Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade

Buddruhs, Nora; Chertkov, Olga; Petersen, Jörn; Fiebig, Anne; Chen, Amy; Pati, Amrita; Ivanova, Natalia; Lapidus, Alla; Goodwin, Lynne; Chain, Patrick; Detter, John C.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Göker, Markus; Klenk, Hans‐Peter

doi:10.4056/sigs.4297965

Cited by 17 publications

(24 citation statements)

References 46 publications

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“…The usual gene organization involves a putative cmuBCA operon and was found in all experimentally characterized chloromethane-degrading bacteria with the cmu pathway except the reference chloromethane-degrading strain M. extorquens CM4, which harbors cmu genes in two clusters ( Figure 1 ). The chloromethane-degrading strain L. methylohalidivorans MB2, in contrast, was known to lack cmu genes ( Schäfer et al, 2007 ), so the recent report of its assembled genome sequence ( Buddruhs et al, 2013 ) was of particular interest.…”

Section: Resultsmentioning

confidence: 99%

Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

et al. 2014

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Chloromethane (CH3Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH3Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH3Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH3Cl. The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH3Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH3Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH3Cl contain part or all of the complement of cmu genes required for CH3Cl degradation. These organisms, unlike bacteria shown to grow with CH3Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans MB2 showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans MB2 suggest that the unknown pathway used by this bacterium for growth with CH3Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH3Cl budget may be teased apart in the future.

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Section: Resultsmentioning

confidence: 99%

Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

et al. 2014

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“…Another reason for the differences between the outcomes of the 16S rRNA gene analyses might be distinct taxon sampling. The 16S rRNA gene tree topologies inferred in the studies on the Leisingera and Phaeobacter genomes varied considerably depending on the included species from other genera (Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Riedel et al, 2013; Breider et al, 2014). This is as expected, since the 16S rRNA gene trees for the group hardly contain branches with relevant support.…”

Section: Discussionmentioning

confidence: 99%

“…Protein sequences from the 14 available type-strain genomes of Leisingera, Phaeobacter, Ruegeria and outgroup ( Oceanibulbus, Roseobacter , and Sediminimonas ) species (Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Riedel et al, 2013; Breider et al, 2014) were retrieved from the IMG website (http://img.jgi.doe.gov/cgi-bin/w/main.cgi) ( L. aquimarina DSM 24565 T , ID 2516653083 = AXBE00000000; L. methylohalidivorans MB2 T , ID 2512564009 = CP006773/CP006774/CP006775; L. nanhaiensis NH52F T , ID 2512047090 = AXBG00000000; P. arcticus DSM 23566 T ; ID 2516653081 = AXBF00000000; P. caeruleus 13 T , ID 2512047087 = AXBI00000000; P. daeponensis TF-218 T , ID 2516493020 = AXBD00000000; P. inhibens T5 T , ID 2516653078 = AXBB00000000; Sediminimonas qiaohouensis DSM 21189 T , ID 2523533612 = AUIJ00000000) or from NCBI ( Oceanibulbus indolifex HEL-45 T , ABID00000000; P. gallaeciensis CIP105210 T , AOQA01000000; Roseobacter denitrificans Och 114 T , CP000362, CP000464, CP000465, CP000466, CP000467; Roseobacter litoralis Och 149 T , CP002623, CP002624, CP002625, CP002626; Ruegeria lacuscaerulensis ITI-1157 T , ACNX00000000; ACNX00000000; Ruegeria pomeroyi DSS-3 T , CP000031, CP000032).…”

Section: Methodsmentioning

confidence: 99%

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Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

et al. 2014

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Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

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“…In addition to the KEGG and TCDB annotation, Pfam models were used to identify siderophore biosynthesis genes and TonB-dependent outer membrane receptors (OMRs). The Roseobacter siderophore biosynthesis proteins determined in previous studies (Thole et al, 2012;Buddruhs et al, 2013;Riedel et al, 2013;Frank et al, 2014;Nandasena et al, 2014;Collins et al, 2015) were searched against the Pfam v29.0 database (Finn et al, 2014) using hmmscan (HMMER3.1b2; http://hmmer.org/) with gathering cutoffs. The lucA/lucC family (PF04183) was assigned to all known Roseobacter siderophore biosynthesis proteins as the best HMM model, and this model was also used in previous studies (Hopkinson and Barbeau, 2012;Hogle et al, 2016).…”

Section: Iron-related Metabolic and Regulatory Pathway Analysismentioning

confidence: 99%

Ecotype diversification of an abundant Roseobacter lineage

Sun

Zhang

Hollibaugh

et al. 2017

Environmental Microbiology

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The Roseobacter DC5-80-3 cluster (also known as the RCA clade) is among the most abundant bacterial lineages in temperate and polar oceans. Previous studies revealed two phylotypes within this cluster that are distinctly distributed in the Antarctic and other ocean provinces. Here, we report a nearly complete genome co-assembly of three closely related single cells co-occurring in the Antarctic, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies.

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Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade

Cited by 17 publications

References 46 publications

Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

Ecotype diversification of an abundant Roseobacter lineage

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