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Hying ZT, Miller TJ, Loh CY, Bazurto JV. Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase. Appl Environ Microbiol 2024; 90:e0209023. [PMID: 38534142 PMCID: PMC11267896 DOI: 10.1128/aem.02090-23] [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: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium Methylorubrum extorquens PA1 might metabolize GB encountered in its native environment. M. extorquens PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that M. extorquens PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative Methylobacterium species and generates the one-carbon metabolism intermediate formaldehyde, which M. extorquens utilizes as a source of energy. Our results support a model where suppressor mutations in Mext_3745 or ftsH (Mext_4840) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.IMPORTANCEOvercoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium Methylorubrum extorquens have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in M. extorquens and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
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Affiliation(s)
- Zachary T. Hying
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Tyler J. Miller
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Chin Yi Loh
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Jannell V. Bazurto
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
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2
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Parekh T, Tsai M, Spiro S. Choline degradation in Paracoccus denitrificans: identification of sources of formaldehyde. J Bacteriol 2024; 206:e0008124. [PMID: 38501746 PMCID: PMC11025334 DOI: 10.1128/jb.00081-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Paracoccus denitrificans is a facultative methylotroph that can grow on methanol and methylamine as sole sources of carbon and energy. Both are oxidized to formaldehyde and then to formate, so growth on C1 substrates induces the expression of genes encoding enzymes required for the oxidation of formaldehyde and formate. This induction involves a histidine kinase response regulator pair (FlhSR) that is likely triggered by formaldehyde. Catabolism of some complex organic substrates (e.g., choline and L-proline betaine) also generates formaldehyde. Thus, flhS and flhR mutants that fail to induce expression of the formaldehyde catabolic enzymes cannot grow on methanol, methylamine, and choline. Choline is oxidized to glycine via glycine betaine, dimethylglycine, and sarcosine. By exploring flhSR growth phenotypes and the activities of a promoter and enzyme known to be upregulated by formaldehyde, we identify the oxidative demethylations of glycine betaine, dimethylglycine, and sarcosine as sources of formaldehyde. Growth on glycine betaine, dimethylglycine, and sarcosine is accompanied by the production of up to three, two, and one equivalents of formaldehyde, respectively. Genetic evidence implicates two orthologous monooxygenases in the oxidation of glycine betaine. Interestingly, one of these appears to be a bifunctional enzyme that also oxidizes L-proline betaine (stachydrine). We present preliminary evidence to suggest that growth on L-proline betaine induces expression of a formaldehyde dehydrogenase distinct from the enzyme induced during growth on other formaldehyde-generating substrates.IMPORTANCEThe bacterial degradation of one-carbon compounds (methanol and methylamine) and some complex multi-carbon compounds (e.g., choline) generates formaldehyde. Formaldehyde is toxic and must be removed, which can be done by oxidation to formate and then to carbon dioxide. These oxidations provide a source of energy; in some species, the CO2 thus generated can be assimilated into biomass. Using the Gram-negative bacterium Paracoccus denitrificans as the experimental model, we infer that oxidation of choline to glycine generates up to three equivalents of formaldehyde, and we identify the three steps in the catabolic pathway that are responsible. Our work sheds further light on metabolic pathways that are likely important in a variety of environmental contexts.
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Affiliation(s)
- Trusha Parekh
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Marcus Tsai
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Stephen Spiro
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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3
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Lipsman V, Shlakhter O, Rocha J, Segev E. Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix. NPJ Biofilms Microbiomes 2024; 10:36. [PMID: 38561371 PMCID: PMC10984933 DOI: 10.1038/s41522-024-00510-y] [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: 10/09/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Marine ecosystems are influenced by phytoplankton aggregation, which affects processes like marine snow formation and harmful events such as marine mucilage outbreaks. Phytoplankton secrete exopolymers, creating an extracellular matrix (ECM) that promotes particle aggregation. This ECM attracts heterotrophic bacteria, providing a nutrient-rich and protective environment. In terrestrial environments, bacterial colonization near primary producers relies on attachment and the formation of multidimensional structures like biofilms. Bacteria were observed attaching and aggregating within algal-derived exopolymers, but it is unclear if bacteria produce an ECM that contributes to this colonization. This study, using Emiliania huxleyi algae and Phaeobacter inhibens bacteria in an environmentally relevant model system, reveals a shared algal-bacterial ECM scaffold that promotes algal-bacterial aggregation. Algal exudates play a pivotal role in promoting bacterial colonization, stimulating bacterial exopolysaccharide (EPS) production, and facilitating a joint ECM formation. A bacterial biosynthetic pathway responsible for producing a specific EPS contributing to bacterial ECM formation is identified. Genes from this pathway show increased expression in algal-rich environments. These findings highlight the underestimated role of bacteria in aggregate-mediated processes in marine environments, offering insights into algal-bacterial interactions and ECM formation, with implications for understanding and managing natural and perturbed aggregation events.
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Affiliation(s)
- Valeria Lipsman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Olesia Shlakhter
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Jorge Rocha
- Programa de Agricultura en Zonas Áridas, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, 23096, México
| | - Einat Segev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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4
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Westermann LM, Lidbury ID, Li CY, Wang N, Murphy AR, Aguilo Ferretjans MDM, Quareshy M, Shanmugan M, Torcello-Requena A, Silvano E, Zhang YZ, Blindauer CA, Chen Y, Scanlan DJ. Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles. SCIENCE ADVANCES 2023; 9:eadf5122. [PMID: 37126561 PMCID: PMC10132767 DOI: 10.1126/sciadv.adf5122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
In marine systems, the availability of inorganic phosphate can limit primary production leading to bacterial and phytoplankton utilization of the plethora of organic forms available. Among these are phospholipids that form the lipid bilayer of all cells as well as released extracellular vesicles. However, information on phospholipid degradation is almost nonexistent despite their relevance for biogeochemical cycling. Here, we identify complete catabolic pathways for the degradation of the common phospholipid headgroups phosphocholine (PC) and phosphorylethanolamine (PE) in marine bacteria. Using Phaeobacter sp. MED193 as a model, we provide genetic and biochemical evidence that extracellular hydrolysis of phospholipids liberates the nitrogen-containing substrates ethanolamine and choline. Transporters for ethanolamine (EtoX) and choline (BetT) are ubiquitous and highly expressed in the global ocean throughout the water column, highlighting the importance of phospholipid and especially PE catabolism in situ. Thus, catabolic activation of the ethanolamine and choline degradation pathways, subsequent to phospholipid metabolism, specifically links, and hence unites, the phosphorus, nitrogen, and carbon cycles.
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Affiliation(s)
- Linda M. Westermann
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Ian D. E. A. Lidbury
- Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Chun-Yang Li
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew R. J. Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | | | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Muralidharan Shanmugan
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | - Eleonora Silvano
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | | | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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5
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Schroer WF, Kepner HE, Uchimiya M, Mejia C, Rodriguez LT, Reisch CR, Moran MA. Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME COMMUNICATIONS 2023; 3:37. [PMID: 37185952 PMCID: PMC10130141 DOI: 10.1038/s43705-023-00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.
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Affiliation(s)
- William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hannah E Kepner
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Catalina Mejia
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | | | - Christopher R Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
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6
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Aminolipids elicit functional trade-offs between competitiveness and bacteriophage attachment in Ruegeria pomeroyi. THE ISME JOURNAL 2023; 17:315-325. [PMID: 36477724 PMCID: PMC9938194 DOI: 10.1038/s41396-022-01346-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Lipids play a crucial role in maintaining cell integrity and homeostasis with the surrounding environment. Cosmopolitan marine roseobacter clade (MRC) and SAR11 clade bacteria are unique in that, in addition to glycerophospholipids, they also produce an array of amino acid-containing lipids that are conjugated with beta-hydroxy fatty acids through an amide bond. Two of these aminolipids, the ornithine aminolipid (OL) and the glutamine aminolipid (QL), are synthesized using the O-acetyltransferase OlsA. Here, we demonstrate that OL and QL are present in both the inner and outer membranes of the Gram-negative MRC bacterium Ruegeria pomeroyi DSS-3. In an olsA mutant, loss of these aminolipids is compensated by a concurrent increase in glycerophospholipids. The inability to produce aminolipids caused significant changes in the membrane proteome, with the membrane being less permeable and key nutrient transporters being downregulated while proteins involved in the membrane stress response were upregulated. Indeed, the import of 14C-labelled choline and dimethylsulfoniopropionate, as a proxy for the transport of key marine nutrients across membranes, was significantly impaired in the olsA mutant. Moreover, the olsA mutant was significantly less competitive than the wild type (WT) being unable to compete with the WT strain in co-culture. However, the olsA mutant unable to synthesize these aminolipids is less susceptible to phage attachment. Together, these data reveal a critical role for aminolipids in the ecophysiology of this important clade of marine bacteria and a trade-off between growth and avoidance of bacteriophage attachment.
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7
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Ferrer-González FX, Hamilton M, Smith CB, Schreier JE, Olofsson M, Moran MA. Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda. ISME COMMUNICATIONS 2023; 3:5. [PMID: 36690682 PMCID: PMC9870897 DOI: 10.1038/s43705-023-00212-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/24/2023]
Abstract
Dissolved primary production released into seawater by marine phytoplankton is a major source of carbon fueling heterotrophic bacterial production in the ocean. The composition of the organic compounds released by healthy phytoplankton is poorly known and difficult to assess with existing chemical methods. Here, expression of transporter and catabolic genes by three model marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) was used as a biological sensor of metabolites released from the picoeukaryote Micromonas commoda RCC299. Bacterial expression responses indicated that the three species together recognized 38 picoeukaryote metabolites. This was consistent with the Micromonas expression of genes for starch metabolism and synthesis of peptidoglycan-like intermediates. A comparison of the hypothesized Micromonas exometabolite pool with that of the diatom Thalassiosira pseudonana CCMP1335, analyzed previously with the same biological sensor method, indicated that both phytoplankton released organic acids, nucleosides, and amino acids, but differed in polysaccharide and organic nitrogen release. Future ocean conditions are expected to favor picoeukaryotic phytoplankton over larger-celled microphytoplankton. Results from this study suggest that such a shift could alter the substrate pool available to heterotrophic bacterioplankton.
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Affiliation(s)
| | - Maria Hamilton
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Christa B Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jeremy E Schreier
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Malin Olofsson
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
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8
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Uchimiya M, Schroer W, Olofsson M, Edison AS, Moran MA. Diel investments in metabolite production and consumption in a model microbial system. THE ISME JOURNAL 2022; 16:1306-1317. [PMID: 34921302 PMCID: PMC9038784 DOI: 10.1038/s41396-021-01172-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 12/01/2022]
Abstract
Organic carbon transfer between surface ocean photosynthetic and heterotrophic microbes is a central but poorly understood process in the global carbon cycle. In a model community in which diatom extracellular release of organic molecules sustained growth of a co-cultured bacterium, we determined quantitative changes in the diatom endometabolome and the bacterial uptake transcriptome over two diel cycles. Of the nuclear magnetic resonance (NMR) peaks in the diatom endometabolites, 38% had diel patterns with noon or mid-afternoon maxima; the remaining either increased (36%) or decreased (26%) through time. Of the genes in the bacterial uptake transcriptome, 94% had a diel pattern with a noon maximum; the remaining decreased over time (6%). Eight diatom endometabolites identified with high confidence were matched to the bacterial genes mediating their utilization. Modeling of these coupled inventories with only diffusion-based phytoplankton extracellular release could not reproduce all the patterns. Addition of active release mechanisms for physiological balance and bacterial recognition significantly improved model performance. Estimates of phytoplankton extracellular release range from only a few percent to nearly half of annual net primary production. Improved understanding of the factors that influence metabolite release and consumption by surface ocean microbes will better constrain this globally significant carbon flux.
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Affiliation(s)
- Mario Uchimiya
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, US
| | - William Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US
| | - Malin Olofsson
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden
| | - Arthur S Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, US
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US.
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9
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Gavira JA, Cámara-Artigas A, Neira JL, Torres de Pinedo JM, Sánchez P, Ortega E, Martinez-Rodríguez S. Structural insights into choline- O-sulfatase reveal the molecular determinants for ligand binding. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:669-682. [PMID: 35503214 PMCID: PMC9063841 DOI: 10.1107/s2059798322003709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022]
Abstract
The first structures of a choline-O-sulfatase bound to different ligands are reported. Choline-O-sulfatase (COSe; EC 3.1.6.6) is a member of the alkaline phosphatase (AP) superfamily, and its natural function is to hydrolyze choline-O-sulfate into choline and sulfate. Despite its natural function, the major interest in this enzyme resides in the landmark catalytic/substrate promiscuity of sulfatases, which has led to attention in the biotechnological field due to their potential in protein engineering. In this work, an in-depth structural analysis of wild-type Sinorhizobium (Ensifer) meliloti COSe (SmeCOSe) and its C54S active-site mutant is reported. The binding mode of this AP superfamily member to both products of the reaction (sulfate and choline) and to a substrate-like compound are shown for the first time. The structures further confirm the importance of the C-terminal extension of the enzyme in becoming part of the active site and participating in enzyme activity through dynamic intra-subunit and inter-subunit hydrogen bonds (Asn146A–Asp500B–Asn498B). These residues act as the ‘gatekeeper’ responsible for the open/closed conformations of the enzyme, in addition to assisting in ligand binding through the rearrangement of Leu499 (with a movement of approximately 5 Å). Trp129 and His145 clamp the quaternary ammonium moiety of choline and also connect the catalytic cleft to the C-terminus of an adjacent protomer. The structural information reported here contrasts with the proposed role of conformational dynamics in promoting the enzymatic catalytic proficiency of an enzyme.
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10
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Boysen AK, Durham BP, Kumler W, Key RS, Heal KR, Carlson L, Groussman RD, Armbrust EV, Ingalls AE. Glycine betaine uptake and metabolism in marine microbial communities. Environ Microbiol 2022; 24:2380-2403. [PMID: 35466501 PMCID: PMC9321204 DOI: 10.1111/1462-2920.16020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/24/2022] [Accepted: 04/15/2022] [Indexed: 11/27/2022]
Abstract
Glycine betaine (GBT) is a compatible solute in high concentrations in marine microorganisms. As a component of labile organic matter, GBT has complex biochemical potential as a substrate for microbial use that is unconstrained in the environment. Here we determine the uptake kinetics and metabolic fate of GBT in two natural microbial communities in the North Pacific characterized by different nitrate concentrations. Dissolved GBT had maximum uptake rates of 0.36 and 0.56 nM h−1 with half‐saturation constants of 79 and 11 nM in the high nitrate and low nitrate stations respectively. During multiday incubations, most GBT taken into cells was retained as a compatible solute. Stable isotopes derived from the added GBT were also observed in other metabolites, including choline, carnitine and sarcosine, suggesting that GBT was used for biosynthesis and for catabolism to pyruvate and ammonium. Where nitrate was scarce, GBT was primarily metabolized via demethylation to glycine. Gene transcript data were consistent with SAR11 using GBT as a source of methyl groups to fuel the methionine cycle. Where nitrate concentrations were higher, more GBT was partitioned for lipid biosynthesis by both bacteria and eukaryotic phytoplankton. Our data highlight unexpected metabolic pathways and potential routes of microbial metabolite exchange.
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Affiliation(s)
- Angela K Boysen
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Bryndan P Durham
- Department of Biology, Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - William Kumler
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Rebecca S Key
- Department of Biology, Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Laura Carlson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Ryan D Groussman
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | | | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
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11
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Luo D, Wang X, Feng X, Tian M, Wang S, Tang SL, Ang P, Yan A, Luo H. Population differentiation of Rhodobacteraceae along with coral compartments. THE ISME JOURNAL 2021; 15:3286-3302. [PMID: 34017056 PMCID: PMC8528864 DOI: 10.1038/s41396-021-01009-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/04/2023]
Abstract
Coral mucus, tissue, and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we sampled bacteria inhabiting a prevalent coral species Platygyra acuta and sequenced genomes of 234 isolates comprising two populations in Rhodobacteraceae, an alphaproteobacterial lineage representing a significant but variable proportion (5-50%) of the coral microbiota. The Ruegeria population (20 genomes) contains three clades represented by eight, six, and six isolates predominantly sampled from the skeleton (outgroup), mucus (clade-M), and skeleton (clade-S), respectively. The clade-M possesses functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine, and L-proline), whereas the clade-S uniquely harbors traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including genomes of 24 related isolates (including seven new genomes) from other marine environments suggest that clade-M and clade-S may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The unassigned Rhodobacteraceae population (214 genomes) varies only at a few dozen nucleotide sites across the whole genomes, but the number of between-compartment migration events predicted by the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism diversifying microbial populations. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.
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Affiliation(s)
- Danli Luo
- grid.10784.3a0000 0004 1937 0482Simon 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 ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaojun Wang
- grid.10784.3a0000 0004 1937 0482Simon 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 ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaoyuan Feng
- grid.10784.3a0000 0004 1937 0482Simon 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 ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mengdan Tian
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- grid.10784.3a0000 0004 1937 0482Simon 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
| | - Sen-Lin Tang
- grid.506939.0Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Put Ang
- grid.10784.3a0000 0004 1937 0482Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Aixin Yan
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Shatin, Hong Kong SAR
| | - Haiwei Luo
- grid.10784.3a0000 0004 1937 0482Simon 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 ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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12
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Murphy ARJ, Scanlan DJ, Chen Y, Adams NBP, Cadman WA, Bottrill A, Bending G, Hammond JP, Hitchcock A, Wellington EMH, Lidbury IDEA. Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle. Nat Commun 2021; 12:4554. [PMID: 34315891 PMCID: PMC8316502 DOI: 10.1038/s41467-021-24646-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
The planktonic synthesis of reduced organophosphorus molecules, such as alkylphosphonates and aminophosphonates, represents one half of a vast global oceanic phosphorus redox cycle. Whilst alkylphosphonates tend to accumulate in recalcitrant dissolved organic matter, aminophosphonates do not. Here, we identify three bacterial 2-aminoethylphosphonate (2AEP) transporters, named AepXVW, AepP and AepSTU, whose synthesis is independent of phosphate concentrations (phosphate-insensitive). AepXVW is found in diverse marine heterotrophs and is ubiquitously distributed in mesopelagic and epipelagic waters. Unlike the archetypal phosphonate binding protein, PhnD, AepX has high affinity and high specificity for 2AEP (Stappia stellulata AepX Kd 23 ± 4 nM; methylphosphonate Kd 3.4 ± 0.3 mM). In the global ocean, aepX is heavily transcribed (~100-fold>phnD) independently of phosphate and nitrogen concentrations. Collectively, our data identifies a mechanism responsible for a major oxidation process in the marine phosphorus redox cycle and suggests 2AEP may be an important source of regenerated phosphate and ammonium, which are required for oceanic primary production.
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Affiliation(s)
- Andrew R J Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Nathan B P Adams
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
- Nanotemper Technologies GmbH, Flößergasse 4, Munich, Germany
| | - William A Cadman
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Andrew Bottrill
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Gary Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - John P Hammond
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Ian D E A Lidbury
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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13
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de Bruyn WJ, Clark CD, Harrison AW, Senstad M, Hok S. The degradation of acetaldehyde in estuary waters in Southern California, USA. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:35811-35821. [PMID: 33675494 DOI: 10.1007/s11356-021-13232-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Acetaldehyde plays an important role in oxidative cycles in the troposphere. Estimates of its air-water flux are important in global models. Biological degradation is believed to be the dominant loss process in water, but there have been few measurements, none in estuaries. Acetaldehyde degradation rates were measured in surface waters at the inflow to the Upper Newport Back Bay estuary in Orange County, Southern California, USA, over a 6-month period including the rainy winter season. Deuterated acetaldehyde was added to filtered and unfiltered water samples incubated in glass syringes, and its loss analyzed by purge and trap gas chromatography mass spectrometry. Filtered samples showed no significant degradation, suggesting that particle-mediated degradation is the dominant removal process. Correlation between measured degradation rate constants in unfiltered incubations and bacteria counts suggests the loss is due to microorganisms. Degradation in unfiltered samples followed first-order kinetics, with rate constants ranging from 0.0006 to 0.025 min-1 (k; average 0.0043 ± 0.006 min-1). Turnover (1/k) ranged from 40 to 1667 min, consistent with prior studies in coastal waters. Acetaldehyde concentrations in the estuary are estimated to range from 30 to ~500 nM (average ~250 nM). Results suggest the estuary is a source of acetaldehyde to the atmosphere.
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Affiliation(s)
- Warren J de Bruyn
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 98266, USA
| | - Catherine D Clark
- Department of Chemistry, College of Science and Engineering, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA.
| | - Aaron W Harrison
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 98266, USA
| | - Mary Senstad
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 98266, USA
| | - Sovanndara Hok
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 98266, USA
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14
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Abstract
Reports of biogenic methane (CH4) synthesis associated with a range of organisms have steadily accumulated in the literature. This has not happened without controversy and in most cases the process is poorly understood at the gene and enzyme levels. In marine and freshwater environments, CH4 supersaturation of oxic surface waters has been termed the "methane paradox" because biological CH4 synthesis is viewed to be a strictly anaerobic process carried out by O2-sensitive methanogens. Interest in this phenomenon has surged within the past decade because of the importance of understanding sources and sinks of this potent greenhouse gas. In our work on Yellowstone Lake in Yellowstone National Park, we demonstrate microbiological conversion of methylamine to CH4 and isolate and characterize an Acidovorax sp. capable of this activity. Furthermore, we identify and clone a gene critical to this process (encodes pyridoxylamine phosphate-dependent aspartate aminotransferase) and demonstrate that this property can be transferred to Escherichia coli with this gene and will occur as a purified enzyme. This previously unrecognized process sheds light on environmental cycling of CH4, suggesting that O2-insensitive, ecologically relevant aerobic CH4 synthesis is likely of widespread distribution in the environment and should be considered in CH4 modeling efforts.
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15
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Kröber E, Cunningham MR, Peixoto J, Spurgin L, Wischer D, Kruger R, Kumaresan D. Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:195-208. [PMID: 33484104 DOI: 10.1111/1758-2229.12927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 05/22/2023]
Abstract
Methylated amines are ubiquitous in the environment and play a role in regulating the earth's climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph, Gemmobacter sp. LW-1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilization as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilization is within members of the bacterial genus Gemmobacter. Seven genomes of different Gemmobacter species isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that methylamine utilization is a distinctive feature of selected members of the genus Gemmobacter, namely G. aquatilis, G. lutimaris, G. sp. HYN0069, G. caeni and G. sp. LW-1 have the genetic potential while others (G. megaterium and G. nectariphilus) have not.
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Affiliation(s)
- Eileen Kröber
- Department of Symbiosis, Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mark R Cunningham
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Julianna Peixoto
- Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Lewis Spurgin
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Daniela Wischer
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Ricardo Kruger
- Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Deepak Kumaresan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
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16
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Ngugi DK, Ziegler M, Duarte CM, Voolstra CR. Genomic Blueprint of Glycine Betaine Metabolism in Coral Metaorganisms and Their Contribution to Reef Nitrogen Budgets. iScience 2020; 23:101120. [PMID: 32438323 PMCID: PMC7240134 DOI: 10.1016/j.isci.2020.101120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
The osmolyte glycine betaine (GB) ranks among the few widespread biomolecules in all three domains of life. In corals, tissue concentrations of GB are substantially higher than in the ambient seawater. However, the synthetic routes remain unresolved, questioning whether intracellular GB originates from de novo synthesis or heterotrophic input. Here we show that the genomic blueprint of coral metaorganisms encode the biosynthetic and degradation machinery for GB. Member organisms also adopted the prokaryotic high-affinity carrier-mediated uptake of exogenous GB, rendering coral reefs potential sinks of marine dissolved GB. The machinery metabolizing GB is highly expressed in the coral model Aiptasia and its microalgal symbionts, signifying GB's role in the cnidarian-dinoflagellate symbiosis. We estimate that corals store between 106–109 grams of GB globally, representing about 16% of their nitrogen biomass. Our findings provide a framework for further mechanistic studies addressing GB's role in coral biology and reef ecosystem nitrogen cycling. Coral tissues contain high concentrations of the osmolyte glycine betaine Corals and their microbial symbionts can produce and degrade glycine betaine High gene expression patterns signifies role in coral-microbial symbiosis Glycine betaine is estimated to encompass 16% of the coral's nitrogen biomass
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Affiliation(s)
- David K Ngugi
- Leibniz Institute DSMZ - German Culture Collection for Microorganisms and Cell Cultures, Braunschweig, Germany; Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Maren Ziegler
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Animal Ecology and Systematics, Justus-Liebig-University, Giessen, Germany
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Biology, University of Konstanz, Konstanz 78457, Germany.
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17
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de la Haba RR, López-Hermoso C, Sánchez-Porro C, Konstantinidis KT, Ventosa A. Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio. Front Microbiol 2019; 10:2104. [PMID: 31572321 PMCID: PMC6749099 DOI: 10.3389/fmicb.2019.02104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 12/02/2022] Open
Abstract
In the genomic era phylogenetic relationship among prokaryotes can be inferred from the core orthologous genes (OGs) or proteins in order to elucidate their evolutionary history and current taxonomy should benefits of that. The genus Salinivibrio belongs to the family Vibrionaceae and currently includes only five halophilic species, in spite the fact that new strains are very frequently isolated from hypersaline environments. Species belonging to this genus have undergone several reclassifications and, moreover, there are many strains of Salinivibrio with available genomes which have not been affiliated to the existing species or have been wrongly designated. Therefore, a phylogenetic study using the available genomic information is necessary to clarify the relationships of existing strains within this genus and to review their taxonomic affiliation. For that purpose, we have also sequenced the first complete genome of a Salinivibrio species, Salinivibrio kushneri AL184T, which was employed as a reference to order the contigs of the draft genomes of the type strains of the current species of this genus, as well as to perform a comparative analysis with all the other available Salinivibrio sp. genomes. The genome of S. kushneri AL184T was assembled in two circular chromosomes (with sizes of 2.84 Mb and 0.60 Mb, respectively), as typically occurs in members of the family Vibrionaceae, with nine complete ribosomal operons, which might explain the fast growing rate of salinivibrios cultured under laboratory conditions. Synteny analysis among the type strains of the genus revealed a high level of genomic conservation in both chromosomes, which allow us to hypothesize a slow speciation process or homogenization events taking place in this group of microorganisms to be tested experimentally in the future. Phylogenomic and orthologous average nucleotide identity (OrthoANI)/average amino acid identity (AAI) analyses also evidenced the elevated level of genetic relatedness within members of this genus and allowed to group all the Salinivibrio strains with available genomes in seven separated species. Genome-scale attribute study of the salinivibrios identified traits related to polar flagellum, facultatively anaerobic growth and osmotic response, in accordance to the phenotypic features described for species of this genus.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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18
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Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux. ISME JOURNAL 2019; 13:2536-2550. [PMID: 31227817 DOI: 10.1038/s41396-019-0455-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/08/2019] [Accepted: 05/03/2019] [Indexed: 11/09/2022]
Abstract
Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.
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19
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Wang C, Wang Z, You Y, Xu W, Lv Z, Liu Z, Chen W, Shi Y. Response of Arthrobacter QD 15-4 to dimethyl phthalate by regulating energy metabolism and ABC transporters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:146-152. [PMID: 30825737 DOI: 10.1016/j.ecoenv.2019.02.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Ubiquitous dimethyl phthalate (DMP) has severely threatened environmental safety and the health of organisms. Therefore, it is necessary to degrade DMP, removing it from the environment. Microbiological degradation is an efficient and safe method for degrading DMP. In this study, the response of Arthrobacter QD 15-4 to DMP was investigated. The results showed that the growth of Arthrobacter QD 15-4 was not impacted by DMP and Arthrobacter QD 15-4 could degrade DMP. RNA-Seq and RT-qPCR results showed that DMP treatment caused some changes in the expression of key genes in Arthrobacter QD 15-4. The transcriptional expressions of pstSCAB and phoU were downregulated by DMP. The transcriptional expressions of potACD, gluBC, oppAB, pdhAB, aceAF, gltA were upregulated by DMP. The genes are mainly involved in regulating energy metabolism and ATP-binding cassette (ABC) transporters. The increasing of pyruvic acid and citrate in Arthrobacter QD 15-4 further supported the energy metabolism was improved by DMP. It was clearly shown that Arthrobacter QD 15-4 made response to dimethyl phthalate by regulating energy metabolism and ABC transporters.
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Affiliation(s)
- Chunlong Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China.
| | - Yimin You
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zhihang Lv
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zeping Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Wenjing Chen
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yiran Shi
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
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20
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Martínez-Pérez C, Mohr W, Schwedt A, Dürschlag J, Callbeck CM, Schunck H, Dekaezemacker J, Buckner CRT, Lavik G, Fuchs BM, Kuypers MMM. Metabolic versatility of a novel N 2 -fixing Alphaproteobacterium isolated from a marine oxygen minimum zone. Environ Microbiol 2018; 20:755-768. [PMID: 29194930 DOI: 10.1111/1462-2920.14008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 11/27/2022]
Abstract
The N2 -fixing (diazotrophic) community in marine ecosystems is dominated by non-cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru. The new species belongs to the genus Sagittula (Rhodobacteraceae, Alphaproteobacteria) and its capability to fix N2 was confirmed in laboratory experiments. Genome sequencing revealed that it is a strict heterotroph with a high versatility in substrate utilization and energy acquisition mechanisms. Pathways for sulfide oxidation and nitrite reduction to nitrous oxide are encoded in the genome and might explain the presence throughout the Peruvian OMZ. The genome further indicates that this novel organism could be in direct interaction with other microbes or particles. NanoSIMS analyses were used to compare the metabolic potential of S. castanea with single-cell activity in situ; however, N2 fixation by this diazotroph could not be detected at the isolation site. While the biogeochemical impact of S. castanea is yet to be resolved, its abundance and widespread distribution suggests that its potential to contribute to the marine N input could be significant at a larger geographical scale.
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Affiliation(s)
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anne Schwedt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Julia Dürschlag
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Harald Schunck
- Institute for General Microbiology, University of Kiel, Kiel, Germany
| | | | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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21
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Schulz A, Hermann L, Freibert SA, Bönig T, Hoffmann T, Riclea R, Dickschat JS, Heider J, Bremer E. Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues. Environ Microbiol 2017; 19:4599-4619. [PMID: 28892254 DOI: 10.1111/1462-2920.13924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 01/04/2023]
Abstract
Ectoine and hydroxyectoine are effective microbial osmostress protectants, but can also serve as versatile nutrients for bacteria. We have studied the genetic regulation of ectoine and hydroxyectoine import and catabolism in the marine Roseobacter species Ruegeria pomeroyi and identified three transcriptional regulators involved in these processes: the GabR/MocR-type repressor EnuR, the feast and famine-type regulator AsnC and the two-component system NtrYX. The corresponding genes are widely associated with ectoine and hydroxyectoine uptake and catabolic gene clusters (enuR, asnC), and with microorganisms predicted to consume ectoines (ntrYX). EnuR contains a covalently bound pyridoxal-5'-phosphate as a co-factor and the chemistry underlying the functioning of MocR/GabR-type regulators typically requires a system-specific low molecular mass effector molecule. Through ligand binding studies with purified EnuR, we identified N-(alpha)-L-acetyl-2,4-diaminobutyric acid and L-2,4-diaminobutyric acid as inducers for EnuR that are generated through ectoine catabolism. AsnC/Lrp-type proteins can wrap DNA into nucleosome-like structures, and we found that the asnC gene was essential for use of ectoines as nutrients. Furthermore, we discovered through transposon mutagenesis that the NtrYX two-component system is required for their catabolism. Database searches suggest that our findings have important ramifications for an understanding of the molecular biology of most microbial consumers of ectoines.
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Affiliation(s)
- Annina Schulz
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Sven-Andreas Freibert
- Department of Medicine, Institute for Cytobiology and Cytopathology, Philipps-University Marburg, Robert-Koch Str. 6, D-35032 Marburg, Germany
| | - Tobias Bönig
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Ramona Riclea
- Institute of Organic Chemistry, Technical University Braunschweig, D-38106 Braunschweig, Germany.,Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University Braunschweig, D-38106 Braunschweig, Germany.,Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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22
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Quantification of glycine betaine, choline and trimethylamine N-oxide in seawater particulates: Minimisation of seawater associated ion suppression. Anal Chim Acta 2016; 938:114-22. [PMID: 27619093 DOI: 10.1016/j.aca.2016.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/11/2016] [Accepted: 07/17/2016] [Indexed: 11/22/2022]
Abstract
A liquid chromatography/mass spectrometry (LC/MS, electrospray ionisation) method has been developed for the quantification of nitrogenous osmolytes (N-osmolytes) in the particulate fraction of natural water samples. Full method validation demonstrates the validity of the method for measuring glycine betaine (GBT), choline and trimethylamine N-oxide (TMAO) in particulates from seawater. Limits of detection were calculated as 3.5, 1.2 and 5.9 pg injected onto column (equivalent to 1.5, 0.6 and 3.9 nmol per litre) for GBT, choline and TMAO respectively. Precision of the method was typically 3% for both GBT and choline and 6% for TMAO. Collection of the particulate fraction of natural samples was achieved via in-line filtration. Resulting chromatography and method sensitivity was assessed and compared for the use of both glass fibre and polycarbonate filters during sample collection. Ion suppression was shown to be a significant cause of reduced instrument response to N-osmolytes and was associated with the presence of seawater in the sample matrix.
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23
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Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y, Schäfer H. A mechanism for bacterial transformation of dimethylsulfide to dimethylsulfoxide: a missing link in the marine organic sulfur cycle. Environ Microbiol 2016; 18:2754-66. [PMID: 27114231 DOI: 10.1111/1462-2920.13354] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/19/2016] [Indexed: 11/30/2022]
Abstract
The volatile organosulfur compound, dimethylsulfide (DMS), plays an important role in climate regulation and global sulfur biogeochemical cycles. Microbial oxidation of DMS to dimethylsulfoxide (DMSO) represents a major sink of DMS in surface seawater, yet the underlying molecular mechanisms and key microbial taxa involved are not known. Here, we reveal that Ruegeria pomeroyi, a model marine heterotrophic bacterium, can oxidize DMS to DMSO using trimethylamine monooxygenase (Tmm). Purified Tmm oxidizes DMS to DMSO at a 1:1 ratio. Mutagenesis of the tmm gene in R. pomeroyi completely abolished DMS oxidation and subsequent DMSO formation. Expression of Tmm and DMS oxidation in R. pomeroyi is methylamine-dependent and regulated at the post-transcriptional level. Considering that Tmm is present in approximately 20% of bacterial cells inhabiting marine surface waters, particularly the marine Roseobacter clade and the SAR11 clade, our observations contribute to a mechanistic understanding of biological DMSO production in surface seawater.
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Affiliation(s)
- Ian Lidbury
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Eileen Kröber
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agriculture Sciences, Urumqi, 830091, China
| | - Yijun Zhu
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK
| | - Yin Chen
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Hendrik Schäfer
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
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Abstract
Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
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Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. Appl Environ Microbiol 2016; 82:2100-2111. [PMID: 26826224 DOI: 10.1128/aem.03678-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/20/2016] [Indexed: 01/28/2023] Open
Abstract
Members of the marine Roseobacter clade are major participants in global carbon and sulfur cycles. While roseobacters are well represented in cultures, several abundant pelagic lineages, including SAG-O19, DC5-80-3, and NAC11-7, remain largely uncultivated and show evidence of genome streamlining. Here, we analyzed the partial genomes of three single cells affiliated with CHAB-I-5, another abundant but exclusively uncultivated Roseobacter lineage. Members of this lineage encode several metabolic potentials that are absent in streamlined genomes. Examples are quorum sensing and type VI secretion systems, which enable them to effectively interact with host and other bacteria. Further analysis of the CHAB-I-5 single-cell amplified genomes (SAGs) predicted that this lineage comprises members with relatively large genomes (4.1 to 4.4 Mbp) and a high fraction of noncoding DNA (10 to 12%), which is similar to what is observed in many cultured, nonstreamlined Roseobacter lineages. The four uncultured lineages, while exhibiting highly variable geographic distributions, together represent >60% of the global pelagic roseobacters. They are consistently enriched in genes encoding the capabilities of light harvesting, oxidation of "energy-rich" reduced sulfur compounds and methylated amines, uptake and catabolism of various carbohydrates and osmolytes, and consumption of abundant exudates from phytoplankton. These traits may define the global prevalence of the four lineages among marine bacterioplankton.
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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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