Genome Characteristics of a Generalist Marine Bacterial Lineage
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.
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Download (.pdf) Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134
by Pere Puigbò
González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, Jaenicke S, Gómez-Consarnau L, Fernàndez-Guerra A, Goesmann A, Pedrós-Alió C.
Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine... more Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle.
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.
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Diseases Affect Cold-Water Corals Too: Eunicella Verrucosa (Cnidaria: Gorgonacea) Necrosis In SW England
http://www.int-res.com/articles/dao_oa/d076p087.pdf
The first recorded incidence of cold-water coral disease was noted in Eunicella verrucosa, a coral on the... more
The first recorded incidence of cold-water coral disease was noted in Eunicella verrucosa, a coral on the international ‘red list’ of threatened species, at a marine protected area in SW England in 2002. Video surveys of 634 separate colonies at 13 sites revealed that disease outbreaks were widespread in SW England from 2003 to 2006. Coenchyme became necrotic in diseased specimens, leading to tissue sloughing and exposing skeletal gorgonin to settlement by fouling organisms.
Sites where necrosis was found had significantly higher incidences of fouling. No fungi were isolated from diseased or healthy tissue, but significantly higher concentrations of bacteria occurred in diseased specimens. Of 21 distinct bacteria isolated from diseased tissues, 19 were Vibrionaceae, 15 were strains of Vibrio splendidus and 2 others closely matched Vibrio tasmaniensis. Vibrios isolated from E. verrucosa did not induce disease at 15°C, but, at 20°C, controls remained healthy and test gorgonians became diseased, regardless of whether vibrios were isolated from diseased or healthy colonies. Bacteria associated with diseased tissue produced proteolytic and cytolytic enzymes that damaged E. verrucosa tissue and may be responsible for the necrosis observed. Monitoring at the site where the disease was first noted showed new gorgonian recruitment from 2003 to 2006; some individuals had died and become completely overgrown, whereas others had continued to grow around a dead central area.
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.