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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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52
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Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322. J Microbiol 2019; 57:676-687. [PMID: 31201724 DOI: 10.1007/s12275-019-9001-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/11/2019] [Accepted: 04/16/2019] [Indexed: 01/21/2023]
Abstract
Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.
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53
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Abstract
The organosulfur metabolite dimethylsulfoniopropionate (DMSP) and its enzymatic breakdown product dimethyl sulfide (DMS) have important implications in the global sulfur cycle and in marine microbial food webs. Enormous amounts of DMSP are produced in marine environments where microbial communities import and catabolize it via either the demethylation or the cleavage pathways. The enzymes that cleave DMSP are termed "DMSP lyases" and generate acrylate or hydroxypropionate, and ~107tons of DMS annually. An important environmental factor affecting DMS generation by the DMSP lyases is the availability of metal ions as these enzymes use various cofactors for catalysis. This chapter summarizes advances on bacterial DMSP catabolism, with an emphasis on various biochemical methods employed for the isolation and characterization of bacterial DMSP lyases. Strategies are presented for the purification of DMSP lyases expressed in bacterial cells. Specific conditions for the efficient isolation of apoproteins in Escherichia coli are detailed. DMSP cleavage is effectively inferred, utilizing the described HPLC-based acrylate detection assay. Finally, substrate and metal binding interactions are examined using fluorescence and UV-visible assays. Together, these methods are rapid and well suited for the biochemical and structural characterization of DMSP lyases and in the assessment of uncharacterized DMSP catabolic enzymes, and new metalloenzymes in general.
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54
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Shao X, Cao HY, Zhao F, Peng M, Wang P, Li CY, Shi WL, Wei TD, Yuan Z, Zhang XH, Chen XL, Todd JD, Zhang YZ. Mechanistic insight into 3-methylmercaptopropionate metabolism and kinetical regulation of demethylation pathway in marine dimethylsulfoniopropionate-catabolizing bacteria. Mol Microbiol 2019; 111:1057-1073. [PMID: 30677184 PMCID: PMC6850173 DOI: 10.1111/mmi.14211] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2019] [Indexed: 01/25/2023]
Abstract
The vast majority of oceanic dimethylsulfoniopropionate (DMSP) is thought to be catabolized by bacteria via the DMSP demethylation pathway. This pathway contains four enzymes termed DmdA, DmdB, DmdC and DmdD/AcuH, which together catabolize DMSP to acetylaldehyde and methanethiol as carbon and sulfur sources respectively. While molecular mechanisms for DmdA and DmdD have been proposed, little is known of the catalytic mechanisms of DmdB and DmdC, which are central to this pathway. Here, we undertake physiological, structural and biochemical analyses to elucidate the catalytic mechanisms of DmdB and DmdC. DmdB, a 3-methylmercaptopropionate (MMPA)-coenzyme A (CoA) ligase, undergoes two sequential conformational changes to catalyze the ligation of MMPA and CoA. DmdC, a MMPA-CoA dehydrogenase, catalyzes the dehydrogenation of MMPA-CoA to generate MTA-CoA with Glu435 as the catalytic base. Sequence alignment suggests that the proposed catalytic mechanisms of DmdB and DmdC are likely widely adopted by bacteria using the DMSP demethylation pathway. Analysis of the substrate affinities of involved enzymes indicates that Roseobacters kinetically regulate the DMSP demethylation pathway to ensure DMSP functioning and catabolism in their cells. Altogether, this study sheds novel lights on the catalytic and regulative mechanisms of bacterial DMSP demethylation, leading to a better understanding of bacterial DMSP catabolism.
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Affiliation(s)
- Xuan Shao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Fang Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Suzhou Institute of Shandong University, Suzhou, 215123, China
| | - Wei-Ling Shi
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Tian-Di Wei
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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55
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Gardner SG, Camp EF, Smith DJ, Kahlke T, Osman EO, Gendron G, Hume BCC, Pogoreutz C, Voolstra CR, Suggett DJ. Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave. Ecol Evol 2019; 9:938-956. [PMID: 30805132 PMCID: PMC6374667 DOI: 10.1002/ece3.4662] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/30/2022] Open
Abstract
Repeat marine heat wave-induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral-associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad-scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2-sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host-specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching-resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome community profiles. These profiles were conserved across bleached and unbleached colonies of all coral species. As this pattern could also reflect a parallel response of the microbiome to environmental changes, the detailed functional associations will need to be determined in future studies. Further understanding such microbiome-environmental interactions is likely critical to target more effective management within oceanically isolated reefs of Seychelles.
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Affiliation(s)
| | - Emma F. Camp
- University of Technology SydneyClimate Change ClusterUltimo NSW 2007Australia
| | - David J. Smith
- Coral Reef Research Unit, School of Biological SciencesUniversity of EssexColchesterUK
| | - Tim Kahlke
- University of Technology SydneyClimate Change ClusterUltimo NSW 2007Australia
| | - Eslam O. Osman
- Coral Reef Research Unit, School of Biological SciencesUniversity of EssexColchesterUK
- Marine Biology Department, Faculty of ScienceAl‐Azhar UniversityCairoEgypt
| | | | - Benjamin C. C. Hume
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Claudia Pogoreutz
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David J. Suggett
- University of Technology SydneyClimate Change ClusterUltimo NSW 2007Australia
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56
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Barriers to 3-Hydroxypropionate-Dependent Growth of Rhodobacter sphaeroides by Distinct Disruptions of the Ethylmalonyl Coenzyme A Pathway. J Bacteriol 2019; 201:JB.00556-18. [PMID: 30455284 DOI: 10.1128/jb.00556-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides is able to use 3-hydroxypropionate as the sole carbon source through the reductive conversion of 3-hydroxypropionate to propionyl coenzyme A (propionyl-CoA). The ethylmalonyl-CoA pathway is not required in this process because a crotonyl-CoA carboxylase/reductase (Ccr)-negative mutant still grew with 3-hydroxypropionate. Much to our surprise, a mutant defective for another specific enzyme of the ethylmalonyl-CoA pathway, mesaconyl-CoA hydratase (Mch), lost its ability for 3-hydroxypropionate-dependent growth. Interestingly, the Mch-deficient mutant was rescued either by introducing an additional ccr in-frame deletion that resulted in the blockage of an earlier step in the pathway or by heterologously expressing a gene encoding a thioesterase (YciA) that can act on several CoA intermediates of the ethylmalonyl-CoA pathway. The mch mutant expressing yciA metabolized only less than half of the 3-hydroxypropionate supplied, and over 50% of that carbon was recovered in the spent medium as free acids of the key intermediates mesaconyl-CoA and methylsuccinyl-CoA. A gradual increase in growth inhibition due to the blockage of consecutive steps of the ethylmalonyl-CoA pathway by gene deletions suggests that the growth defects were due to the titration of free CoA and depletion of the CoA pool in the cell rather than to detrimental effects arising from the accumulation of a specific metabolite. Recovery of carbon in mesaconate for the wild-type strain expressing yciA demonstrated that carbon flux through the ethylmalonyl-CoA pathway occurs during 3-hydroxypropionate-dependent growth. A possible role of the ethylmalonyl-CoA pathway is proposed that functions outside its known role in providing tricarboxylic acid intermediates during acetyl-CoA assimilation.IMPORTANCE Mutant analysis is an important tool utilized in metabolic studies to understand which role a particular pathway might have under certain growth conditions for a given organism. The importance of the enzyme and of the pathway in which it participates is discretely linked to the resulting phenotype observed after mutation of the corresponding gene. This work highlights the possibility of incorrectly interpreting mutant growth results that are based on studying a single unit (gene and encoded enzyme) of a metabolic pathway rather than the pathway in its entirety. This work also hints at the possibility of using an enzyme as a drug target although the enzyme may participate in a nonessential pathway and still be detrimental to the cell when inhibited.
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57
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González JM, Hernández L, Manzano I, Pedrós-Alió C. Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate. ISME JOURNAL 2019; 13:1183-1197. [PMID: 30643200 DOI: 10.1038/s41396-019-0347-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/22/2018] [Accepted: 12/25/2018] [Indexed: 11/09/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is produced mainly by phytoplankton and bacteria. It is relatively abundant and ubiquitous in the marine environment, where bacterioplankton make use of it readily as both carbon and sulfur sources. In one transformation pathway, part of the molecule becomes dimethylsulfide (DMS), which escapes into the atmosphere and plays an important role in the sulfur exchange between oceans and atmosphere. Through its other dominant catabolic pathway, bacteria are able to use it as sulfur source. During the past few years, a number of genes involved in its transformation have been characterized. Identifying genes in taxonomic groups not amenable to conventional methods of cultivation is challenging. Indeed, functional annotation of genes in environmental studies is not straightforward, considering that particular taxa are not well represented in the available sequence databases. Furthermore, many genes belong to families of paralogs with similar sequences but perhaps different functions. In this study, we develop in silico approaches to infer protein function of an environmentally important gene (dmdA) that carries out the first step in the sulfur assimilation from DMSP. The method combines a set of tools to annotate a targeted gene in genome databases and metagenome assemblies. The method will be useful to identify genes that carry out key biochemical processes in the environment.
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Affiliation(s)
- José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain.
| | - Laura Hernández
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Iris Manzano
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Carlos Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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58
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Liu J, Liu J, Zhang SH, Liang J, Lin H, Song D, Yang GP, Todd JD, Zhang XH. Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea. Front Microbiol 2018; 9:3206. [PMID: 30622530 PMCID: PMC6309047 DOI: 10.3389/fmicb.2018.03206] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The compatible solute dimethylsulfoniopropionate (DMSP), made by many marine organisms, is one of Earth's most abundant organosulfur molecules. Many marine bacteria import DMSP and can degrade it as a source of carbon and/or sulfur via DMSP cleavage or DMSP demethylation pathways, which can generate the climate active gases dimethyl sulfide (DMS) or methanthiol (MeSH), respectively. Here we used culture-dependent and -independent methods to study bacteria catabolizing DMSP in the East China Sea (ECS). Of bacterial isolates, 42.11% showed DMSP-dependent DMS (Ddd+) activity, and 12.28% produced detectable levels of MeSH. Interestingly, although most Ddd+ isolates were Alphaproteobacteria (mainly Roseobacters), many gram-positive Actinobacteria were also shown to cleave DMSP producing DMS. The mechanism by which these Actinobacteria cleave DMSP is unknown, since no known functional ddd genes have been identified in genome sequences of Ddd+Microbacterium and Agrococcus isolates or in any other sequenced Actinobacteria genomes. Gene probes to the DMSP demethylation gene dmdA and the DMSP lyase gene dddP demonstrated that these DMSP-degrading genes are abundant and widely distributed in ECS seawaters. dmdA was present in relatively high proportions in both surface (19.53% ± 6.70%) and bottom seawater bacteria (16.00% ± 8.73%). In contrast, dddP abundance positively correlated with chlorophyll a, and gradually decreased with the distance from land, which implies that the bacterial DMSP lyase gene dddP might be from bacterial groups that closely associate with phytoplankton. Bacterial community analysis showed positive correlations between Rhodobacteraceae abundance and concentrations of DMS and DMSP, further confirming the link between this abundant bacterial class and the environmental DMSP cycling.
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Affiliation(s)
- Jingli Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Ji Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Sheng-Hui Zhang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Jinchang Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Heyu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Delei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Gui-Peng Yang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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59
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Lavoie M, Galí M, Sévigny C, Kieber DJ, Sunda WG, Spiese CE, Maps F, Levasseur M. Modelling dimethylsulfide diffusion in the algal external boundary layer: implications for mutualistic and signalling roles. Environ Microbiol 2018; 20:4157-4169. [DOI: 10.1111/1462-2920.14417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 08/26/2018] [Accepted: 09/07/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Michel Lavoie
- Québec‐Océan and Unité Mixte Internationale Takuvik Ulaval‐CNRS, Département de Biologie Université Laval Québec Québec G1V 0A6 Canada
| | - Martí Galí
- Québec‐Océan and Unité Mixte Internationale Takuvik Ulaval‐CNRS, Département de Biologie Université Laval Québec Québec G1V 0A6 Canada
| | - Caroline Sévigny
- Institut des sciences de la mer de Rimouski Université du Québec à Rimouski 310 allée des Ursulines, Québec G5L 3A1 Canada
| | - David J. Kieber
- Department of Chemistry State University of New York, College of Environmental Science and Forestry Syracuse, NY 13210 USA
| | - William G. Sunda
- Department of Marine Sciences University of North Carolina 292 Old Piedmont Circle, Chapel Hill NC 27516 USA
| | - Christopher E. Spiese
- Donald J. Bettinger Department of Chemistry and Biochemistry Ohio Northern University 525 South Main St, Ada OH 45810 USA
| | - Frédéric Maps
- Québec‐Océan and Unité Mixte Internationale Takuvik Ulaval‐CNRS, Département de Biologie Université Laval Québec Québec G1V 0A6 Canada
| | - Maurice Levasseur
- Québec‐Océan and Unité Mixte Internationale Takuvik Ulaval‐CNRS, Département de Biologie Université Laval Québec Québec G1V 0A6 Canada
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60
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Barak-Gavish N, Frada MJ, Ku C, Lee PA, DiTullio GR, Malitsky S, Aharoni A, Green SJ, Rotkopf R, Kartvelishvily E, Sheyn U, Schatz D, Vardi A. Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP. SCIENCE ADVANCES 2018; 4:eaau5716. [PMID: 30397652 PMCID: PMC6200362 DOI: 10.1126/sciadv.aau5716] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/17/2018] [Indexed: 05/12/2023]
Abstract
Emiliania huxleyi is a bloom-forming microalga that affects the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide. Top-down regulation of E. huxleyi blooms has been attributed to viruses and grazers; however, the possible involvement of algicidal bacteria in bloom demise has remained elusive. We demonstrate that a Roseobacter strain, Sulfitobacter D7, that we isolated from a North Atlantic E. huxleyi bloom, exhibited algicidal effects against E. huxleyi upon coculturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying algal-bacterial interactions in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in an algal strain typically resistant to the bacterial pathogen. This enhanced virulence was highly specific to DMSP compared to addition of propionate and glycerol which had no effect on bacterial virulence. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions among marine organisms, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.
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Affiliation(s)
- Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miguel José Frada
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- The Interuniversity Institute for Marine Sciences, Eilat 88103, Israel
- Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Chuan Ku
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Peter A. Lee
- Hollings Marine Laboratory, College of Charleston, Charleston, SC 29412, USA
| | - Giacomo R. DiTullio
- Hollings Marine Laboratory, College of Charleston, Charleston, SC 29412, USA
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ron Rotkopf
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Kartvelishvily
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Sheyn
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Corresponding author.
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61
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Töpel M, Pinder MIM, Johansson ON, Kourtchenko O, Godhe A, Clarke AK. Whole-Genome Sequence of the Novel Antarctobacter heliothermus Strain SMS3, Found in Association with the Marine Diatom Skeletonema marinoi. J Genomics 2018; 6:113-116. [PMID: 30310524 PMCID: PMC6170321 DOI: 10.7150/jgen.27637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/26/2018] [Indexed: 11/30/2022] Open
Abstract
As part of an ongoing investigation into the microbiome of the marine diatom Skeletonema marinoi, the bacterial strain SMS3 was isolated from a culture of S. marinoi strain ST54, which had been propagated from a sample of top layer marine sediments taken from the Swedish west coast. We present here the sequenced genome of this bacterium, which we place in the taxon Antarctobacter heliothermus, based on a phylotaxonomic analysis and its high 16S rRNA sequence similarity to the A. heliothermus type strain DSM 11445T. Its 5,331,190 bp genome consists of a circular chromosome and three circular plasmids, and contains 5,019 CDSs. Strain SMS3 contains a phosphatidylcholine synthase gene, as well as genes involved in DMSP degradation, both of which imply a potential symbiotic relationship with its host.
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Affiliation(s)
- Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Matthew I M Pinder
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Oskar N Johansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Adrian K Clarke
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
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62
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Akob DM, Sutton JM, Fierst JL, Haase KB, Baesman S, Luther GW, Miller LG, Oremland RS. Acetylenotrophy: a hidden but ubiquitous microbial metabolism? FEMS Microbiol Ecol 2018; 94:5026170. [PMID: 29933435 PMCID: PMC7190893 DOI: 10.1093/femsec/fiy103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/29/2018] [Indexed: 11/12/2022] Open
Abstract
Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.
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Affiliation(s)
- Denise M Akob
- U. S. Geological Survey, 12201 Sunrise Valley Dr, MS 430, Reston, VA 20192 USA
| | - John M Sutton
- Department of Biological Sciences, The University of Alabama, SEC 2328, Box 870344, Tuscaloosa, AL 35487 USA
| | - Janna L Fierst
- Department of Biological Sciences, The University of Alabama, SEC 2328, Box 870344, Tuscaloosa, AL 35487 USA
| | - Karl B Haase
- U. S. Geological Survey, 12201 Sunrise Valley Dr, MS 430, Reston, VA 20192 USA
| | - Shaun Baesman
- U. S. Geological Survey, 345 Middlefield Road, MS 480, Menlo Park, CA 94025 USA
| | - George W Luther
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, Cannon Laboratory 218, Lewes, DE 19958, USA
| | - Laurence G Miller
- U. S. Geological Survey, 345 Middlefield Road, MS 480, Menlo Park, CA 94025 USA
| | - Ronald S Oremland
- U. S. Geological Survey, 345 Middlefield Road, MS 480, Menlo Park, CA 94025 USA
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63
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Lei L, Alcolombri U, Tawfik DS. Biochemical Profiling of DMSP Lyases. Methods Enzymol 2018; 605:269-289. [PMID: 29909827 DOI: 10.1016/bs.mie.2018.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dimethyl sulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms release DMS via cleavage of dimethylsulfoniopropionate (DMSP). DMSP lyases have been identified in various organisms, including bacteria, coral, and algae, thus comprising a range of gene families putatively assigned as DMSP lyases. Metagenomics may therefore provide insight regarding the presence of DMSP lyases in various marine environments, thereby promoting a better understanding of global DMS emission. However, gene counts, and even mRNA levels, do not necessarily reflect the level of DMSP cleavage activity in a given environmental sample, especially because some of the families assigned as DMSP lyases may merely exhibit promiscuous lyase activity. Here, we describe a range of biochemical profiling methods that can assign an observed DMSP lysis activity to a specific gene family. These methods include selective inhibitors and DMSP substrate analogues. Combined with genomics and metagenomics, biochemical profiling may enable a more reliable identification of the origins of DMS release in specific organisms and in crude environmental samples.
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Affiliation(s)
- Lei Lei
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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64
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Burkhardt I, Lauterbach L, Brock NL, Dickschat JS. Chemical differentiation of three DMSP lyases from the marine Roseobacter group. Org Biomol Chem 2018; 15:4432-4439. [PMID: 28485454 DOI: 10.1039/c7ob00913e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) catabolism of marine bacteria plays an important role in marine and global ecology. The genome of Ruegeria pomeroyi DSS-3, a model organism from the Roseobacter group, harbours no less than three genes for different DMSP lyases (DddW, DddP and DddQ) that catalyse the degradation of DMSP to dimethyl sulfide (DMS) and acrylate. Despite their apparent similar function these enzymes show no significant overall sequence identity. In this work DddQ and DddW from R. pomeroyi and the DddP homolog from Phaeobacter inhibens DSM 17395 were functionally characterised and their substrate scope was tested using several synthetic DMSP analogues. Comparative kinetic assays revealed differences in the conversion of DMSP and its analogues in terms of selectivity and overall velocity, giving additional insights into the molecular mechanisms of DMSP lyases and into their putatively different biological functions.
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Affiliation(s)
- Immo Burkhardt
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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65
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Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M. Genome sequence of Planktotalea frisia type strain (SH6-1 T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Genomic Sci 2018; 13:7. [PMID: 29682168 PMCID: PMC5896138 DOI: 10.1186/s40793-018-0311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome sequence and annotation of the type strain SH6-1T. The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system. This indicates not only adaptation to a free-living lifestyle of P. frisia but points also to interactions with prokaryotic or eukaryotic organisms.
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Affiliation(s)
- Insa Bakenhus
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Sonja Voget
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
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66
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Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi. GENOME ANNOUNCEMENTS 2018; 6:6/12/e01558-17. [PMID: 29567748 PMCID: PMC5864940 DOI: 10.1128/genomea.01558-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the genome sequence of Loktanella vestfoldensis strain SMR4r, isolated from the marine diatom Skeletonema marinoi strain RO5AC. Its 3,987,360-bp genome consists of a circular chromosome and two circular plasmids, one of which appears to be shared with an S. marinoi-associated Roseovarius species.
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67
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Lei L, Cherukuri KP, Alcolombri U, Meltzer D, Tawfik DS. The Dimethylsulfoniopropionate (DMSP) Lyase and Lyase-Like Cupin Family Consists of Bona Fide DMSP lyases as Well as Other Enzymes with Unknown Function. Biochemistry 2018; 57:3364-3377. [DOI: 10.1021/acs.biochem.8b00097] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lei Lei
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Uria Alcolombri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Diana Meltzer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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68
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Seng S, Picone AL, Bava YB, Juncal LC, Moreau M, Ciuraru R, George C, Romano RM, Sobanska S, Tobon YA. Photodegradation of methyl thioglycolate particles as a proxy for organosulphur containing droplets. Phys Chem Chem Phys 2018; 20:19416-19423. [DOI: 10.1039/c7cp08658j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical generation of elemental sulphur and sulphate at the gas–liquid interface by heterogeneous interaction with gaseous O2and H2O.
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69
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Eyice Ö, Myronova N, Pol A, Carrión O, Todd JD, Smith TJ, Gurman SJ, Cuthbertson A, Mazard S, Mennink-Kersten MA, Bugg TD, Andersson KK, Johnston AW, Op den Camp HJ, Schäfer H. Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. ISME JOURNAL 2017; 12:145-160. [PMID: 29064480 PMCID: PMC5739008 DOI: 10.1038/ismej.2017.148] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/07/2017] [Accepted: 07/27/2017] [Indexed: 12/05/2022]
Abstract
Oxidation of methanethiol (MT) is a significant step in the sulfur cycle. MT is an intermediate of metabolism of globally significant organosulfur compounds including dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS), which have key roles in marine carbon and sulfur cycling. In aerobic bacteria, MT is degraded by a MT oxidase (MTO). The enzymatic and genetic basis of MT oxidation have remained poorly characterized. Here, we identify for the first time the MTO enzyme and its encoding gene (mtoX) in the DMS-degrading bacterium Hyphomicrobium sp. VS. We show that MTO is a homotetrameric metalloenzyme that requires Cu for enzyme activity. MTO is predicted to be a soluble periplasmic enzyme and a member of a distinct clade of the Selenium-binding protein (SBP56) family for which no function has been reported. Genes orthologous to mtoX exist in many bacteria able to degrade DMS, other one-carbon compounds or DMSP, notably in the marine model organism Ruegeria pomeroyi DSS-3, a member of the Rhodobacteraceae family that is abundant in marine environments. Marker exchange mutagenesis of mtoX disrupted the ability of R. pomeroyi to metabolize MT confirming its function in this DMSP-degrading bacterium. In R. pomeroyi, transcription of mtoX was enhanced by DMSP, methylmercaptopropionate and MT. Rates of MT degradation increased after pre-incubation of the wild-type strain with MT. The detection of mtoX orthologs in diverse bacteria, environmental samples and its abundance in a range of metagenomic data sets point to this enzyme being widely distributed in the environment and having a key role in global sulfur cycling.
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Affiliation(s)
- Özge Eyice
- School of Life Sciences, University of Warwick, Coventry, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Tom J Smith
- Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Stephen J Gurman
- Department of Physics and Astronomy, University of Leicester, Leicester, UK
| | | | - Sophie Mazard
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Monique Ash Mennink-Kersten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Timothy Dh Bugg
- Department of Chemistry, University of Warwick, Coventry, UK
| | | | | | - Huub Jm Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
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70
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Ferla MP, Brewster JL, Hall KR, Evans GB, Patrick WM. Primordial‐like enzymes from bacteria with reduced genomes. Mol Microbiol 2017. [DOI: 10.1111/mmi.13737] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matteo P. Ferla
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
| | - Jodi L. Brewster
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
| | - Kelsi R. Hall
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
| | - Gary B. Evans
- Ferrier Research InstituteVictoria UniversityLower Hutt New Zealand
| | - Wayne M. Patrick
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
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71
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Bava YB, Tamone LM, Juncal LC, Seng S, Tobón YA, Sobanska S, Picone AL, Romano RM. Gas-phase and matrix-isolation photochemistry of methyl thioglycolate, CH 3 OC(O)CH 2 SH: Influence of the presence of molecular oxygen in the photochemical mechanisms. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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72
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Schnicker NJ, De Silva SM, Todd JD, Dey M. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry 2017; 56:2873-2885. [DOI: 10.1021/acs.biochem.7b00099] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas J. Schnicker
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Saumya M. De Silva
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Jonathan D. Todd
- School
of Biological Sciences, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Mishtu Dey
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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73
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Dani KGS, Loreto F. Trade-Off Between Dimethyl Sulfide and Isoprene Emissions from Marine Phytoplankton. TRENDS IN PLANT SCIENCE 2017; 22:361-372. [PMID: 28242195 DOI: 10.1016/j.tplants.2017.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/04/2017] [Accepted: 01/24/2017] [Indexed: 05/14/2023]
Abstract
Marine phytoplankton emit volatile organic compounds (VOCs) such as dimethyl sulfide (DMS) and isoprene that influence air quality, cloud dynamics, and planetary albedo. We show that globally (i) marine phytoplankton taxa tend to emit either DMS or isoprene, and (ii) sea-water surface concentration and emission hotspots of DMS and isoprene have opposite latitudinal gradients. We argue that a convergence of antioxidant functions between DMS and isoprene is possible, driven by potential metabolic competition for photosynthetic substrates. Linking phytoplankton emission traits to their latitudinal niches, we hypothesize that natural selection favors DMS emission in cold (polar) waters and isoprene emission in warm (tropical) oceans, and that global warming may expand the geographic range of marine isoprene-emitters. A trade-off between DMS and isoprene at metabolic, organismal, and geographic levels may have important consequences for future marine biosphere-atmosphere interactions.
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Affiliation(s)
- K G Srikanta Dani
- Istituto per lo Studio degli Ecosistemi, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, Sesto Fiorentino, 50019 Firenze, Italy; School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695016 Kerala, India.
| | - Francesco Loreto
- Dipartimento di Scienze Bio-Agroalimentari, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro 7, 00185 Roma, Italy.
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74
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Bullock HA, Luo H, Whitman WB. Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria. Front Microbiol 2017; 8:637. [PMID: 28469605 PMCID: PMC5395565 DOI: 10.3389/fmicb.2017.00637] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/28/2017] [Indexed: 11/13/2022] Open
Abstract
The elucidation of the pathways for dimethylsulfoniopropionate (DMSP) synthesis and metabolism and the ecological impact of DMSP have been studied for nearly 70 years. Much of this interest stems from the fact that DMSP metabolism produces the climatically active gas dimethyl sulfide (DMS), the primary natural source of sulfur to the atmosphere. DMSP plays many important roles for marine life, including use as an osmolyte, antioxidant, predator deterrent, and cryoprotectant for phytoplankton and as a reduced carbon and sulfur source for marine bacteria. DMSP is hypothesized to have become abundant in oceans approximately 250 million years ago with the diversification of the strong DMSP producers, the dinoflagellates. This event coincides with the first genome expansion of the Roseobacter clade, known DMSP degraders. Structural and mechanistic studies of the enzymes of the bacterial DMSP demethylation and cleavage pathways suggest that exposure to DMSP led to the recruitment of enzymes from preexisting metabolic pathways. In some cases, such as DmdA, DmdD, and DddP, these enzymes appear to have evolved to become more specific for DMSP metabolism. By contrast, many of the other enzymes, DmdB, DmdC, and the acrylate utilization hydratase AcuH, have maintained broad functionality and substrate specificities, allowing them to carry out a range of reactions within the cell. This review will cover the experimental evidence supporting the hypothesis that, as DMSP became more readily available in the marine environment, marine bacteria adapted enzymes already encoded in their genomes to utilize this new compound.
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Affiliation(s)
- Hannah A Bullock
- Department of Microbiology, University of Georgia, AthensGA, USA
| | - Haiwei Luo
- School of Life Sciences, The Chinese University of Hong KongHong Kong, Hong Kong
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75
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Alcolombri U, Lei L, Meltzer D, Vardi A, Tawfik DS. Assigning the Algal Source of Dimethylsulfide Using a Selective Lyase Inhibitor. ACS Chem Biol 2017; 12:41-46. [PMID: 28103686 DOI: 10.1021/acschembio.6b00844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS originates from Alma lyase(s). This biochemical profiling may complement meta-genomics and transcriptomics to provide better understanding of the marine sulfur cycle.
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Affiliation(s)
- Uria Alcolombri
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lei Lei
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Meltzer
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
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76
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Enzymology of Microbial Dimethylsulfoniopropionate Catabolism. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:195-222. [DOI: 10.1016/bs.apcsb.2017.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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77
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Haworth M, Catola S, Marino G, Brunetti C, Michelozzi M, Riggi E, Avola G, Cosentino SL, Loreto F, Centritto M. Moderate Drought Stress Induces Increased Foliar Dimethylsulphoniopropionate (DMSP) Concentration and Isoprene Emission in Two Contrasting Ecotypes of Arundo donax. FRONTIERS IN PLANT SCIENCE 2017; 8:1016. [PMID: 28659959 PMCID: PMC5468454 DOI: 10.3389/fpls.2017.01016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/26/2017] [Indexed: 05/14/2023]
Abstract
The function of dimethylsulphoniopropionate (DMSP) in plants is unclear. It has been proposed as an antioxidant, osmolyte and overflow for excess energy under stress conditions. The formation of DMSP is part of the methionine (MET) pathway that is involved in plant stress responses. We used a new analytical approach to accurately quantify the changes in DMSP concentration that occurred in two ecotypes of the biomass crop Arundo donax subject to moderate drought stress under field conditions. The ecotypes of A. donax were from a hot semi-arid habitat in Morocco and a warm-humid environment in Central Italy. The Moroccan ecotype showed more pronounced reductions in photosynthesis, stomatal conductance and photochemical electron transport than the Italian ecotype. An increase in isoprene emission occurred in both ecotypes alongside enhanced foliar concentrations of DMSP, indicative of a protective function of these two metabolites in the amelioration of the deleterious effects of excess energy and oxidative stress. This is consistent with the modification of carbon within the methyl-erythritol and MET pathways responsible for increased synthesis of isoprene and DMSP under moderate drought. The results of this study indicate that DMSP is an important adaptive component of the stress response regulated via the MET pathway in A. donax. DMSP is likely a multifunctional molecule playing a number of roles in the response of A. donax to reduced water availability.
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Affiliation(s)
- Matthew Haworth
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
| | - Stefano Catola
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
| | - Giovanni Marino
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
| | - Cecilia Brunetti
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
- Department of Agrifood Production and Environmental Sciences, University of FlorenceSesto Fiorentino, Italy
| | - Marco Michelozzi
- Institute of Biosciences and Bioresources, National Research CouncilSesto Fiorentino, Italy
| | - Ezio Riggi
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
| | - Giovanni Avola
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
| | - Salvatore L. Cosentino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di CataniaCatania, Italy
| | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences, National Research CouncilRome, Italy
| | - Mauro Centritto
- Tree and Timber Institute, National Research CouncilSesto Fiorentino, Italy
- *Correspondence: Mauro Centritto,
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78
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Watson SB, Jüttner F. Malodorous volatile organic sulfur compounds: Sources, sinks and significance in inland waters. Crit Rev Microbiol 2016; 43:210-237. [DOI: 10.1080/1040841x.2016.1198306] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Susan B. Watson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Canada Center for Inland Waters, Burlington, Ontario, Canada
| | - Friedrich Jüttner
- University of Zurich, Department of Limnology, Limnological Station, Kilchberg, Switzerland
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79
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Brummett AE, Dey M. New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Biochemistry 2016; 55:6162-6174. [PMID: 27755868 DOI: 10.1021/acs.biochem.6b00585] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates ∼300 million tons of dimethyl sulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ, reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily on the basis of structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP β-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses ∼0.5 Fe/subunit. The UV-visible spectrum exhibited a feature at 550 nm, consistent with a tyrosinate-Fe(III) ligand-to-metal charge transfer transition. Incubation of as-isolated DddQ with added iron increases the intensity of the 550 nm peak, whereas addition of dithionite causes a bleaching as Fe(III) is reduced. Both the Fe(III) oxidized and Fe(II) reduced species are active, with similar kcat values and 2-fold differences in their Km values for DMSP. The slow turnover of Fe(III)-bound DddQ allowed us to capture a substrate-bound form of the enzyme. Our DMSP-Fe(III)-DddQ structure reveals conformational changes associated with substrate binding and shows that DMSP is positioned optimally to bind iron and is in the proximity of Tyr 120 that acts as a Lewis base to initiate catalysis. The structures of Tris-, DMSP-, and acrylate-bound forms of Fe(III)-DddQ reported here illustrate various states of the enzyme along the reaction pathway. These results provide new insights into DMSP lyase catalysis and have broader significance for understanding the mechanism of oceanic DMS production.
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Affiliation(s)
- Adam E Brummett
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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80
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Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden. Sci Rep 2016; 6:33031. [PMID: 27604458 PMCID: PMC5015088 DOI: 10.1038/srep33031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/19/2016] [Indexed: 11/08/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world's oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.
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81
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Mayers TJ, Bramucci AR, Yakimovich KM, Case RJ. A Bacterial Pathogen Displaying Temperature-Enhanced Virulence of the Microalga Emiliania huxleyi. Front Microbiol 2016; 7:892. [PMID: 27379036 PMCID: PMC4904034 DOI: 10.3389/fmicb.2016.00892] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023] Open
Abstract
Emiliania huxleyi is a globally abundant microalga that plays a significant role in biogeochemical cycles. Over the next century, sea surface temperatures are predicted to increase drastically, which will likely have significant effects on the survival and ecology of E. huxleyi. In a warming ocean, this microalga may become increasingly vulnerable to pathogens, particularly those with temperature-dependent virulence. Ruegeria is a genus of Rhodobacteraceae whose population size tracks that of E. huxleyi throughout the alga’s bloom–bust lifecycle. A representative of this genus, Ruegeria sp. R11, is known to cause bleaching disease in a red macroalga at elevated temperatures. To investigate if the pathogenicity of R11 extends to microalgae, it was co-cultured with several cell types of E. huxleyi near the alga’s optimum (18°C), and at an elevated temperature (25°C) known to induce virulence in R11. The algal populations were monitored using flow cytometry and pulse-amplitude modulated fluorometry. Cultures of algae without bacteria remained healthy at 18°C, but lower cell counts in control cultures at 25°C indicated some stress at the elevated temperature. Both the C (coccolith-bearing) and S (scale-bearing swarming) cell types of E. huxleyi experienced a rapid decline resulting in apparent death when co-cultured with R11 at 25°C, but had no effect on N (naked) cell type at either temperature. R11 had no initial negative impact on C and S type E. huxleyi population size or health at 18°C, but caused death in older co-cultures. This differential effect of R11 on its host at 18 and 25°C suggest it is a temperature-enhanced opportunistic pathogen of E. huxleyi. We also detected caspase-like activity in dying C type cells co-cultured with R11, which suggests that programmed cell death plays a role in the death of E. huxleyi triggered by R11 – a mechanism induced by viruses (EhVs) and implicated in E. huxleyi bloom collapse. Given that E. huxleyi has recently been shown to have acquired resistance against EhVs at elevated temperature, bacterial pathogens with temperature-dependent virulence, such as R11, may become much more important in the ecology of E. huxleyi in a warming climate.
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Affiliation(s)
- Teaghan J Mayers
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Anna R Bramucci
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Kurt M Yakimovich
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
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82
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Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AWB, Davie-Martin CL, Halsey KH, Giovannoni SJ. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nat Microbiol 2016; 1:16065. [PMID: 27573103 DOI: 10.1038/nmicrobiol.2016.65] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 01/20/2023]
Abstract
Marine phytoplankton produce ∼10(9) tonnes of dimethylsulfoniopropionate (DMSP) per year(1,2), an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide(3,4). SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemo-organotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell's unusual requirement for reduced sulfur(5,6). Here, we report that Pelagibacter HTCC1062 produces the gas methanethiol, and that a second DMSP catabolic pathway, mediated by a cupin-like DMSP lyase, DddK, simultaneously shunts as much as 59% of DMSP uptake to dimethyl sulfide production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of dimethyl sulfide as the supply of DMSP exceeds cellular sulfur demands for biosynthesis.
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Affiliation(s)
- Jing Sun
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - J Cameron Thrash
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Yanping Qian
- Department of Food Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Michael C Qian
- Department of Food Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Ben Temperton
- Department of Biosciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Jiazhen Guo
- Qingdao Aquarium, Qingdao, Shandong 266003, China
| | - Emily K Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Joshua T Aldrich
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Carrie D Nicora
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Richard D Smith
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Patrick De Leenheer
- Department of Mathematics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Samuel H Payne
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Andrew W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Cleo L Davie-Martin
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Kimberly H Halsey
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
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83
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Enzymatic breakage of dimethylsulfoniopropionate — a signature molecule for life at sea. Curr Opin Chem Biol 2016; 31:58-65. [DOI: 10.1016/j.cbpa.2016.01.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/18/2022]
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84
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Johnson WM, Kido Soule MC, Kujawinski EB. Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP. ISME JOURNAL 2016; 10:2304-16. [PMID: 26882264 PMCID: PMC4989321 DOI: 10.1038/ismej.2016.6] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/17/2015] [Accepted: 12/24/2015] [Indexed: 11/09/2022]
Abstract
Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter.
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Affiliation(s)
- Winifred M Johnson
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Melissa C Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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85
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Do H, Lee CW, Lee SG, Kang H, Park CM, Kim HJ, Park H, Park H, Lee JH. Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii. J Microbiol 2016; 54:114-21. [PMID: 26832667 DOI: 10.1007/s12275-016-5549-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 11/24/2022]
Abstract
The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NAD-dependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.
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Affiliation(s)
- Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea
| | - Chang Woo Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea
| | - Sung Gu Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea
| | - Hara Kang
- Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea
| | - Chul Min Park
- Medicinal Chemistry Research Center, Bio-Organic Division, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan, 608-739, Republic of Korea
| | - Hyun Park
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. .,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.
| | - HaJeung Park
- X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL, 33458, USA.
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. .,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.
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86
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Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. ISME JOURNAL 2016; 10:1902-14. [PMID: 26784354 PMCID: PMC5029164 DOI: 10.1038/ismej.2015.260] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/24/2015] [Accepted: 12/10/2015] [Indexed: 11/08/2022]
Abstract
Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner–Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.
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87
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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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88
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Alcolombri U, Ben-Dor S, Feldmesser E, Levin Y, Tawfik DS, Vardi A. MARINE SULFUR CYCLE. Identification of the algal dimethyl sulfide-releasing enzyme: A missing link in the marine sulfur cycle. Science 2015; 348:1466-9. [PMID: 26113722 DOI: 10.1126/science.aab1586] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Algal blooms produce large amounts of dimethyl sulfide (DMS), a volatile with a diverse signaling role in marine food webs that is emitted to the atmosphere, where it can affect cloud formation. The algal enzymes responsible for forming DMS from dimethylsulfoniopropionate (DMSP) remain unidentified despite their critical role in the global sulfur cycle. We identified and characterized Alma1, a DMSP lyase from the bloom-forming algae Emiliania huxleyi. Alma1 is a tetrameric, redox-sensitive enzyme of the aspartate racemase superfamily. Recombinant Alma1 exhibits biochemical features identical to the DMSP lyase in E. huxleyi, and DMS released by various E. huxleyi isolates correlates with their Alma1 levels. Sequence homology searches suggest that Alma1 represents a gene family present in major, globally distributed phytoplankton taxa and in other marine organisms.
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Affiliation(s)
- Uria Alcolombri
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ester Feldmesser
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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89
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Methylotrophs in natural habitats: current insights through metagenomics. Appl Microbiol Biotechnol 2015; 99:5763-79. [PMID: 26051673 DOI: 10.1007/s00253-015-6713-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 01/10/2023]
Abstract
The focus of this review is on the recent data from the omics approaches, measuring the presence of methylotrophs in natural environments. Both Bacteria and Archaea are considered. The data are discussed in the context of the current knowledge on the biochemistry of methylotrophy and the physiology of cultivated methylotrophs. One major issue discussed is the recent metagenomic data pointing toward the activity of "aerobic" methanotrophs, such as Methylobacter, in microoxic or hypoxic conditions. A related issue of the metabolic distinction between aerobic and "anaerobic" methylotrophy is addressed in the light of the genomic and metagenomic data for respective organisms. The role of communities, as opposed to single-organism activities in environmental cycling of single-carbon compounds, such as methane, is also discussed. In addition, the emerging issue of the role of non-traditional methylotrophs in global metabolism of single-carbon compounds and the role of methylotrophy pathways in non-methylotrophs is briefly mentioned.
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90
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Brummett AE, Schnicker NJ, Crider A, Todd JD, Dey M. Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW--A Mononuclear Iron-Dependent DMSP Lyase. PLoS One 2015; 10:e0127288. [PMID: 25993446 PMCID: PMC4437653 DOI: 10.1371/journal.pone.0127288] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
The osmolyte dimethylsulfoniopropionate (DMSP) is a key nutrient in marine environments and its catabolism by bacteria through enzymes known as DMSP lyases generates dimethylsulfide (DMS), a gas of importance in climate regulation, the sulfur cycle, and signaling to higher organisms. Despite the environmental significance of DMSP lyases, little is known about how they function at the mechanistic level. In this study we biochemically characterize DddW, a DMSP lyase from the model roseobacter Ruegeria pomeroyi DSS-3. DddW is a 16.9 kDa enzyme that contains a C-terminal cupin domain and liberates acrylate, a proton, and DMS from the DMSP substrate. Our studies show that as-purified DddW is a metalloenzyme, like the DddQ and DddP DMSP lyases, but contains an iron cofactor. The metal cofactor is essential for DddW DMSP lyase activity since addition of the metal chelator EDTA abolishes its enzymatic activity, as do substitution mutations of key metal-binding residues in the cupin motif (His81, His83, Glu87, and His121). Measurements of metal binding affinity and catalytic activity indicate that Fe(II) is most likely the preferred catalytic metal ion with a nanomolar binding affinity. Stoichiometry studies suggest DddW requires one Fe(II) per monomer. Electronic absorption and electron paramagnetic resonance (EPR) studies show an interaction between NO and Fe(II)-DddW, with NO binding to the EPR silent Fe(II) site giving rise to an EPR active species (g = 4.29, 3.95, 2.00). The change in the rhombicity of the EPR signal is observed in the presence of DMSP, indicating that substrate binds to the iron site without displacing bound NO. This work provides insight into the mechanism of DMSP cleavage catalyzed by DddW.
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Affiliation(s)
- Adam E. Brummett
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Nicholas J. Schnicker
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexander Crider
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Mishtu Dey
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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91
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Brock NL, Menke M, Klapschinski TA, Dickschat JS. Marine bacteria from the Roseobacter clade produce sulfur volatiles via amino acid and dimethylsulfoniopropionate catabolism. Org Biomol Chem 2015; 12:4318-23. [PMID: 24848489 DOI: 10.1039/c4ob00719k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is a versatile sulfur source for the production of sulfur-containing secondary metabolites by marine bacteria from the Roseobacter clade. (34)S-labelled DMSP and cysteine, and several DMSP derivatives with modified S-alkyl groups were synthesised and used in feeding experiments that gave insights into the biosynthesis of sulfur volatiles from these bacteria.
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Affiliation(s)
- Nelson L Brock
- Institut für Organische Chemie, Hagenring 30, 38106 Braunschweig, Germany.
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92
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Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M, Klenk HP. Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. Stand Genomic Sci 2015; 10:17. [PMID: 26203330 PMCID: PMC4511512 DOI: 10.1186/1944-3277-10-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 12/10/2014] [Indexed: 02/01/2023] Open
Abstract
Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Anne Fiebig
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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93
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Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species. J Bacteriol 2015; 197:1515-24. [PMID: 25691524 DOI: 10.1128/jb.02605-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Methanosarcina acetivorans uses a variety of methylated sulfur compounds as carbon and energy sources. Previous studies implicated the mtsD, mtsF, and mtsH genes in catabolism of dimethylsulfide, but the genes required for use of other methylsulfides have yet to be established. Here, we show that a four-gene locus, designated mtpCAP-msrH, is specifically required for growth on methylmercaptopropionate (MMPA). The mtpC, mtpA, and mtpP genes encode a putative corrinoid protein, a coenzyme M (CoM) methyltransferase, and a major facilitator superfamily (MFS) transporter, respectively, while msrH encodes a putative transcriptional regulator. Mutants lacking mtpC or mtpA display a severe growth defect in MMPA medium but are unimpaired during growth on other substrates. The mtpCAP genes comprise a transcriptional unit that is highly and specifically upregulated during growth on MMPA, whereas msrH is monocistronic and constitutively expressed. Mutants lacking msrH fail to transcribe mtpCAP and grow poorly in MMPA medium, consistent with the assignment of its product as a transcriptional activator. The mtpCAP-msrH locus is conserved in numerous marine methanogens, including eight Methanosarcina species that we showed are capable of growth on MMPA. Mutants lacking the mtsD, mtsF, and mtsH genes display a 30% reduction in growth yield when grown on MMPA, suggesting that these genes play an auxiliary role in MMPA catabolism. A quadruple ΔmtpCAP ΔmtsD ΔmtsF ΔmtsH mutant strain was incapable of growth on MMPA. Reanalysis of mtsD, mtsF, and mtsH mutants suggests that the preferred substrate for MtsD is dimethylsulfide, while the preferred substrate for MtsF is methanethiol. IMPORTANCE Methylated sulfur compounds play pivotal roles in the global sulfur and carbon cycles and contribute to global temperature homeostasis. Although the degradation of these molecules by aerobic bacteria has been well studied, relatively little is known regarding their fate in anaerobic ecosystems. In this study, we identify the genetic basis for metabolism of methylmercaptopropionate, dimethylsulfide, and methanethiol by strictly anaerobic methanogens of the genus Methanosarcina. These data will aid the development of predictive sulfur cycle models and enable molecular ecological approaches for the study of methylated sulfur metabolism in anaerobic ecosystems.
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94
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Pyrosequencing revealed SAR116 clade as dominant dddP-containing bacteria in oligotrophic NW Pacific Ocean. PLoS One 2015; 10:e0116271. [PMID: 25615446 PMCID: PMC4304780 DOI: 10.1371/journal.pone.0116271] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/03/2014] [Indexed: 11/19/2022] Open
Abstract
Dimethyl sulfide (DMS) is a climatically active gas released into the atmosphere from oceans. It is produced mainly by bacterial enzymatic cleavage of dimethylsulfoniopropionate (DMSP), and six DMSP lyases have been identified to date. To determine the biogeographical distribution of bacteria relevant to DMS production, we investigated the diversity of dddP—the most abundant DMS-producing gene—in the northwestern Pacific Ocean using newly developed primers and the pyrosequencing method. Consistent with previous studies, the major dddP-containing bacteria in coastal areas were those belonging to the Roseobacter clade. However, genotypes closely related to the SAR116 group were found to represent a large portion of dddP-containing bacteria in the surface waters of the oligotrophic ocean. The addition of DMSP to a culture of the SAR116 strain Candidatus Puniceispirillum marinum IMCC1322 resulted in the production of DMS and upregulated expression of the dddP gene. Considering the large area of oligotrophic water and the wide distribution of the SAR116 group in oceans worldwide, we propose that these bacteria may play an important role in oceanic DMS production and biogeochemical sulfur cycles, especially via bacteria-mediated DMSP degradation.
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95
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Broy S, Chen C, Hoffmann T, Brock NL, Nau-Wagner G, Jebbar M, Smits SHJ, Dickschat JS, Bremer E. Abiotic stress protection by ecologically abundant dimethylsulfoniopropionate and its natural and synthetic derivatives: insights from Bacillus subtilis. Environ Microbiol 2014; 17:2362-78. [PMID: 25384455 DOI: 10.1111/1462-2920.12698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/28/2014] [Indexed: 12/01/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant osmolyte and anti-stress compound produced primarily in marine ecosystems. After its release into the environment, microorganisms can exploit DMSP as a source of sulfur and carbon, or accumulate it as an osmoprotectant. However, import systems for this ecophysiologically important compatible solute, and its stress-protective properties for microorganisms that do not produce it are insufficiently understood. Here we address these questions using a well-characterized set of Bacillus subtilis mutants to chemically profile the influence of DMSP import on stress resistance, the osmostress-adaptive proline pool and on osmotically controlled gene expression. We included in this study the naturally occurring selenium analogue of DMSP, dimethylseleniopropionate (DMSeP), as well as a set of synthetic DMSP derivatives. We found that DMSP is not a nutrient for B. subtilis, but it serves as an excellent stress protectant against challenges conferred by sustained high salinity or lasting extremes in both low and high growth temperatures. DMSeP and synthetic DMSP derivatives retain part of these stress protective attributes, but DMSP is clearly the more effective stress protectant. We identified the promiscuous and widely distributed ABC transporter OpuC as a high-affinity uptake system not only for DMSP, but also for its natural and synthetic derivatives.
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Affiliation(s)
- Sebastian Broy
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Chiliang Chen
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Gabriele Nau-Wagner
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Mohamed Jebbar
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,Laboratory of Microbiology of Extreme Environments, UMR 6197 (CNRS - Ifremer - UBO), European Institute of Marine Studies, University of West Brittany (Brest), Technopole Brest-Iroise, F-29280, Plouzané, France
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitäts Str. 1, D-40225, Düsseldorf, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany.,Kekule-Institute for Organic Chemistry and Biochemistry, Friedrich Wilhelms-University Bonn, Gerhard-Domagk-Str. 1, D-53121, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
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96
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Salinity as a regulator of DMSP degradation in Ruegeria pomeroyi DSS-3. J Microbiol 2014; 52:948-54. [PMID: 25277409 DOI: 10.1007/s12275-014-4409-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/27/2014] [Indexed: 10/24/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an important carbon and sulfur source to marine bacterial communities and the main precursor of dimethylsulfide (DMS), a gas that influences atmospheric chemistry and potentially the global climate. In nature, bacterial DMSP catabolism can yield different proportions of DMS and methanethiol (MeSH), but relatively little is known about the factors controlling the pathways of bacterial degradation that select between their formation (cleavage vs. demethiolation). In this study, we carried out experiments to evaluate the influence of salinity on the routes of DMSP catabolism in Ruegeria pomeroyi DSS-3. We monitored DMS and MeSH accumulation in cell suspensions grown in a range of salinities (10, 20, 30 ppt) and with different DMSP amendments (0, 50, 500 µM). Significantly higher concentrations of DMS accumulated in low salinity treatments (10 ppt; P < 0.001), in both Marine Basal Medium (MBM) and half-strength Yeast Tryptone Sea Salts (1/2 YTSS) media. Results showed a 47.1% and 87.5% decrease of DMS accumulation, from salinity 10 to 20 ppt, in MBM and 1/2 YTSS media, respectively. On the other hand, MeSH showed enhanced accumulations at higher salinities (20, 30 ppt), with a 90.6% increase of MeSH accumulation from the 20 ppt to the 30 ppt salinity treatments. Our results with R. pomeroyi DSS-3 in culture are in agreement with previous results from estuarine sediments and demonstrate that salinity can modulate selection of the DMSP enzymatic degradation routes, with a consequent potential impact on DMS and MeSH liberation into the atmosphere.
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97
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Alcolombri U, Laurino P, Lara-Astiaso P, Vardi A, Tawfik DS. DddD Is a CoA-Transferase/Lyase Producing Dimethyl Sulfide in the Marine Environment. Biochemistry 2014; 53:5473-5. [DOI: 10.1021/bi500853s] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Uria Alcolombri
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Paola Laurino
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Pedro Lara-Astiaso
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Vardi
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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98
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Hehemann JH, Law A, Redecke L, Boraston AB. The structure of RdDddP from Roseobacter denitrificans reveals that DMSP lyases in the DddP-family are metalloenzymes. PLoS One 2014; 9:e103128. [PMID: 25054772 PMCID: PMC4108388 DOI: 10.1371/journal.pone.0103128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 Å resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 Å apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Adrienne Law
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation of the Universities of Hamburg and Lübeck, c/o DESY, Hamburg, Germany
| | - Alisdair B. Boraston
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
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99
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Ambiguous evidence for assigning DddQ as a dimethylsulfoniopropionate lyase and oceanic dimethylsulfide producer. Proc Natl Acad Sci U S A 2014; 111:E2078-9. [PMID: 24760823 DOI: 10.1073/pnas.1401685111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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100
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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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