Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum 'Verrucomicrobia', and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae

Yoon, Jaewoo; Matsuo, Yoshihide; Adachi, Kyoko; Nozawa, Midori; Matsuda, Satoru; Kasai, Hiroaki; Yokota, Akira

doi:10.1099/ijs.0.65520-0

Cited by 116 publications

(52 citation statements)

References 38 publications

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“…Algal diversity is positively correlated with mean productivity (Pearson R ϭ 0.33, P ϭ 1.1 ϫ 10 Ϫ1 ) and negatively correlated with standard deviation in productivity (Pearson R ϭ Ϫ0.6, P ϭ 1.9 ϫ 10 Ϫ3 ). Luteolibacter yonseiensis and Luteolibacter algae (46,47). Community composition also showed seasonal shifts comparable to natural assemblages (48), even though the environment was managed to achieve relative homeostasis.…”

Section: Figmentioning

confidence: 80%

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

Beyter

Tang

Becker

et al. 2016

Appl Environ Microbiol

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f Managing ecosystems to maintain biodiversity may be one approach to ensuring their dynamic stability, productivity, and delivery of vital services. The applicability of this approach to industrial ecosystems that harness the metabolic activities of microbes has been proposed but has never been tested at relevant scales. We used a tag-sequencing approach with bacterial small subunit rRNA (16S) genes and eukaryotic internal transcribed spacer 2 (ITS2) to measuring the taxonomic composition and diversity of bacteria and eukaryotes in an open pond managed for bioenergy production by microalgae over a year. Periods of high eukaryotic diversity were associated with high and more-stable biomass productivity. In addition, bacterial diversity and eukaryotic diversity were inversely correlated over time, possibly due to their opposite responses to temperature. The results indicate that maintaining diverse communities may be essential to engineering stable and productive bioenergy ecosystems using microorganisms.

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Section: Figmentioning

confidence: 80%

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

Beyter

Tang

Becker

et al. 2016

Appl Environ Microbiol

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“…This little-known group is widely distributed in soils, sediments, and aquatic and gastrointestinal habitats (49,67,81) and makes up as much as 12% of soil bacterial communities (68). In comparison, the Verrucomicrobia constituted up to 31% (EFK6.3) of the communities explored in this study.…”

Section: Discussionmentioning

confidence: 99%

Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams

Vishnivetskaya

Mosher

Palumbo

et al. 2011

Appl Environ Microbiol

141

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High concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, including Proteobacteria (ranging from 22.9 to 58.5% per sample), Cyanobacteria (0.2 to 32.0%), Acidobacteria (1.6 to 30.6%), Verrucomicrobia (3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within the Proteobacteria group that includes sulfate-reducing bacteria and within the Verrucomicrobia group appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on the in situ microbial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.

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“…Recently, subdivisions 1, 2 and 4 have been presented as the classes Verrucomicrobiae, 'Spartobacteria' and Opitutae, respectively (7,36,61). To verify the phylogenetic positions and novelty of the isolates we obtained, a phylogenetic tree was constructed using almost full-length 16S rRNA gene sequences of all isolates of RFLP groups (A, I, P and Q), and those of previously known strains together with environmental clones within the Verrucomicrobia (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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Cited by 116 publications

References 38 publications

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams

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

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