccharides available as detritus or in dissolved phase. Besides utilizing high molecular weight organic biopolymers, this strain appears to accomplish assimilatory sulfate reduction, sulfide oxidation, and acquisition and inter-conversion of inorganic carbon. Genes encoding zeaxanthin and three different kinds of DNA photolyase/cryptochrome (senses blue light) were present, while genes that code for blue light sensing BLUF domain proteins and red/far-red light sensing phytochromes were absent. Furthermore, CC-SAMT-1T lacked the rhodopsin photosystem and all other genes that confer any other known forms of phototrophy. The genomic data revealed that CC-SAMT-1T is highly adapted to sulfur-rich coastal environments, where it most likely contributes to marine carbon and sulfur cycles by metabolizing sulfated polysaccharides as well as inorganic sulfur.
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Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsin-Chieh Huang
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 1427 College Plaza, Edmonton, Canada
| | - Chiu-Chung Young
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan.
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11
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Guerrero LD, Vikram S, Makhalanyane TP, Cowan DA. Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems. Environ Microbiol 2017; 19:3755-3767. [PMID: 28752953 DOI: 10.1111/1462-2920.13877] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022]
Abstract
Microorganisms able to synthesize rhodopsins have the capacity to translocate ions through their membranes, using solar energy to generate a proton motive force. Rhodopsins are the most abundant phototrophic proteins in oceanic surface waters and are key constituents in marine bacterial ecology. However, it remains unclear how rhodopsins are used in most microorganisms. Despite their abundance in marine and fresh-water systems, the presence of functional rhodopsin systems in edaphic habitats has never been reported. Here, we show the presence of several new putative H+ , Na+ and Cl+ pumping rhodopsins identified by metagenomic analysis of Antarctic desert hypolithic communities. Reconstruction of two Proteobacteria genomes harboring xanthorhodopsin-like proteins and one Bacteroidetes genome with a Na-pumping-like rhodopsin indicated that these bacteria were aerobic heterotrophs possessing the apparent capacity for the functional expression of rhodopsins. The existence of these protein systems in hypolithic bacteria expands the known role of rhodopsins to include terrestrial environments and suggests a possible predominant function as heterotrophic energy supply proteins, a feasible microbial adaptation to the harsh conditions prevalent in Antarctic edaphic systems.
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Affiliation(s)
- Leandro D Guerrero
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
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12
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Yoon K, Song JY, Kwak MJ, Kwon SK, Kim JF. Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5. J Microbiol 2017; 55:561-567. [DOI: 10.1007/s12275-017-6427-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/06/2017] [Accepted: 03/22/2017] [Indexed: 11/30/2022]
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13
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Muthusamy S, Lundin D, Mamede Branca RM, Baltar F, González JM, Lehtiö J, Pinhassi J. Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. Environ Microbiol 2017; 19:2301-2319. [PMID: 28371138 DOI: 10.1111/1462-2920.13725] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/05/2017] [Indexed: 11/30/2022]
Abstract
Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.
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Affiliation(s)
- Saraladevi Muthusamy
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Rui Miguel Mamede Branca
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, Stockholm, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden.,Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, ES-38200, Spain
| | - Janne Lehtiö
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, Stockholm, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
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14
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Smith MW, Herfort L, Fortunato CS, Crump BC, Simon HM. Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary. Microbiologyopen 2017; 6. [PMID: 28318115 PMCID: PMC5552926 DOI: 10.1002/mbo3.467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/02/2017] [Accepted: 02/14/2017] [Indexed: 11/25/2022] Open
Abstract
Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3‐μm prefilter and 0.2‐μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES‐5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES‐5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free‐living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low‐salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical “hotspot,” which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater–brackish water interface in the fast‐flowing Columbia River estuary.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | | | - Byron C Crump
- Oregon State University, College of Earth, Ocean and Atmospheric Sciences, Corvallis, OR, USA
| | - Holly M Simon
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
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15
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Wissuwa J, Bauer SLM, Steen IH, Stokke R. Complete genome sequence of Lutibacter profundi LP1 T isolated from an Arctic deep-sea hydrothermal vent system. Stand Genomic Sci 2017; 12:5. [PMID: 28078050 PMCID: PMC5219744 DOI: 10.1186/s40793-016-0219-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki's Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. A substantial number of genes encoding for extracellular polysaccharide synthesis pathways, curli fibres and attachment to surfaces could mediate adhesion in the biofilm and may contribute to the biofilm formation. In addition to aerobic respiration, the complete denitrification pathway and genes for sulphide oxidation e.g. sulphide:quinone reductase are present in the genome. sulphide:quinone reductase and denitrification may serve as detoxification systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched environment. The information gained from the genome gives a greater insight in the functional role of L. profundi LP1T in the biofilm and its adaption strategy in an extreme environment.
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Affiliation(s)
- Juliane Wissuwa
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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16
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Baltar F, Lundin D, Palovaara J, Lekunberri I, Reinthaler T, Herndl GJ, Pinhassi J. Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO 2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic. Front Microbiol 2016; 7:1670. [PMID: 27818655 PMCID: PMC5073097 DOI: 10.3389/fmicb.2016.01670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/06/2016] [Indexed: 02/05/2023] Open
Abstract
To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
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Affiliation(s)
- Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
- Department of Marine Sciences, University of OtagoDunedin, New Zealand
- National Institute of Water and Atmospheric Research (NIWA)/University of Otago Research Centre for OceanographyDunedin, New Zealand
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
| | - Joakim Palovaara
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
| | - Itziar Lekunberri
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
- Institut Català de Recerca de l'AiguaGirona, Spain
| | - Thomas Reinthaler
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
| | - Gerhard J. Herndl
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
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17
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Song Y, Kaster AK, Vollmers J, Song Y, Davison PA, Frentrup M, Preston GM, Thompson IP, Murrell JC, Yin H, Hunter CN, Huang WE. Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea. Microb Biotechnol 2016; 10:125-137. [PMID: 27748032 PMCID: PMC5270752 DOI: 10.1111/1751-7915.12420] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 07/19/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022] Open
Abstract
Cell sorting coupled with single-cell genomics is a powerful tool to circumvent cultivation of microorganisms and reveal microbial 'dark matter'. Single-cell Raman spectra (SCRSs) are label-free biochemical 'fingerprints' of individual cells, which can link the sorted cells to their phenotypic information and ecological functions. We employed a novel Raman-activated cell ejection (RACE) approach to sort single bacterial cells from a water sample in the Red Sea based on SCRS. Carotenoids are highly diverse pigments and play an important role in phototrophic bacteria, giving strong and distinctive Raman spectra. Here, we showed that individual carotenoid-containing cells from a Red Sea sample were isolated based on the characteristic SCRS. RACE-based single-cell genomics revealed putative novel functional genes related to carotenoid and isoprenoid biosynthesis, as well as previously unknown phototrophic microorganisms including an unculturable Cyanobacteria spp. The potential of Raman sorting coupled to single-cell genomics has been demonstrated.
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Affiliation(s)
- Yizhi Song
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Anne-Kristin Kaster
- Leibniz Institute DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - John Vollmers
- Leibniz Institute DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - Yanqing Song
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Martinique Frentrup
- Leibniz Institute DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Huabing Yin
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
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18
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Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiol Mol Biol Rev 2016; 80:929-54. [PMID: 27630250 DOI: 10.1128/mmbr.00003-16] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
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19
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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: 462] [Impact Index Per Article: 51.3] [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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20
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Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME JOURNAL 2015; 10:1102-12. [PMID: 26574687 DOI: 10.1038/ismej.2015.196] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 01/17/2023]
Abstract
Proteorhodopsins (PR) are light-driven proton pumps widely distributed in bacterioplankton. Although they have been thoroughly studied for more than a decade, it is still unclear how the proton motive force (pmf) generated by PR is used in most organisms. Notably, very few PR-containing bacteria show growth enhancement in the light. It has been suggested that the presence of specific functions within a genome may define the different PR-driven light responses. Thus, comparing closely related organisms that respond differently to light is an ideal setup to identify the mechanisms involved in PR light-enhanced growth. Here, we analyzed the transcriptomes of three PR-harboring Flavobacteria strains of the genus Dokdonia: Dokdonia donghaensis DSW-1(T), Dokdonia MED134 and Dokdonia PRO95, grown in identical seawater medium in light and darkness. Although only DSW-1(T) and MED134 showed light-enhanced growth, all strains expressed their PR genes at least 10 times more in the light compared with dark. According to their genomes, DSW-1(T) and MED134 are vitamin-B1 auxotrophs, and their vitamin-B1 TonB-dependent transporters (TBDT), accounted for 10-18% of all pmf-dependent transcripts. In contrast, the expression of vitamin-B1 TBDT was 10 times lower in the prototroph PRO95, whereas its vitamin-B1 synthesis genes were among the highest expressed. Our data suggest that light-enhanced growth in DSW-1(T) and MED134 derives from the use of PR-generated pmf to power the uptake of vitamin-B1, essential for central carbon metabolism, including the TCA cycle. Other pmf-generating mechanisms available in darkness are probably insufficient to power transport of enough vitamin-B1 to support maximum growth of these organisms.
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21
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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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22
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Feng S, Powell SM, Wilson R, Bowman JP. Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels. J Proteome Res 2015; 14:3848-58. [DOI: 10.1021/acs.jproteome.5b00241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shi Feng
- Food
Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Hobart, Tasmania 7005, Australia
| | - Shane M. Powell
- Food
Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Hobart, Tasmania 7005, Australia
| | - Richard Wilson
- Central
Science Laboratory, University of Tasmania, Sandy Bay, Hobart, Tasmania 7005, Australia
| | - John P. Bowman
- Food
Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Hobart, Tasmania 7005, Australia
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23
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Courties A, Riedel T, Rapaport A, Lebaron P, Suzuki MT. Light-driven increase in carbon yield is linked to maintenance in the proteorhodopsin-containing Photobacterium angustum S14. Front Microbiol 2015. [PMID: 26217320 PMCID: PMC4498439 DOI: 10.3389/fmicb.2015.00688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A type of photoheterotrophic bacteria contain a transmembrane light-driven proton pump called proteorhodopsins (PRs). Due to the prevalence of these organisms in the upper water column of the World's Ocean, and their potential for light-driven ATP generation, they have been suggested to significantly influence energy and matter flows in the biosphere. To date, evidence for the significance of the light-driven metabolism of PR-containing prokaryotes has been obtained by comparing growth in batch culture, under light versus dark conditions, and it appears that responses to light are linked to unfavorable conditions, which so far have not been well parameterized. We studied light responses to carbon yields of the PR-containing Photobacterium angustum S14 using continuous culture conditions and light-dark cycles. We observed significant effects of light-dark cycles compared to dark controls, as well as significant differences between samples after 12 h illumination versus 12 h darkness. However, these effects were only observed under higher cell counts and lower pH associated with higher substrate concentrations. Under these substrate levels Pirt's maintenance coefficient was higher when compared to lower substrate dark controls, and decreased under light-dark cycles. It appears that light responses by P. angustum S14 are induced by the energetic status of the cells rather than by low substrate concentrations.
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Affiliation(s)
- Alicia Courties
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique , Banyuls-sur-Mer, France
| | - Thomas Riedel
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique , Banyuls-sur-Mer, France
| | - Alain Rapaport
- INRA-Supagro, UMR MISTEA , Montpellier, France ; INRA-INRIA, MODEMIC Team , Sophia Antipolis, France
| | - Philippe Lebaron
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique , Banyuls-sur-Mer, France
| | - Marcelino T Suzuki
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique , Banyuls-sur-Mer, France
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24
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Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. ISME JOURNAL 2014; 9:1410-22. [PMID: 25478683 DOI: 10.1038/ismej.2014.225] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 11/08/2022]
Abstract
Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.
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25
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Leneveu-Jenvrin C, Connil N, Bouffartigues E, Papadopoulos V, Feuilloley MGJ, Chevalier S. Structure-to-function relationships of bacterial translocator protein (TSPO): a focus on Pseudomonas. Front Microbiol 2014; 5:631. [PMID: 25477872 PMCID: PMC4237140 DOI: 10.3389/fmicb.2014.00631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 11/04/2014] [Indexed: 12/21/2022] Open
Abstract
The translocator protein (TSPO), which was previously designated as the peripheral-type benzodiazepine receptor, is a 3.5 billion year-old evolutionarily conserved protein expressed by most Eukarya, Archae and Bacteria, but its organization and functions differ remarkably. By taking advantage of the genomic data available on TSPO, we focused on bacterial TSPO and attempted to define functions of TSPO in Pseudomonas via in silico approaches. A tspo ortholog has been identified in several fluorescent Pseudomonas. This protein presents putative binding motifs for cholesterol and PK 11195, which is a specific drug ligand of mitochondrial TSPO. While it is a common surface distribution, the sense of insertion and membrane localization differ between α- and γ-proteobacteria. Experimental published data and STRING analysis of common TSPO partners in fluorescent Pseudomonas indicate a potential role of TSPO in the oxidative stress response, iron homeostasis and virulence expression. In these bacteria, TSPO could also take part in signal transduction and in the preservation of membrane integrity.
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Affiliation(s)
- Charlène Leneveu-Jenvrin
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Nathalie Connil
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Vassilios Papadopoulos
- Department of Medicine, Research Institute of the McGill University Health Centre, McGill University Montreal, QC, Canada
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
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Ng KK, Shi X, Yao Y, Ng HY. Bio-entrapped membrane reactor and salt marsh sediment membrane bioreactor for the treatment of pharmaceutical wastewater: treatment performance and microbial communities. BIORESOURCE TECHNOLOGY 2014; 171:265-273. [PMID: 25203236 DOI: 10.1016/j.biortech.2014.08.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/14/2014] [Accepted: 08/17/2014] [Indexed: 06/03/2023]
Abstract
In this study, a bio-entrapped membrane reactor (BEMR) and a salt marsh sediment membrane bioreactor (SMSMBR) were evaluated to study the organic treatment performance of pharmaceutical wastewater. The influences of hydraulic retention time (HRT) and salinity were also studied. The conventional biomass in the BEMR cannot tolerate well of the hypersaline conditions, resulting in total chemical oxygen demand (TCOD) removal efficiency of 54.2-68.0%. On the other hand, microorganisms in the SMSMBR, which was seeded from coastal shore, strived and was able to degrade the complex organic in the presence of salt effectively, achieving 74.7-90.9% of TCOD removal efficiencies. Marine microorganisms able to degrade recalcitrant compounds and utilize hydrocarbon compounds were found in the SMSMBR, which resulted in higher organic removal efficiency than the BEMR. However, specific nitrifying activity decreased and inhibited due to the saline effect that led to poor ammonia nitrogen removal.
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Affiliation(s)
- Kok Kwang Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Xueqing Shi
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Yinuo Yao
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - How Yong Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore.
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Tully BJ, Sachdeva R, Heidelberg KB, Heidelberg JF. Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data. MICROBIOME 2014; 2:34. [PMID: 25258679 PMCID: PMC4164334 DOI: 10.1186/2049-2618-2-34] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/20/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome. RESULTS Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment. CONCLUSIONS Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.
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Affiliation(s)
- Benjamin J Tully
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
| | - Rohan Sachdeva
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
| | - Karla B Heidelberg
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
| | - John F Heidelberg
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
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Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol 2014; 12:686-98. [PMID: 25134618 DOI: 10.1038/nrmicro3326] [Citation(s) in RCA: 538] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Marine phytoplankton blooms are annual spring events that sustain active and diverse bloom-associated bacterial populations. Blooms vary considerably in terms of eukaryotic species composition and environmental conditions, but a limited number of heterotrophic bacterial lineages - primarily members of the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria - dominate these communities. In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling. On the basis of selected field and laboratory-based studies of flavobacteria and roseobacters, distinct metabolic strategies are emerging for these archetypal phytoplankton-associated taxa, which provide insights into the underlying mechanisms that dictate their behaviours during blooms.
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Affiliation(s)
- Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845, USA
| | - Gary R LeCleir
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845, USA
| | - Christopher A Gulvik
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - José M González
- Department of Microbiology, University of La Laguna, ES-38200 La Laguna, Spain
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Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria. Proc Natl Acad Sci U S A 2014; 111:E3650-8. [PMID: 25136122 DOI: 10.1073/pnas.1402617111] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proteorhodopsin (PR) is present in half of surface ocean bacterioplankton, where its light-driven proton pumping provides energy to cells. Indeed, PR promotes growth or survival in different bacteria. However, the metabolic pathways mediating the light responses remain unknown. We analyzed growth of the PR-containing Dokdonia sp. MED134 (where light-stimulated growth had been found) in seawater with low concentrations of mixed [yeast extract and peptone (YEP)] or single (alanine, Ala) carbon compounds as models for rich and poor environments. We discovered changes in gene expression revealing a tightly regulated shift in central metabolic pathways between light and dark conditions. Bacteria showed relatively stronger light responses in Ala compared with YEP. Notably, carbon acquisition pathways shifted toward anaplerotic CO2 fixation in the light, contributing 31 ± 8% and 24 ± 6% of the carbon incorporated into biomass in Ala and YEP, respectively. Thus, MED134 was a facultative double mixotroph, i.e., photo- and chemotrophic for its energy source and using both bicarbonate and organic matter as carbon sources. Unexpectedly, relative expression of the glyoxylate shunt genes (isocitrate lyase and malate synthase) was >300-fold higher in the light--but only in Ala--contributing a more efficient use of carbon from organic compounds. We explored these findings in metagenomes and metatranscriptomes and observed similar prevalence of the glyoxylate shunt compared with PR genes and highest expression of the isocitrate lyase gene coinciding with highest solar irradiance. Thus, regulatory interactions between dissolved organic carbon quality and central metabolic pathways critically determine the fitness of surface ocean bacteria engaging in PR phototrophy.
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Lekunberri I, Gasol JM, Acinas SG, Gómez-Consarnau L, Crespo BG, Casamayor EO, Massana R, Pedrós-Alió C, Pinhassi J. The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea. Syst Appl Microbiol 2014; 37:216-28. [PMID: 24462268 DOI: 10.1016/j.syapm.2013.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/10/2013] [Accepted: 11/13/2013] [Indexed: 10/25/2022]
Abstract
Microbial isolates are useful models for physiological and ecological studies and can also be used to reassemble genomes from metagenomic analyses. However, the phylogenetic diversity that can be found among cultured marine bacteria may vary significantly depending on the isolation. Therefore, this study describes a set of 136 bacterial isolates obtained by traditional isolation techniques from the Blanes Bay Microbial Observatory, of which seven strains have had the whole genome sequenced. The complete set was compared to a series of environmental sequences obtained by culture-independent techniques (60 DGGE sequences and 303 clone library sequences) previously obtained by molecular methods. In this way, each isolate was placed in both its "ecological" (time of year, nutrient limitation, chlorophyll and temperature values) context or setting, and its "phylogenetic" landscape (i.e. similar organisms that were found by culture-independent techniques, when they were relevant, and when they appeared). Nearly all isolates belonged to the Gammaproteobacteria, Alphaproteobacteria, or the Bacteroidetes (70, 40 and 20 isolates, respectively). Rarefaction analyses showed similar diversity patterns for sequences from isolates and molecular approaches, except for Alphaproteobacteria where cultivation retrieved a higher diversity per unit effort. Approximately 30% of the environmental clones and isolates formed microdiversity clusters constrained at 99% 16S rRNA gene sequence identity, but the pattern was different in Bacteroidetes (less microdiversity) than in the other main groups. Seventeen cases (12.5%) of nearly complete (98-100%) rRNA sequence identity between isolates and environmental sequences were found: nine in the Alphaproteobacteria, five in the Gammaproteobacteria, and three in the Bacteroidetes, indicating that cultivation could be used to obtain at least some organisms representative of the various taxa detected by molecular methods. Collectively, these results illustrated the largely unexplored potential of culturing on standard media for complementing the study of microbial diversity by culture-independent techniques and for obtaining phylogenetically distinct model organisms from natural seawater.
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Affiliation(s)
- Itziar Lekunberri
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Laura Gómez-Consarnau
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain; Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182 Kalmar, Sweden
| | - Bibiana G Crespo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Emilio O Casamayor
- Centre d'Estudis Avançats de Blanes - CSIC, Accés a la cala Sant Francesc 14, 17300 Blanes, Catalunya, Spain
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Carlos Pedrós-Alió
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182 Kalmar, Sweden.
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Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, Huettel B, Stüber K, Reinhardt R, Harder J, Glöckner FO, Amann RI, Teeling H. The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. Appl Environ Microbiol 2013; 79:6813-22. [PMID: 23995932 PMCID: PMC3811500 DOI: 10.1128/aem.01937-13] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/26/2013] [Indexed: 11/20/2022] Open
Abstract
In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901(T)), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.
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Affiliation(s)
- Alexander J. Mann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | | | - Sixing Huang
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Johannes Werner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | - Peng Xing
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tristan Barbeyron
- National Center of Scientific Research/Pierre and Marie Curie University Paris 6, UMR 7139 Marine Plants and Biomolecules, Roscoff, Bretagne, France
| | | | - Kurt Stüber
- Max Planck Genome Centre Cologne, Cologne, Germany
| | | | - Jens Harder
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013; 8:e76704. [PMID: 24086761 PMCID: PMC3784431 DOI: 10.1371/journal.pone.0076704] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022] Open
Abstract
Flavobacteria are important members of aquatic and terrestrial bacterial communities, displaying extreme variations in lifestyle, geographical distribution and genome size. They are ubiquitous in soil, but are often strongly enriched in the rhizosphere and phyllosphere of plants. In this study, we compared the genome of a root-associated Flavobacterium that we recently isolated, physiologically characterized and sequenced, to 14 additional Flavobacterium genomes, in order to pinpoint characteristics associated with its high abundance in the rhizosphere. Interestingly, flavobacterial genomes vary in size by approximately two-fold, with terrestrial isolates having predominantly larger genomes than those from aquatic environments. Comparative functional gene analysis revealed that terrestrial and aquatic Flavobacteria generally segregated into two distinct clades. Members of the aquatic clade had a higher ratio of peptide and protein utilization genes, whereas members of the terrestrial clade were characterized by a significantly higher abundance and diversity of genes involved in metabolism of carbohydrates such as xylose, arabinose and pectin. Interestingly, genes encoding glycoside hydrolase (GH) families GH78 and GH106, responsible for rhamnogalacturonan utilization (exclusively associated with terrestrial plant hemicelluloses), were only present in terrestrial clade genomes, suggesting adaptation of the terrestrial strains to plant-related carbohydrate metabolism. The Peptidase/GH ratio of aquatic clade Flavobacteria was significantly higher than that of terrestrial strains (1.7±0.7 and 9.7±4.7, respectively), supporting the concept that this relation can be used to infer Flavobacterium lifestyles. Collectively, our research suggests that terrestrial Flavobacteria are highly adapted to plant carbohydrate metabolism, which appears to be a key to their profusion in plant environments.
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Affiliation(s)
- Max Kolton
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
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Kwon SK, Kim BK, Song JY, Kwak MJ, Lee CH, Yoon JH, Oh TK, Kim JF. Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. Genome Biol Evol 2013; 5:187-99. [PMID: 23292138 PMCID: PMC3595038 DOI: 10.1093/gbe/evs134] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rhodopsin-containing marine microbes such as those in the class Flavobacteriia play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488–494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.
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Affiliation(s)
- Soon-Kyeong Kwon
- Systems and Synthetic Biology Research Center, Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
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Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One 2013; 8:e57487. [PMID: 23526944 PMCID: PMC3587595 DOI: 10.1371/journal.pone.0057487] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/22/2013] [Indexed: 01/10/2023] Open
Abstract
Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.
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Affiliation(s)
- Thomas Riedel
- Helmholtz-Centre for Infection Research, Braunschweig, Germany.
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Akram N, Palovaara J, Forsberg J, Lindh MV, Milton DL, Luo H, González JM, Pinhassi J. Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp. AND4. Environ Microbiol 2013; 15:1400-15. [PMID: 23379752 DOI: 10.1111/1462-2920.12085] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/08/2013] [Indexed: 01/21/2023]
Abstract
Proteorhodopsin (PR), a ubiquitous membrane photoprotein in marine environments, acts as a light-driven proton pump and can provide energy for bacterial cellular metabolism. However, knowledge of factors that regulate PR gene expression in different bacteria remains strongly limited. Here, experiments with Vibrio sp. AND4 showed that PR phototrophy promoted survival only in cells from stationary phase and not in actively growing cells. PR gene expression was tightly regulated, with very low values in exponential phase, a pronounced peak at the exponential/stationary phase intersection, and a marked decline in stationary phase. Thus, PR gene expression at the entry into stationary phase preceded, and could therefore largely explain, the stationary phase light-induced survival response in AND4. Further experiments revealed nutrient limitation, not light exposure, regulated this differential PR expression. Screening of available marine vibrios showed that the PR gene, and thus the potential for PR phototrophy, is found in at least three different clusters in the genus Vibrio. In an ecological context, our findings suggest that some PR-containing bacteria adapted to the exploitation of nutrient-rich micro-environments rely on a phase of relatively slowly declining resources to mount a cellular response preparing them for adverse conditions dispersed in the water column.
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Affiliation(s)
- Neelam Akram
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, SE-39182, Kalmar, Sweden
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Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, Pedrós-Alió C. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME JOURNAL 2013; 7:1026-37. [PMID: 23303374 DOI: 10.1038/ismej.2012.169] [Citation(s) in RCA: 408] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Fernández-Gómez B, Fernàndez-Guerra A, Casamayor EO, González JM, Pedrós-Alió C, Acinas SG. Patterns and architecture of genomic islands in marine bacteria. BMC Genomics 2012; 13:347. [PMID: 22839777 PMCID: PMC3478194 DOI: 10.1186/1471-2164-13-347] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance. RESULTS We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the β-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome. CONCLUSIONS Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Pg Marítim de la Barceloneta 37-49, ES-08003 Barcelona, Spain
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