Marine Microbiology

Genome Characteristics of a Generalist Marine Bacterial Lineage

by Clinton Oakley

Ryan J Newton, Laura E Griffin, Kathy M Bowles, Christof Meile, Scott Gifford, Carrie E Givens, Erinn C Howard, Eric King, Clinton A Oakley, Chris R Reisch, Johanna M Rinta-Kanto, Shalabh Sharma, Shulei Sun, Vanessa Varaljay, Maria Vila-Costa, Jason R Westrich and Mary Ann Moran. The ISME Journal (2010), 1–15

Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there... more Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there will be challenges in assigning well-delineated ecological roles and biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/ pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat surprisingly, phylogenetic tree topology was not the best model for organizing genome characteristics or distribution patterns of individual genes/pathways, although it provided some predictive power. The lifestyle framework, established by grouping isolates according to evidence for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this lineage. The environment framework had a weak predictive power for the overall genome content of each strain, but explained the distribution of several individual genes/pathways, including those related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale geographical signal in some Roseobacter genes. The primary findings emerging from this comparative genome analysis are that members of the lineage cannot be easily collapsed into just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates); the strongest framework for predicting genome content is trophic strategy, but no single framework gives robust predictions; and previously unknown homologs to genes for H2 oxidation, proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO2 fixation by Form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms for energy and carbon acquisition in this remarkably versatile bacterial lineage.

Regulatory effects of mussel (Aulacomya maoriana Iredale 1915) larval settlement by neuroactive compounds, amino acids and bacterial biofilms

by Tim Young

Published in 'Aquaculture' Volumes 322–323, 21 December 2011, Pages 158–168

Larval settlement responses of the ribbed mussel, Aulacomya maoriana Iredale 1915, were investigated after exposure to... more Larval settlement responses of the ribbed mussel, Aulacomya maoriana Iredale 1915, were investigated after exposure to various chemicals and mono-species bacteria. Identification of settlement inductive compounds assists in the elucidation of intermediary biochemical mechanisms involved in the neuronal control of settlement behaviour downstream from primary cue reception. Neuroactive compounds and amino acids (potassium ions, GABA, acetylcholine, l-Phenylalanine, l-Tyrosine, dopamine, epinephrine, l-Tryptophan, and 5-HTP) and planktonic bacteria, biofilms and biofilm exudates of Macrococcus sp. AMGM1, Bacillus sp. AMGB1, and Pseudoalteromonas sp. AMGP1 were tested for their abilities to induce larval settlement. Toxicity effects of each treatment also were simultaneously identified by recording larval mortalities. Results indicate that all chemicals used induced larvae to settle, with acetylcholine being the most effective (~ 24% at 10−6 M compared to < 2% in control assays). Toxicities of treatment compounds were low at optimal settlement inducing concentrations, except for l-Tryptophan (~ 32%) and GABA (~ 59%). Our data suggest that catecholamines (and their precursors) play an important role in the biochemical mechanisms of settlement for A. maoriana. While serotonin precursors did induce low levels of larval settlement at some concentrations, high toxicity responses to 5-HTP at 10−5 M, combined with complete settlement inhibition indicate that the mechanism of action may be more complex than can be elucidated in this study. Larval settlement responses to bacterial treatments were low for planktonic and biofilm phases across all three strains, and settlement inhibition was observed when larvae were exposed to biofilm exudates of all bacterial strains. Comparisons of A. maoriana responses to other endemic and worldwide distributed mussel species are provided as a means to highlight potential evolutionary differences in chemoreception mechanisms.

Diversity of the marine cyanobacterium Trichodesmium: characterization of the Woods Hole culture collection and quantification of field populations

by Annette Hynes

Dimethylsulfide is an energy source for the heterotrophic marine bacterium Sagittula stellata

by Rich Boden

Co-authored with Hendrik Schäfer and J. Colin Murrell.

Dimethylsulfide (DMS) is a volatile organosulfur compound, ubiquitous in the oceans, that has been credited with... more Dimethylsulfide (DMS) is a volatile organosulfur compound, ubiquitous in the oceans, that has been credited with various roles in biogeochemical cycling and in climate control. Various oceanic sinks of DMS are known – both chemical and biological – although they are poorly understood. In addition to the utilization of DMS as a carbon or a sulfur source, some Bacteria are known to oxidize it to dimethylsulfoxide (DMSO). Sagittula stellata is a heterotrophic member of the Alphaproteobacteria found in marine environments. It has been shown to oxidize DMS during heterotrophic growth on sugars, but the reasons for and the mechanisms of this oxidation have not been investigated. Here, we show that the oxidation of DMS to DMSO is coupled to ATP synthesis in S. stellata and that DMS acts as an energy source during chemoorganoheterotrophic growth of the organism on fructose and on succinate. DMS dehydrogenase (which is responsible for the oxidation of DMS to DMSO in other marine Bacteria) and DMSO reductase activities were absent from cells grown in the presence of DMS, indicating an alternative route of DMS oxidation in this organism.

Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

by Rich Boden

Many co-authors. Projected completed as part of the OMeGA sequencing consortium.

Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria,... more Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph

Photosynthetic performance of healthy and virus-infected Feldmannia irregularis and F. simplex (Phaeophyceae)

by Daniel Robledo

Co-authored with P. A. SOSA, G. GARCIA-REINA AND D. G. MULLER

The filamentous brown algae Feldmannia simplex and F. irregular~ are attacked by aquatic viruses, which propagate in... more The filamentous brown algae Feldmannia simplex and F. irregular~ are attacked by aquatic viruses, which propagate in deformed sporangia of the host plants. In order to evaluate a possible detrimental effect of the pathogen, photosynthesis-irradiance response curves and pigment concentrations of healthy and infected plants were compared. Photosynthetic performance of infected plants was significantly reduced and associated with a decrease in chlorophyll a and c content. In Feldmannia irregularis, which had a relatively low photosynthetic
capacity, the virus infection produced a more severe effect than in F. simplex.

Substrate-Specific Clades of Active Marine Methylotrophs Associated With a Phytoplankton Bloom In a Temperate Coastal Environment

by Rich Boden

Applied and Environmental Microbiology

Authors:

Neufeld J, Boden R, Moussard H, Schäfer H & Murrell JC.

Marine microorganisms that consume one-carbon (C1) compounds are poorly described, despite their impact on global... more Marine microorganisms that consume one-carbon (C1) compounds are poorly described, despite their impact on global climate via an influence on aquatic and atmospheric chemistry. This study investigated marine bacterial communities involved in the metabolism of C1 compounds. These communities were of relevance to surface seawater and atmospheric chemistry in the context of a bloom that was dominated by phytoplankton known to produce dimethylsulfoniopropionate. In addition to using 16S rRNA gene fingerprinting and clone libraries to characterize samples taken from a bloom transect in July 2006, seawater samples from the phytoplankton bloom were incubated with 13C labeled methanol, monomethylamine, dimethylamine, methyl bromide, and dimethyl sulfide to identify microbial populations involved in the turnover of C1 compounds, using DNA stable isotope probing. The [13C]DNA samples from a single time point were characterized and compared using denaturing gradient gel electrophoresis (DGGE), fingerprint cluster analysis, and 16S rRNA gene clone library analysis. Bacterial community DGGE fingerprints from 13C-labeled DNA were distinct from those obtained with the DNA of the nonlabeled community DNA and suggested some overlap in substrate utilization between active methylotroph populations growing on different C1 substrates. Active methylotrophs were affiliated with Methylophaga spp. and several clades of undescribed Gammaproteobacteria that utilized methanol, methylamines (both monomethylamine and dimethylamine), and dimethyl sulfide. rRNA gene sequences corresponding to populations assimilating 13C-labeled methyl bromide and other substrates were associated with members of the Alphaproteobacteria (e.g., the family Rhodobacteraceae), the Cytophaga-Flexibacter-Bacteroides group, and unknown taxa. This study expands the known diversity of marine methylotrophs in surface seawater and provides a comprehensive data set for focused cultivation and metagenomic analyses in the future.

Stable-Isotope Probing Implicates Methylophaga Spp and Novel Gammaproteobacteria In Marine Methanol and Methylamine Metabolism

by Rich Boden

ISME Journal

Authors:

Neufeld J, Schaefer H, Cox MJ, Boden R, McDonald IR, Murrell JC

The metabolism of one-carbon (C1) compounds in the marine environment affects global warming, seawater ecology and... more The metabolism of one-carbon (C1) compounds in the marine environment affects global warming, seawater ecology and atmospheric chemistry. Despite their global significance, marine microorganisms that consume C1 compounds in situ remain poorly characterized. Stable-isotope probing (SIP) is an ideal tool for linking the function and phylogeny of methylotrophic organisms by the metabolism and incorporation of stable-isotope-labelled substrates into nucleic acids. By combining DNA-SIP and time-series sampling, we characterized the organisms involved in the assimilation of methanol and methylamine in coastal sea water (Plymouth, UK). Labelled nucleic acids were analysed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA genes. In addition, we characterized the functional gene complement of labelled nucleic acids with an improved primer set targeting methanol dehydrogenase (mxaF) and newly designed primers for methylamine dehydrogenase (mauA). Predominant DGGE phylotypes, 16S rRNA, methanol and methylamine dehydrogenase gene sequences, and cultured isolates all implicated Methylophaga spp, moderately halophilic marine methylotrophs, in the consumption of both methanol and methylamine. Additionally, an mxaF sequence obtained from DNA extracted from sea water clustered with those detected in 13C-DNA, suggesting a predominance of Methylophaga spp among marine methylotrophs. Unexpectedly, most predominant 16S rRNA and functional gene sequences from 13C-DNA were clustered in distinct substrate-specific clades, with 16S rRNA genes clustering with sequences from the Gammaproteobacteria. These clades have no cultured representatives and reveal an ecological adaptation of particular uncultured methylotrophs to specific C1 compounds in the coastal marine environment.

Draft genome sequence of the chemolithoheterotrophic halophilic methylotroph Methylophaga thiooxydans DMS010

by Rich Boden

Journal of Bacteriology

Authors:

Boden R, Ferriera S, Johnson J, Kelly DP, Murrell JC & Schäfer H.

Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of methylotrophic growth on... more Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of methylotrophic growth on a range of one-carbon compounds as well as chemolithoheterotrophic growth at the expense of thiosulfate. Here we present the draft genome sequence of Methylophaga thiooxydans DMS010 (DSM 22068T, VKM B2586T), the type strain of the species, which has allowed prediction of the genes involved in one-carbon metabolism, nitrogen metabolism and other aspects of central metabolism.

Marinobacter adhaerens sp. nov., prominent in aggregate formation with the diatom Thalassiosira weissflogii

by Eva Sonnenschein (Kaeppel)

Kaeppel EC, Gärdes A, Seebah S, Grossart HP, Ullrich MS (2011) Int J Syst Evol Microbiol

The Gram-negative, motile, and rod-shaped bacterial strain, HP15T, was isolated from particles sampled in surface... more The Gram-negative, motile, and rod-shaped bacterial strain, HP15T, was isolated from particles sampled in surface waters of the German Wadden Sea. It was identified among 82 other marine isolates due to its high potential to induce production of transparent exopolymeric particles and aggregate formation while interacting with the diatom, Thalassiosira weissflogii. HP15T grew optimally at a range of 34-38 °C, a pH of 7-8.5, and was able to tolerate salt concentrations between 0.5-20 % (w/v) NaCl. HP15T was chemotaxonomically characterized by possessing ubiquinone-9 as the major respiratory lipoquinone as well as C16:0, C18:1ω9c, and C16:1ω7c/C15:0 iso 2-OH as predominant fatty acids. The G+C content of its DNA was 56.9 mol%. The closest relative by means of 16S rRNA sequence analysis was Marinobacter flavimaris with a similarity level of 99 %. The whole-genome relatedness of HP15T to M. flavimaris, M. salsuginis, M. lipolyticus, and M. algicola was determined to be lower than 70 % by DNA-DNA hybridization. On the basis of phenotypic and chemotaxonomic properties as well as phylogenetic analyses, strain HP15T (=DSM 23420T = CIP 110141T) is proposed to represent the novel species, Marinobacter adhaerens sp. nov.

Oxidation of Dimethylsulfide to Tetrathionate by Methylophaga Thiooxidans Sp. Nov.: a New Link In the Sulfur Cycle

by Rich Boden

Environmental Microbiology.

Authors:

Boden R, Kelly DP, Murrell JC, Schaefer H.

A new pathway of dimethylsulfide (DMS) metabolism was identified in a novel species of Gammaproteobacteria,... more A new pathway of dimethylsulfide (DMS) metabolism was identified in a novel species of Gammaproteobacteria, Methylophaga thiooxidans sp. nov., in which tetrathionate (S(4)O(6)(2-)) was the end-product of DMS oxidation. Inhibitor evidence indicated that DMS degradation was initiated by demethylation, catalysed by a corrinoid demethylase. Thiosulfate was an intermediate, which was oxidized to tetrathionate by a cytochrome-linked thiosulfate dehydrogenase. Thiosulfate oxidation was coupled to ATP synthesis, and M. thiooxidans could also use exogenous thiosulfate as an energy source during chemolithoheterotrophic growth on DMS or methanol. Cultures grown on a variety of substrates oxidized thiosulfate, indicating that thiosulfate oxidation was constitutive. The observations have relevance to interactions among sulfur-metabolizing bacteria in the marine environment. The production of tetrathionate from an organosulfur precursor is previously undocumented and represents a potential step in the biogeochemical sulfur cycle, providing a 'shunt' across the cycle

Constrained water access to the active site of cytochrome P450 from the piezophilic bacterium Photobacterium profundum

by Elena Sineva

ELENA V SINEVA AND DMITRI R. DAVYDOV High Pressure research, 2010, 30(4): 466 - 474

Living species inhabiting ocean deeps must adapt to high hydrostatic pressure. This adaptation, which must enable... more Living species inhabiting ocean deeps must adapt to high hydrostatic pressure. This adaptation, which must enable functioning under conditions of promoted protein hydration, is especially important for proteins such as cytochromes P450 that exhibit functionally important hydration-dehydration dynamics. Here we study the interactions of substrates with cytochrome P450-SS9, a putative fatty acid hydroxylase from the piezophilic bacterium Photobacterium profundum SS9, and characterize the protein’s barotropic properties. Comparison of P450-SS9 with cytochrome P450BM-3, a mesophilic fatty acid hydroxylase, suggests that P450-SS9 is characterized by severely confined accessibility and low water occupancy of the active site. This feature may reveal a mechanism of structural adaptation of the piezophilic enzyme. We also demonstrate that saturated and unsaturated fatty acids exert opposite effects on solvent accessibility and hydration of the active site. Modulation of the protein conformation by fatty acids is hypothesized to have an important physiological function in the piezophile.