Genome Sequence of Strain IMCC2047, a Novel Marine Member of the Gammaproteobacteria

Kang, Ilnam; Kang, Dongmin; Oh, Hyun-Myung; Kim, Hana; Kim, Hee‐Jin; Kang, Tae-Wook; Kim, Seon‐Young; Cho, Jang-Cheon

doi:10.1128/jb.05226-11

Cited by 8 publications

(4 citation statements)

References 13 publications

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“…RuBisCO, the key enzyme that fixes CO 2 in the Calvin cycle, has been found in strain IMCC2047 (Gammaproteobacteria), which also has a rhodopsin (61). Still, rhodopsin-driven proton pumping does not directly generate the reductant necessary for CO 2 fixation, as does, for example, oxygenic photosynthesis.…”

Section: Discussionmentioning

confidence: 99%

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Pinhassi

DeLong

Béjà

et al. 2016

Microbiol Mol Biol Rev

166

172

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SUMMARYThe recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of “heterotrophic” bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.

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Section: Discussionmentioning

confidence: 99%

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Pinhassi

DeLong

Béjà

et al. 2016

Microbiol Mol Biol Rev

166

172

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“…No further genes encoding enzymes involved in C1 metabolism were found in the genome of this organism. The presence of a proteorhodopsin for light driven formation of a proton gradient is described in strain IMCC2047 (Kang et al, 2011). The combination of proteorhodopsin and the CBB cycle has been suggested to enable photoheterotrophic growth of strain IMCC2047, with reducing power obtained from exogenous chemical compounds (Pinhassi et al, 2016) such as methylamine.…”

Section: Genomic and Proteomic Analysis Of The Metabolism Of Methylammentioning

confidence: 99%

Methylamine as a nitrogen source for microorganisms from a coastal marine environment

Taubert

Grob

Howat

et al. 2017

Environmental Microbiology

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Nitrogen is a key limiting resource for biomass production in the marine environment. Methylated amines, released from the degradation of osmolytes, could provide a nitrogen source for marine microbes. Thus far, studies in aquatic habitats on the utilization of methylamine, the simplest methylated amine, have mainly focussed on the fate of the carbon from this compound. Various groups of methylotrophs, microorganisms that can grow on one-carbon compounds, use methylamine as a carbon source. Non-methylotrophic microorganisms may also utilize methylamine as a nitrogen source, but little is known about their diversity, especially in the marine environment. In this proof-of-concept study, stable isotope probing (SIP) was used to identify microorganisms from a coastal environment that assimilate nitrogen from methylamine. SIP experiments using N methylamine combined with metagenomics and metaproteomics facilitated identification of active methylamine-utilizing Alpha- and Gammaproteobacteria. The draft genomes of two methylamine utilizers were obtained and their metabolism with respect to methylamine was examined. Both bacteria identified in these SIP experiments used the γ-glutamyl-methylamide pathway, found in both methylotrophs and non-methylotrophs, to metabolize methylamine. The utilization of N methylamine also led to the release of N ammonium that was used as nitrogen source by other microorganisms not directly using methylamine.

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“…CCS2 strain belonging to the Roseobacter genus was obtained from Pacific coastal waters and showed as an aerobic anoxygenic phototroph (AAnP) (Slightom, Buchan, 2009). Gamma proteobacterium IMCC2047 strain was isolated from a surface sea in the Yellow Sea, Korea (Kang et al, 2011). Thiobacillus thioparus species is a sulfur-oxidizing bacteria which can be isolated from marine microbial mat (Van den Ende, Gemerden, 1993).…”

Section: Onmentioning

confidence: 99%

Analysis of microbial communities in Binh Chau hot spring through metagenomic DNA sequencing

Thủy

Lan

Tung

et al. 2022

Vietnam J. Biotechnol.

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Binh Chau hot spring locates in Bung Rieng commune, Xuyen Moc district, Ba Ria - Vung Tau province, and is the second hottest hot spring in Vietnam. Up to date, the microbial diversity of this hot spring has been mainly evaluated using the culture-dependent methods, thus, it could not be able to assess all of microorganisms there. In this report, the microbial community of Binh Chau hot spring was investigated by meta-analysis using Hiseq Illumina for sequencing. The results revealed that only 106,903 genes were annotated and 49,190 genes were unknown among 156,093 potential ORFs. The annotated genes consisted of 29,069 bacterial genes, 1,416 archaeal genes, 4 eukaryotic genes, 3 viral genes, and 76,411 unclassified genes. Among the annotated and classified genes, the microbial community of Binh Chau hot spring was characterized by the predominance of bacteria over archaea. At the phylum level, the most abundant phyla in Binh Chau hot spring were followed as Proteobacteria > Firmicutes > Cyanobacteria > Bacteroidetes > Planctomycetes > Thaumarchaeota > Actinobacteria > Euryarchaeota. These belonged mainly to the thermophilic group. A number of the phyla are reported to grow at high temperature, alkaline pH, and high salt concentrations. In addition to the culturable species, the metagenomic data is also indicated the presence of unculturable groups, for example phylum Acidobacteria and Chloroflexi of bacteria. The order Thermoplasmata, which is classified to class Thermoplasmatales of the phylum Euryarchaeota, as well as ultra-small cell and symbiotic archaea including phyla Parvarchaeota, Nanohaloarchaeota, and Nanoarchaeota were detected. The results in this study indicated an important insight into the microbial communities of Binh Chau hot spring, which revealed a promising thermophilic gene sources for their exploitation and conservation in Vietnam.

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Genome Sequence of Strain IMCC2047, a Novel Marine Member of the Gammaproteobacteria

Cited by 8 publications

References 13 publications

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Methylamine as a nitrogen source for microorganisms from a coastal marine environment

Analysis of microbial communities in Binh Chau hot spring through metagenomic DNA sequencing

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