Rhizomicrobium palustre gen. nov., sp. nov., a facultatively anaerobic, fermentative stalked bacterium in the class Alphaproteobacteria isolated from rice plant roots

Ueki, Atsuko; Kodama, Yoshio; Kaku, Nobuo; Shiromura, Takuya; Satoh, Atsuya; Watanabe, Kazuya; Ueki, Katsuji

doi:10.2323/jgam.56.193

Cited by 43 publications

(18 citation statements)

References 43 publications

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“…Members of these lineages have been detected in soil habitats 56, 57 , but not specifically associated with plant roots. Soil isolates belonging to the order Ellin329 metabolize xylan, arabinose, rhamnose, and starch 58, 59 , and are speculated to play a role in plant litter decomposition 59 . Whether these unfamiliar root-associated taxa are actively recruited into the root microbiome, are root-proximal opportunists feeding on rhizodeposits, or interact only with other root-associated bacteria remains to be determined.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

et al. 2017

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Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history.

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Section: Resultsmentioning

confidence: 99%

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

et al. 2017

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“…Gram staining and oxidase/catalase tests were conducted according to standard procedures (Smibert & Krieg, 1994). The presence of heat-tolerant cells was examined as described by Ueki et al (2010).…”

Section: Routine Cultivation Of Strain Mfc52mentioning

confidence: 99%

“…The second closest relative was Rhizomicrobium palustre A48 T (97.3 %), isolated from roots of rice plants grown in flooded rice field soil (Ueki et al, 2010). Other sequences in the databases were not highly similar; e.g.…”

Section: Strain Mfc52mentioning

confidence: 99%

Rhizomicrobium electricum sp. nov., a facultatively anaerobic, fermentative, prosthecate bacterium isolated from a cellulose-fed microbial fuel cell

Kodama

Watanabe

2011

International Journal of Systematic and Evolutionary Microbiology

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Rhizomicrobium electricum sp. nov., a facultatively anaerobic, fermentative, prosthecate bacterium isolated from a cellulose-fed microbial fuel cell Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter (Logan et al., 2006;Watanabe, 2008). In our previous study, MFCs were developed with rice-paddy field soil as a source of micro-organisms and crystalline cellulose as the sole fuel, and microbial communities attaching onto graphite anodes in these MFCs were analysed (Ishii et al., 2008a, b). Results showed that rod-shaped members of the class Alphaproteobacteria possessing prosthecae-like appendages (represented by phylotype Mfc-9) were abundantly present in anode biofilm communities (Ishii et al., 2008a), suggesting that they may have played important roles in the cellulose/electricity conversion in these MFCs. In order to investigate their ecological roles, we isolated these bacterial strains (including strain Mfc52 T ) and examined their ability to generate electric currents . It was revealed that strain Mfc52T generated electricity in pureculture MFCs by oxidizing intermediate metabolites (e.g. lactate and acetate) from cellulose degradation, and most cells of strain Mfc52T had long prosthecae similar to those observed in scanning electron micrographs of the anode biofilm in the cellulose-fed MFC . Strain Mfc52T is the first isolate of prosthecate bacteria with the ability to generate electricity in MFCs. In our phylogenetic analysis , strain Mfc52 T was deeply branched within the class Alphaproteobacteria and closely related to Rhizomicrobium palustre A48 T , a facultatively anaerobic, fermentative stalked bacterium isolated from rice plant roots (Ueki et al., 2010). In the present study, we performed further physiological and taxonomic analyses of strain Mfc52 T . Based on the results, we propose that strain Mfc52T represents a novel species in the genus Rhizomicrobium. Routine cultivation of strain Mfc52T was done without shaking at 30 u C in 1/10 PYGV medium supplemented with 1 g glucose l 21 under oxygen-free N 2 gas in culture bottles capped with Tefloncoated butyl rubber septa and sealed with aluminium crimps. Growth in liquid medium was monitored by measuring optical density at 660 nm (OD 660 ) using a spectrophotometer (U-1100, Hitachi), and cell concentration was determined by directly counting 49, 6-diamidino-2-phenylindole (DAPI)-stained cells under an epifluorescence microscope as described elsewhere (Kodama & Watanabe, 2003). Cells of Mfc52T were stored at 280 u C in liquid 1/10 PYGV medium supplemented with 15 % (v/v) glycerol.Cell morphology was examined by transmission electron microscopy (Beveridge et al., 1994). Cells were fixed with glutaraldehyde (2.5 %, w/v), negatively stained with Abbreviation: MFCs, microbial fuel cells.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain Mfc52T is AB365487.

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“…This electrophoresis analysis detected several intense bands that specifically occurred on the anode or cathode of the power-generation system; sequence analyses revealed that bands from the anode were related to Natronocella acetinitrilica (Sorokin et al 2007) and Rhizobiales bacterium A48 (Satoh et al, 2002), while that from the cathode was related to Rhodobacter gluconicum (Do et al 2003). Among them, A48 was isolated from a rice root surface (Satoh et al, 2002), and its taxonomy has recently been described as the genus Rhizomicrobium gen nov. (Ueki et al 2010). In addition, closely related bacteria were detected in laboratory MFCs operated with cellulose as the sole fuel (Ishii et al 2008a;Ishii et al 2008b).…”

Section: Rice Paddy-field Smfcmentioning

confidence: 99%

Electric Power from Rice Paddy Fields

Watanabe¹,

Nishio²

2010

Paths to Sustainable Energy

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Rhizomicrobium palustre gen. nov., sp. nov., a facultatively anaerobic, fermentative stalked bacterium in the class Alphaproteobacteria isolated from rice plant roots

Cited by 43 publications

References 43 publications

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

Rhizomicrobium electricum sp. nov., a facultatively anaerobic, fermentative, prosthecate bacterium isolated from a cellulose-fed microbial fuel cell

Electric Power from Rice Paddy Fields

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