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Imaura Y, Okamoto S, Hino T, Ogami Y, Katayama YA, Tanimura A, Inoue M, Kamikawa R, Yoshida T, Sako Y. Isolation, Genomic Sequence and Physiological Characterization of Parageobacillus sp. G301, an Isolate Capable of Both Hydrogenogenic and Aerobic Carbon Monoxide Oxidation. Appl Environ Microbiol 2023; 89:e0018523. [PMID: 37219438 PMCID: PMC10304674 DOI: 10.1128/aem.00185-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023] Open
Abstract
Prokaryotes that can oxidize carbon monoxide (CO oxidizers) can use this gas as a source of carbon or energy. They oxidize carbon monoxide with carbon monoxide dehydrogenases (CODHs): these are divided into nickel-containing CODH (Ni-CODH), which are sensitive to O2, and molybdenum-containing CODH (Mo-CODH), which can function aerobically. The oxygen conditions required for CO oxidizers to oxidize CO may be limited, as those which have been isolated and characterized so far contain either Ni- or Mo-CODH. Here, we report a novel CO oxidizer, Parageobacillus sp. G301, which is capable of CO oxidation using both types of CODH based on genomic and physiological characterization. This thermophilic, facultatively anaerobic Bacillota bacterium was isolated from the sediments of a freshwater lake. Genomic analyses revealed that strain G301 possessed both Ni-CODH and Mo-CODH. Genome-based reconstruction of its respiratory machinery and physiological investigations indicated that CO oxidation by Ni-CODH was coupled with H2 production (proton reduction), whereas CO oxidation by Mo-CODH was coupled with O2 reduction under aerobic conditions and nitrate reduction under anaerobic conditions. G301 would thus be able to thrive via CO oxidation under a wide range of conditions, from aerobic environments to anaerobic environments, even with no terminal electron acceptors other than protons. Comparative genome analyses revealed no significant differences in genome structures and encoded cellular functions, except for CO oxidation between CO oxidizers and non-CO oxidizers in the genus Parageobacillus; CO oxidation genes are retained exclusively for CO metabolism and related respiration. IMPORTANCE Microbial CO oxidation has received much attention because it contributes to global carbon cycling in addition to functioning as a remover of CO, which is toxic to many organisms. Some microbial CO oxidizers, including both bacteria and archaea, exhibit sister relationships with non-CO oxidizers even in genus-level monophyletic groups. In this study, we demonstrated that a new isolate, Parageobacillus sp. G301, is capable of both anaerobic (hydrogenogenic) and aerobic CO oxidation, which has not been previously reported. The discovery of this new isolate, which is versatile in CO metabolism, will accelerate research on CO oxidizers with diverse CO metabolisms, expanding our understanding of microbial diversity. Through comparative genomic analyses, we propose that CO oxidation genes are not essential genetic elements in the genus Parageobacillus, providing insights into the factors which shape the punctate distribution of CO oxidizers in the prokaryote tree, even in genus-level monophyletic groups.
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Affiliation(s)
| | | | - Taiki Hino
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yusuke Ogami
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Ayumi Tanimura
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- R-GIRO, Ritsumeikan University, Kusatsu, Shiga, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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2
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Molecular hydrogen in seawater supports growth of diverse marine bacteria. Nat Microbiol 2023; 8:581-595. [PMID: 36747116 DOI: 10.1038/s41564-023-01322-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
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3
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Basaltic Lava Tube Hosts a Putative Novel Genus in the Family Solirubrobacteraceae. Microbiol Resour Announc 2022; 11:e0049922. [PMID: 36190248 PMCID: PMC9583782 DOI: 10.1128/mra.00499-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of a putative new genus and species, Siliceabacter maunaloa, in the family Solirubrobacteraceae. The members of this family of Actinobacteria are generally Gram positive and mesophilic. Found within a Hawaiian lava tube, this microbe illuminates the types of prokaryotes inhabiting secondary minerals in subsurface basaltic environments.
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4
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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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5
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Giebel HA, Wolterink M, Brinkhoff T, Simon M. Complementary energy acquisition via aerobic anoxygenic photosynthesis and carbon monoxide oxidation by Planktomarina temperata of the Roseobacter group. FEMS Microbiol Ecol 2020; 95:5437672. [PMID: 31055603 DOI: 10.1093/femsec/fiz050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
In marine pelagic ecosystems energy is often the limiting factor for growth of heterotrophic bacteria. Aerobic anoxygenic photosynthesis (AAP) and oxidation of carbon monoxide (CO) are modes to acquire complementary energy, but their significance in abundant and characteristic pelagic marine bacteria has not been well studied. In long-term batch culture experiments we found that Planktomarina temperata RCA23, representing the largest and most prominent subcluster of the Roseobacter group, maintains 2-3-fold higher cell numbers in the stationary and declining phase when grown in a light-dark cycle relative to dark conditions. Light enables P. temperata to continue to replicate its DNA during the stationary phase relative to a dark control such that when reinoculated into fresh medium growth resumed two days earlier than in control cultures. In cultures grown in the dark and supplemented with CO, cell numbers in the stationary phase remained significantly higher than in an unsupplemented control. Furthermore, repeated spiking with CO until day 372 resulted in significant CO consumption relative to an unsupplemented control. P. temperata represents a prominent marine pelagic bacterium for which AAP and CO consumption, to acquire complementary energy, have been documented.
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Affiliation(s)
- Helge-Ansgar Giebel
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Mathias Wolterink
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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6
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Alonso-Sáez L, Morán XAG, González JM. Transcriptional Patterns of Biogeochemically Relevant Marker Genes by Temperate Marine Bacteria. Front Microbiol 2020; 11:465. [PMID: 32265888 PMCID: PMC7098952 DOI: 10.3389/fmicb.2020.00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Environmental microbial gene expression patterns remain largely unexplored, particularly at interannual time scales. We analyzed the variability in the expression of marker genes involved in ecologically relevant biogeochemical processes at a temperate Atlantic site over two consecutive years. Most of nifH transcripts, involved in nitrogen (N) fixation, were affiliated with the symbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa, suggesting a key role as N providers in this system. The expression of nifH and amoA (i.e., marker for ammonia oxidation) showed consistent maxima in summer and autumn, respectively, suggesting a temporal succession of these important N cycling processes. The patterns of expression of genes related to the oxidation of carbon monoxide (coxL) and reduced sulfur (soxB) were different from that of amoA, indicating alternate timings for these energy conservation strategies. We detected expression of alkaline phosphatases, induced under phosphorus limitation, in agreement with the reported co-limitation by this nutrient at the study site. In contrast, low-affinity phosphate membrane transporters (pit) typically expressed under phosphorus luxury conditions, were mainly detected in post-bloom conditions. Rhodobacteraceae dominated the expression of soxB, coxL and ureases, while Pelagibacteraceae dominated the expression of proteorhodopsins. Bacteroidetes and Gammaproteobacteria were major contributors to the uptake of inorganic nutrients (pit and amt transporters). Yet, in autumn, Thauma- and Euryarchaeota unexpectedly contributed importantly to the uptake of ammonia and phosphate, respectively. We provide new hints on the active players and potential dynamics of ecologically relevant functions in situ, highlighting the potential of metatranscriptomics to provide significant input to future omics-driven marine ecosystem assessment.
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Affiliation(s)
- Laura Alonso-Sáez
- Marine Research Division, AZTI, Sukarrieta, Spain.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
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7
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Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME JOURNAL 2019; 13:2868-2881. [PMID: 31358912 PMCID: PMC6794299 DOI: 10.1038/s41396-019-0479-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/22/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022]
Abstract
Carbon monoxide (CO) is a ubiquitous atmospheric trace gas produced by natural and anthropogenic sources. Some aerobic bacteria can oxidize atmospheric CO and, collectively, they account for the net loss of ~250 teragrams of CO from the atmosphere each year. However, the physiological role, genetic basis, and ecological distribution of this process remain incompletely resolved. In this work, we addressed these knowledge gaps through culture-based and culture-independent work. We confirmed through shotgun proteomic and transcriptional analysis that the genetically tractable aerobic soil actinobacterium Mycobacterium smegmatis upregulates expression of a form I molydenum-copper carbon monoxide dehydrogenase by 50-fold when exhausted for organic carbon substrates. Whole-cell biochemical assays in wild-type and mutant backgrounds confirmed that this organism aerobically respires CO, including at sub-atmospheric concentrations, using the enzyme. Contrary to current paradigms on CO oxidation, the enzyme did not support chemolithoautotrophic growth and was dispensable for CO detoxification. However, it significantly enhanced long-term survival, suggesting that atmospheric CO serves a supplemental energy source during organic carbon starvation. Phylogenetic analysis indicated that atmospheric CO oxidation is widespread and an ancestral trait of CO dehydrogenases. Homologous enzymes are encoded by 685 sequenced species of bacteria and archaea, including from seven dominant soil phyla, and we confirmed genes encoding this enzyme are abundant and expressed in terrestrial and marine environments. On this basis, we propose a new survival-centric model for the evolution of aerobic CO oxidation and conclude that, like atmospheric H2, atmospheric CO is a major energy source supporting persistence of aerobic heterotrophic bacteria in deprived or changeable environments.
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8
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Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. Metabolic potential and
in situ
activity of marine Marinimicrobia bacteria in an anoxic water column. Environ Microbiol 2017; 19:4392-4416. [DOI: 10.1111/1462-2920.13879] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Cory C. Padilla
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern DenmarkOdense Denmark
| | - Frank J. Stewart
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
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9
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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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10
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Brüggemann M, Hayeck N, Bonnineau C, Pesce S, Alpert PA, Perrier S, Zuth C, Hoffmann T, Chen J, George C. Interfacial photochemistry of biogenic surfactants: a major source of abiotic volatile organic compounds. Faraday Discuss 2017; 200:59-74. [DOI: 10.1039/c7fd00022g] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Films of biogenic compounds exposed to the atmosphere are ubiquitously found on the surfaces of cloud droplets, aerosol particles, buildings, plants, soils and the ocean. These air/water interfaces host countless amphiphilic compounds concentrated there with respect to in bulk water, leading to a unique chemical environment. Here, photochemical processes at the air/water interface of biofilm-containing solutions were studied, demonstrating abiotic VOC production from authentic biogenic surfactants under ambient conditions. Using a combination of online-APCI-HRMS and PTR-ToF-MS, unsaturated and functionalized VOCs were identified and quantified, giving emission fluxes comparable to previous field and laboratory observations. Interestingly, VOC fluxes increased with the decay of microbial cells in the samples, indicating that cell lysis due to cell death was the main source for surfactants and VOC production. In particular, irradiation of samples containing solely biofilm cells without matrix components exhibited the strongest VOC production upon irradiation. In agreement with previous studies, LC-MS measurements of the liquid phase suggested the presence of fatty acids and known photosensitizers, possibly inducing the observed VOC productionviaperoxy radical chemistry. Up to now, such VOC emissions were directly accounted to high biological activity in surface waters. However, the results obtained suggest that abiotic photochemistry can lead to similar emissions into the atmosphere, especially in less biologically-active regions. Furthermore, chamber experiments suggest that oxidation (O3/OH radicals) of the photochemically-produced VOCs leads to aerosol formation and growth, possibly affecting atmospheric chemistry and climate-related processes, such as cloud formation or the Earth’s radiation budget.
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Affiliation(s)
| | - Nathalie Hayeck
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- IRCELYON
- Villeurbanne
| | - Chloé Bonnineau
- Irstea
- UR MALY
- Centre de Lyon-Villeurbanne
- F-69616 Villeurbanne
- France
| | - Stéphane Pesce
- Irstea
- UR MALY
- Centre de Lyon-Villeurbanne
- F-69616 Villeurbanne
- France
| | - Peter A. Alpert
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- IRCELYON
- Villeurbanne
| | | | - Christoph Zuth
- Institute of Inorganic and Analytical Chemistry
- Johannes Gutenberg-Universität
- 55128 Mainz
- Germany
| | - Thorsten Hoffmann
- Institute of Inorganic and Analytical Chemistry
- Johannes Gutenberg-Universität
- 55128 Mainz
- Germany
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3)
- Fudan Tyndall Centre
- Fudan University
- Shanghai 200433
- China
| | - Christian George
- Univ Lyon
- Université Claude Bernard Lyon 1
- CNRS
- IRCELYON
- Villeurbanne
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11
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Giebel HA, Klotz F, Voget S, Poehlein A, Grosser K, Teske A, Brinkhoff T. Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. Stand Genomic Sci 2016; 11:81. [PMID: 27777651 PMCID: PMC5064897 DOI: 10.1186/s40793-016-0201-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 10/04/2016] [Indexed: 10/24/2022] Open
Abstract
The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community. The draft genome comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and energy source and is able to grow on several hydroxylated and substituted aromatic compounds. Based on 16S rRNA gene comparison the closest described and validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is lacking several phenotypic and genomic characteristics specific for the genus Phaeobacter. Phylogenomic analyses based on the whole genome support extensive genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially by using the secretion system type IV. Our physiological observations are consistent with the genomic and phylogenomic analyses and support that strain O3.65 is a novel species of a new genus within the Rhodobacteraceae.
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Affiliation(s)
- Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Franziska Klotz
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Katrin Grosser
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC USA
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
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12
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Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms. Appl Environ Microbiol 2015; 82:1324-1333. [PMID: 26682854 DOI: 10.1128/aem.03595-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/12/2015] [Indexed: 12/25/2022] Open
Abstract
Surveys of the coxL gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of coxL sequences encompassing the atypical genotype coxL type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available coxL reference genome sequences, this unusual genotype was assigned to an unknown member of the Deltaproteobacteria, with the coxL sequence from Haliangium ochraceum being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the coxL group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of Deltaproteobacteria was too small to account for the abundance of the coxL group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of coxL genotypes and CO uptake activity in soil. We found that most of the coxL genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to Actinobacteria and Alphaproteobacteria. Our analysis did not provide any evidence that coxL group x genotypes belonged to Deltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical coxL group x genotype are mixotrophic K-strategists.
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13
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Cunliffe M. Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3. FEMS Microbiol Ecol 2015; 92:fiv150. [PMID: 26613749 DOI: 10.1093/femsec/fiv150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 11/13/2022] Open
Abstract
Purines are nitrogen-rich compounds that are widely distributed in the marine environment and are an important component of the dissolved organic nitrogen (DON) pool. Even though purines have been shown to be degraded by bacterioplankton, the identities of marine bacteria capable of purine degradation and their underlying catabolic mechanisms are currently unknown. This study shows that Ruegeria pomeroyi, a model marine bacterium and Marine Roseobacter Clade (MRC) representative, utilizes xanthine as a source of carbon and nitrogen. The R. pomeroyi genome contains putative genes that encode xanthine dehydrogenase (XDH), which is expressed during growth with xanthine. RNAseq-based analysis of the R. pomeroyi transcriptome revealed that the transcription of an XDH-initiated catabolic pathway is up-regulated during growth with xanthine, with transcription greatest when xanthine was the only available carbon source. The RNAseq-deduced pathway indicates that glyoxylate and ammonia are the key intermediates from xanthine degradation. Utilising a laboratory model, this study has identified the potential genes and catabolic pathway active during xanthine degradation. The ability of R. pomeroyi to utilize xanthine provides novel insights into the capabilities of the MRC that may contribute to their success in marine ecosystems and the potential biogeochemical importance of the group in processing DON.
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Affiliation(s)
- Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK Marine Biology and Ecology Research Centre, Marine Institute, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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14
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Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark. Curr Opin Microbiol 2015; 25:33-9. [PMID: 25863027 DOI: 10.1016/j.mib.2015.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/07/2015] [Accepted: 03/16/2015] [Indexed: 11/24/2022]
Abstract
Prokaryotes are extremely abundant in the ocean where they drive biogeochemical cycles. The recent development and application of -omics techniques has provided an astonishing amount of information revealing the existence of a vast diversity of functional genes and a large heterogeneity within each gene. The big challenge for microbial ecologists is now to understand the ecological relevance of this variability for ecosystem functioning, a question that remains largely understudied. This brief review highlights some of the latest advances in the study of the diversity of biogeochemically relevant functional genes in the sunlit ocean.
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Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling. ISME JOURNAL 2014; 9:760-9. [PMID: 25148480 DOI: 10.1038/ismej.2014.149] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/03/2014] [Accepted: 07/11/2014] [Indexed: 11/08/2022]
Abstract
Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.
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Hanson BT, Hewson I, Madsen EL. Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling. MICROBIAL ECOLOGY 2014; 67:520-39. [PMID: 24425229 DOI: 10.1007/s00248-013-0346-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/06/2013] [Indexed: 05/15/2023]
Abstract
Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.
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Affiliation(s)
- Buck T Hanson
- Department of Microbiology, B57A Wing Hall, Cornell University, Ithaca, NY, 14853, USA
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Durham BP, Grote J, Whittaker KA, Bender SJ, Luo H, Grim SL, Brown JM, Casey JR, Dron A, Florez-Leiva L, Krupke A, Luria CM, Mine AH, Nigro OD, Pather S, Talarmin A, Wear EK, Weber TS, Wilson JM, Church MJ, DeLong EF, Karl DM, Steward GF, Eppley JM, Kyrpides NC, Schuster S, Rappé MS. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genomic Sci 2014; 9:632-45. [PMID: 25197450 PMCID: PMC4148974 DOI: 10.4056/sigs.4998989] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.
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Affiliation(s)
- Bryndan P Durham
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Jana Grote
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Kerry A Whittaker
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Sara J Bender
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Haiwei Luo
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Sharon L Grim
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Julia M Brown
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - John R Casey
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Antony Dron
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Observatoire Océanologique de Villefranche, Villefranche-sur-mer, France
| | - Lennin Florez-Leiva
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Universidad Del Magdalena, Santa Marta, Colombia
| | - Andreas Krupke
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Max Plank Institute for Marine Microbiology, Bremen, Germany
| | - Catherine M Luria
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
| | - Aric H Mine
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Olivia D Nigro
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Santhiska Pather
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; School for Marine Science and Technology, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, USA
| | - Agathe Talarmin
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Earth System Science, University of California Irvine, Irvine, CA, USA
| | - Emma K Wear
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Thomas S Weber
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Atmospheric and Ocean Sciences, University of California Los Angeles, Los Angeles, California, USA
| | - Jesse M Wilson
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; School of Natural Sciences, University of California Merced, Merced, California, USA
| | - Matthew J Church
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Edward F DeLong
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David M Karl
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Grieg F Steward
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - John M Eppley
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nikos C Kyrpides
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Stephan Schuster
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Singapore Centre on Environmental Life Sciences Engineering, Singapore
| | - Michael S Rappé
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA ; Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
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Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria. Proc Natl Acad Sci U S A 2014; 111:2710-5. [PMID: 24550299 DOI: 10.1073/pnas.1317834111] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) is a common osmolyte found in a variety of marine biota and has been detected at nanomolar concentrations in oceanic surface waters. TMAO can serve as an important nutrient for ecologically important marine heterotrophic bacteria, particularly the SAR11 clade and marine Roseobacter clade (MRC). However, the enzymes responsible for TMAO catabolism and the membrane transporter required for TMAO uptake into microbial cells have yet to be identified. We show here that the enzyme TMAO demethylase (Tdm) catalyzes the first step in TMAO degradation. This enzyme represents a large group of proteins with an uncharacterized domain (DUF1989). The function of TMAO demethylase in a representative from the SAR11 clade (strain HIMB59) and in a representative of the MRC (Ruegeria pomeroyi DSS-3) was confirmed by heterologous expression of tdm (the gene encoding Tdm) in Escherichia coli. In R. pomeroyi, mutagenesis experiments confirmed that tdm is essential for growth on TMAO. We also identified a unique ATP-binding cassette transporter (TmoXWV) found in a variety of marine bacteria and experimentally confirmed its specificity for TMAO through marker exchange mutagenesis and lacZ reporter assays of the promoter for genes encoding this transporter. Both Tdm and TmoXWV are particularly abundant in natural seawater assemblages and actively expressed, as indicated by a number of recent metatranscriptomic and metaproteomic studies. These data suggest that TMAO represents a significant, yet overlooked, nutrient for marine bacteria.
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