Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea

Poddar, Abhijit; Lepcha, Rinchen T.; Mukherjee, Debasish; Bhattacharyya, Dhananjay; Das, Subrata K.

doi:10.1016/j.resmic.2014.07.008

Cited by 18 publications

(14 citation statements)

References 27 publications

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“…The isolate clearly forms a separate branch with A. maris, which is distinct from other members of the family Idiomarinaceae.Analysis of signature bases at nucleotide positions143, 206, 213, 241, 285, 653, 662, 682, 748, 830, 856 and 1256 of species within the family Idiomarinaceae confirmed that there are four broad RNA groups(Supplementary Table S2), similar to that described recently(Zhang et al 2012;Poddar et al 2014). Strain MLST1 T groups with members of the genus Aliidiomarina.…”

supporting

confidence: 69%

“…Idiomarinaceae comprises a variety of Gram-negative salt-requiring bacteria distinguished from related families by their fatty acid profiles, inability to use carbohydrates as sole sources of carbon and energy and signature nucleotides in the 16S rRNA gene (Ivanova et al 2004). Species within the family have been isolated from a variety of surface and deep marine waters and sediments, sea salt evaporation ponds, and hypersaline soils (Yoon et al 2007;Taborda et al 2009;Huang et al 2012;Srinivas et al 2012;Zhang et al 2012;Poddar et al 2014). The taxonomy of the family Idiomarinaceae is complex and distinguishing genera and species has been difficult.…”

Section: Introductionmentioning

confidence: 99%

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Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Farooqui

Wright

Greene

2015

Antonie van Leeuwenhoek

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An aerobic haloalkaliphilic bacterium, designated strain MLST1(T), was isolated from filtered (0.22 µm) Mono Lake (USA) waters. The isolate was observed to grow primarily on yeast extract, peptone and tryptone. Optimal growth occurred in media at pH 9.5 containing 5-11 g/l yeast extract, and 70-100 g/l NaCl. When in log phase of growth, cells were found to be mostly curved motile rods (1-3 µm length by 0.4-1 µm diameter). Phylogenetic analysis of the 16S rRNA gene and chemotaxonomic data revealed that the isolate belonged to the family Idiomarinaceae, and is closely related to Aliidiomarina maris (96.67 % sequence similarity). The major fatty acids were identified to be iso-C17:1 ω9c (27.1 %), iso-C17:0 (21.3 %) and iso-C15:0 (12.2 %). Predominant polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and the major respiratory quinone was identified as Q8. The DNA base composition was 46.3 mol% G+C. Survival studies indicated that strain MLST1(T) remains viable after exposure to adverse conditions, particularly in the prolonged absence of a carbon source, at low temperatures and with no NaCl. Under these conditions, the cells shrunk to around 0.2 µm in length by 0.1 µm in diameter and passed through 0.22 µm filters. The ultra-small cells could only be resuscitated in media with low levels of yeast extract, up to 0.6 g/l. Once resuscitated, cells were able to grow to full size. Strain MLST1(T) is clearly a unique bacterium in the waters of Mono Lake and the name Aliidiomarina minuta sp. nov. is proposed. The type strain is MLST1(T) (=JCM 17425(T) = KCTC 23357(T)).

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supporting

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Farooqui

Wright

Greene

2015

Antonie van Leeuwenhoek

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“…Idiomarina was first described as a deep-sea bacterium with particle-associated life style and protein metabolism as an important source of nutrients (Donachie et al, 2003 ; Hou et al, 2004 ), and representatives have since been found in other environments including shallow water and salterns (e.g., Poddar et al, 2014 ; León et al, 2015 ). Isolated Idiomarina strains are described as obligately aerobic and heterotrophic, which is generally consistent with the gene content found in the Idiomarina SAGs.…”

Section: Resultsmentioning

confidence: 99%

Bacterial Succession on Sinking Particles in the Ocean's Interior

2017

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Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio campbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 clade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.

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“…Idiomarina woesei strain W11 T is a Gram-negative, short rod aerobe that belongs to the class Gammaproteobacteria ( 1 ). Its whole-genome sequence will help understand the halophilic lifestyle of this bacterium.…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Idiomarina woesei Strain W11 ^T (DSM 27808 ^T ) Isolated from the Andaman Sea

et al. 2016

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Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea

Cited by 18 publications

References 27 publications

Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Bacterial Succession on Sinking Particles in the Ocean's Interior

Draft Genome Sequence of Idiomarina woesei Strain W11 ^T (DSM 27808 ^T ) Isolated from the Andaman Sea

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Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea

Cited by 18 publications

References 27 publications

Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Bacterial Succession on Sinking Particles in the Ocean's Interior

Draft Genome Sequence of Idiomarina woesei Strain W11 T (DSM 27808 T ) Isolated from the Andaman Sea

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Draft Genome Sequence of Idiomarina woesei Strain W11 ^T (DSM 27808 ^T ) Isolated from the Andaman Sea