ABSTRACT
Oceanic bacteria perform many environmental functions, including biogeochemical cycling of many elements, metabolizing of greenhouse gases, functioning in oceanic food webs (microbial loop), and producing valuable natural products and viruses. We demonstrate that the widespread capability of marine bacteria to participate in horizontal gene transfer (HGT) in coastal and oceanic environments may be the result of gene transfer agents (GTAs), viral-like particles produced by α-Proteobacteria. We documented GTA-mediated gene transfer frequencies a thousand to a hundred million times higher than prior estimates of HGT in the oceans, with as high as 47% of the culturable natural microbial community confirmed as gene recipients. These findings suggest a plausible mechanism by which marine bacteria acquire novel traits, thus ensuring resilience in the face of environmental change.
Subject(s)
Ecosystem , Gene Transfer, Horizontal , Rhodobacteraceae/genetics , Seawater/microbiology , Adaptation, Physiological , DNA Transposable Elements , Drug Resistance, Bacterial/genetics , Flavobacterium/drug effects , Flavobacterium/genetics , Flexibacter/drug effects , Flexibacter/genetics , Kanamycin Resistance/genetics , Oceans and Seas , Prophages/genetics , Rhodobacteraceae/drug effects , Rhodobacteraceae/virology , Streptomycin/metabolism , Streptomycin/pharmacologyABSTRACT
The taxonomic position of the misclassified strains [Flexibacter] tractuosus KCTC 2958T and '[Microscilla] sericea' LMG 13021 was studied using a polyphasic approach. The two strains shared 99.1% 16S rRNA gene sequence similarity and 28% DNA-DNA relatedness. On the basis of the phylogenetic evidence supported by genotypic and phenotypic data [Flexibacter] tractuosus KCTC 2958T and '[Microscilla] sericea' LMG 13021 are classified as two distinct species in a novel genus, Marivirga, in the family 'Flammeovirgaceae', as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov., with strains KCTC 2958T (=ATCC 23168T =CIP 106410T =DSM 4126T =NBRC 15989T =NCIMB 1408T =VKM B-1430T) and LMG 13021T (=ATCC 23182T =NBRC 15983T =NCIMB 1403T), respectively, as the type strains. The type species is Marivirga tractuosa.
Subject(s)
Bacteroidetes/classification , Flexibacter/classification , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Flexibacter/genetics , Flexibacter/isolation & purification , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/geneticsABSTRACT
A Gram-negative, rod-shaped, non-spore-forming bacterium, designated strain R2A36-4T, was isolated from greenhouse soil and subjected to a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Sphingobacteriaceae. Its nearest phylogenetic neighbour was the type strain of [Flexibacter] canadensis CIP 104802T (93.2% 16S rRNA gene sequence similarity). Strain R2A36-4T and [F.] canadensis CIP 104802T fell in a distinct cluster within the family Sphingobacteriaceae. Strain R2A36-4T contained MK-7 as the predominant quinone. Strain R2A36-4T and [F.] canadensis CIP 104802T had iso-C15:0, iso-C17:0 3-OH, summed feature 3 and C15:1omega6c as the major fatty acids. Strain R2A36-4T could be distinguished from [F.] canadensis on the basis of several physiological properties and fatty acid compositions. Based on phenotypic characterization and 16S rRNA gene sequence analysis, strain R2A36-4T represents a novel species within a new genus, for which the name Solitalea koreensis gen. nov., sp. nov. is proposed. The type strain of Solitalea koreensis is strain R2A36-4T (=KACC 12953T=DSM 21342T). It is also proposed that [F.] canadensis be transferred to this genus as Solitalea canadensis comb. nov. (type strain UASM 9DT=ATCC 29591T=CIP 104802T=DSM 3403T=NBRC 15130T=JCM 21819T=KACC 13276T=LMG 8368T).
Subject(s)
Bacteroidetes/classification , Bacteroidetes/isolation & purification , Flexibacter/classification , Soil Microbiology , Bacterial Typing Techniques , Bacteroidetes/genetics , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Flexibacter/genetics , Molecular Sequence Data , Phylogeny , Quinones/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
The taxonomic relationship between [Flexibacter] aggregans IAM 14894(T) and Flexithrix dorotheae NBRC 15987(T) was investigated by means of DNA-DNA hybridization and phenotypic characteristics. On the basis of these results, it is proposed that Flexibacter aggregans (Lewin 1969) Leadbetter 1974 be considered a later heterotypic synonym of Flexithrix dorotheae Lewin 1970. Emended descriptions of the species Flexithrix dorotheae and the genus Flexithrix are also given.
Subject(s)
Flexibacter/classification , Base Composition , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Flexibacter/chemistry , Flexibacter/genetics , Genes, rRNA , Molecular Sequence Data , Nucleic Acid Hybridization , Phylogeny , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sequence Homology, Nucleic AcidABSTRACT
A microbial consortium (AM) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (PAH) mixture of three- and four-ringed PAHs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (DGGE), and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and seven by both DGGE and clone libraries were obtained. The comparison of three variable regions (V3-V5) of the 16S rRNA gene between the sequences obtained yielded 19 different microbial components. Proteobacteria were the dominant group, representing 83% of the total, while the Cytophaga-Flexibacter-Bacteroides group (CFB) was 11% and the Ascomycota fungi 6%. Beta-proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences were achieved by the cultivation method that showed members of the alpha-, beta-, and gamma-Proteobacteria; CFB bacterial group; and Ascomycota fungi. Only six of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1), which were similar to Sphingomonas sp. and Fusarium sp., respectively, achieved the greatest PAH depletion. The results indicate that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium.
