Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan

Yoon, Jaewoo; Yasumoto-Hirose, Mina; Katsuta, Atsuko; Sekiguchi, Hiroshi; Matsuda, Satoru; Kasai, Hiroaki; Yokota, Akira

doi:10.1099/ijs.0.64755-0

Cited by 60 publications

(58 citation statements)

References 21 publications

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“…The data from this study suggest that the different bacterial morphotypes are different taxa occupying separate tubules. Bacterial morphology by itself is not a reliable taxonomic identifier; however, studies of the marine verrucomicrobium Coraliomargarita akajimensis revealed a morphology similar to the LCB morphotype observed in this study (52). The two epithelial morphologies of the ANG tubules are very distinct from one another, suggesting that each tubule fosters a unique microenvironment optimized to contain a specific bacterial taxon or that specific bacteria influence development of different epithelia.…”

Section: Discussionmentioning

confidence: 41%

Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes

Collins

LaBarre

Won

et al. 2012

Appl Environ Microbiol

117

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ABSTRACTMicrobial consortia confer important benefits to animal and plant hosts, and model associations are necessary to examine these types of host/microbe interactions. The accessory nidamental gland (ANG) is a female reproductive organ found among cephalopod mollusks that contains a consortium of bacteria, the exact function of which is unknown. To begin to understand the role of this organ, the bacterial consortium was characterized in the Hawaiian bobtail squid,Euprymna scolopes, a well-studied model organism for symbiosis research. Transmission electron microscopy (TEM) analysis of the ANG revealed dense bacterial assemblages of rod- and coccus-shaped cells segregated by morphology into separate, epithelium-lined tubules. The host epithelium was morphologically heterogeneous, containing ciliated and nonciliated cells with various brush border thicknesses. Hemocytes of the host's innate immune system were also found in close proximity to the bacteria within the tubules. A census of 16S rRNA genes suggested thatRhodobacterales, Rhizobiales, andVerrucomicrobiabacteria were prevalent, with members of the genusPhaeobacterdominating the consortium. Analysis of 454-shotgun sequencing data confirmed the presence of members of these taxa and revealed members of a fourth,Flavobacteriaof theBacteroidetesphylum. 16S rRNA fluorescentin situhybridization (FISH) revealed that many ANG tubules were dominated by members of specific taxa, namely,Rhodobacterales,Verrucomicrobia, orCytophaga-Flavobacteria-Bacteroidetes, suggesting symbiont partitioning to specific host tubules. In addition, FISH revealed that bacteria, includingPhaeobacterspecies from the ANG, are likely deposited into the jelly coat of freshly laid eggs. This report establishes the ANG of the invertebrateE. scolopesas a model to examine interactions between a bacterial consortium and its host.

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Section: Discussionmentioning

confidence: 41%

Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes

Collins

LaBarre

Won

et al. 2012

Appl Environ Microbiol

117

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“…There are nine validly named species within the class Opitutae (subdivision 4) (6,7,56,(58)(59)(60). As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Culture-Dependent and Independent Analyses of the Microbial Communities Inhabiting the Giant Duckweed (Spirodela polyrrhiza) Rhizoplane and Isolation of a Variety of Rarely Cultivated Organisms within the Phylum Verrucomicrobia

et al. 2010

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The microbial communities of the rhizoplane, the surface part of roots, in aquatic plants are not understood at all. In this study, we analyzed microbial communities in the rhizoplane of a floating aquatic plant, giant duckweed (Spirodela polyrrhiza), based on cultivation-dependent and independent analyses. The cultivation-based analysis using agar and gellan gum plates revealed that the rhizoplane isolates were affiliated with four bacterial lineages; the Alphaproteobacteria, Betaproteobacteria, Bacteroidetes and Verrucomicrobia. Interestingly, microbes belonging to the phylum Verrucomicrobia accounted for 24% of all the isolates, suggesting that the rhizoplane of S. polyrrhiza forms a specific habitat for the organisms within this phylum. Culture-independent 16S rRNA gene cloning showed that the clonal sequences were affiliated with eight bacterial classes and phyla: the classes Alphaproteobacteria (14% total clones), Betaproteobacteria (45%), Gammaproteobacteria (2%) and Deltaproteobacteria (2%), and the phyla Bacteroidetes (11%), Verrucomicrobia (2%), Planctomycetes (2%) and Cyanobacteria (22%). Comparative analysis of the microbial communities in the rhizoplane between culture-dependent and independent methods revealed that 33% of the taxonomic groups of bacterial species detected in the molecular analysis were cultivable. Our findings suggest that the microbes in the rhizoplane of giant duckweed are comprised of a diverse array of readily cultured organisms including a variety of strains within the Verrucomicrobia, a well-known phylum that contains a number of yet-to-be cultivated organisms.Key words: duckweed, rhizoplane, Verrucomicrobia, isolation of novel microbeThe rhizosphere, the zone adjacent to and influenced by a plant's roots, and the rhizoplane, the surface part of roots, are of great significance to plant health and the fertility of their surroundings. Many studies on the microbial community structure of the rhizosphere and rhizoplane of terrestrial plants have been conducted using cultivation-based and cultivation-independent methods (12,18,21,22,31,40). These studies have shown that terrestrial plants harbor unique and diverse microbial communities in their rhizoplane probably due to the specific environments formed by the surface structure and exudates released from the roots. Moreover, it has also been revealed that the microbes might exert a beneficial, neutral, or deleterious influence on plant growth (16,32,43,44,55), and they are sometimes involved in the degradation of environmental pollutants (phytoremediation) (4, 14, 52). By contrast, little is known about rhizosphere and rhizoplane microbial communities of aquatic plants, though it has been reported that the microbes would participate in various activities such as nitrogen metabolism (denitrification and nitrification) and the removal of toxic chemicals (1,35,50,51). Giant duckweed, Spirodela polyrrhiza, is an aquatic floating angiosperm that is globally distributed in various water environments such as lakes, paddy fields, ponds, ...

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“…Strain 04OKA010-24 T (DSM 45221 = JCM 23193 = KCTC 12865) is the type strain of the species Coraliomargarita akajimensis and was first described in 2007 by Yoon et al [1]. Strain 04OKA010-24 T was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Okinawa, Japan.…”

Section: Introductionmentioning

confidence: 99%

“…Besides the genus Coraliomargarita [1] the genera Cerasicoccus [10], Pelagicoccus [11], Puniceicoccus [9] belong into the family Puniceicoccaceae . Here we present a summary classification and a set of features for C. akajimensis 04OKA010-24 T , together with the description of the complete genomic sequencing and annotation.…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)

Mavromatis

Abt

Brambilla

et al. 2010

Stand. Genomic Sci.

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Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium that was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of special interest because of its phylogenetic position in a genomically under-studied area of the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

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Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan

Abstract: Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24

Cited by 60 publications

References 21 publications

Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes

Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes

Culture-Dependent and Independent Analyses of the Microbial Communities Inhabiting the Giant Duckweed (Spirodela polyrrhiza) Rhizoplane and Isolation of a Variety of Rarely Cultivated Organisms within the Phylum Verrucomicrobia

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)

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