Linear 3-Hydroxybutyrate Tetramer (HB4) Produced by<i>Sphingomonas</i>sp. Is Characterized as a Growth Promoting Factor for Some Rhizomicrofloral Composers

Ogita, Noriko; Hashidoko, Yasuyuki; Limin, Suwido H.; Tahara, Satoshi

doi:10.1271/bbb.60299

Cited by 17 publications

(17 citation statements)

References 13 publications

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“…2). It was therefore suggested that some MWGЈ-culturable bacteria comprising bacterial microbiota of V5 and V30 soils play a role as helper or stimulus-generating bacteria for the free-living N 2 -fixing bacteria in soil microbiota (25,28,32). We subsequently hypothesized that it is not a single bacterial isolate but is rather rather bacterial consortia that exhibit capabilities of N 2 fixation in the soil, as is similar to other cases of bacterial consortia previously reported (14,25,38).…”

Section: Discussionsupporting

confidence: 54%

“…Recently, it has been reported that a linear type (R)-3-hydroxybutyrate tetramer produced by a Sphingomonas sp. showed a growth-promoting effect on some bacterial cells that was similar to the effect seen with gellan gum (28). It is widely known that (R)-3-hydroxybutyrate polymer is also an extracellular polymeric substance produced by many N 2 -fixing bacteria (23,31).…”

Section: Discussionmentioning

confidence: 52%

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High Rate of N ₂ Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

Hara

Hashidoko

Desyatkin

et al. 2009

Appl Environ Microbiol

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For evaluating N 2 fixation of diazotrophic bacteria, nitrogen-poor liquid media supplemented with at least 0.5% sugar and 0.2% agar are widely used for acetylene reduction assays. In such a soft gel medium, however, many N 2 -fixing soil bacteria generally show only trace acetylene reduction activity. Here, we report that use of a N 2 fixation medium solidified with gellan gum instead of agar promoted growth of some gellan-preferring soil bacteria. In a soft gel medium solidified with 0.3% gellan gum under appropriate culture conditions, bacterial microbiota from boreal forest bed soils and some free-living N 2 -fixing soil bacteria isolated from the microbiota exhibited 10-to 200-fold-higher acetylene reduction than those cultured in 0.2% agar medium. To determine the N 2 fixation-activating mechanism of gellan gum medium, qualitative differences in the colony-forming bacterial components from tested soil microbiota were investigated in plate cultures solidified with either agar or gellan gum for use with modified Winogradsky's medium. On 1.5% agar plates, apparently cryophilic bacterial microbiota showed strictly distinguishable microbiota according to the depth of soil in samples from an eastern Siberian Taiga forest bed. Some pure cultures of proteobacteria, such as Pseudomonas fluorescens and Burkholderia xenovorans, showed remarkable acetylene reduction. On plates solidified with 1.0% gellan gum, some soil bacteria, including Luteibacter sp., Janthinobacterium sp., Paenibacillus sp., and Arthrobacter sp., uniquely grew that had not grown in the presence of the same inoculants on agar plates. In contrast, Pseudomonas spp. and Burkholderia spp. were apparent only as minor colonies on the gellan gum plates. Moreover, only gellan gum plates allowed some bacteria, particularly those isolated from the shallow organic soil layer, to actively swarm. In consequence, gellan gum is a useful gel matrix to bring out growth potential capabilities of many soil diazotrophs and their consortia in communities of soil bacteria.In 1967, Schöllhorn and Burris discovered that nitrogenase from an N 2 -fixing rhizobium of soybean can reduce acetylene to produce ethylene (C 2 H 4 ) (32), a reaction analogous to the conversion of the natural substrate N 2 into ammonia. Shortly afterwards, it was shown that this acetylene reduction activity parallels N 2 reduction by nitrogenase (13), and since then, acetylene reduction assays have been widely used in the evaluation of biological N 2 fixation. An acetylene reduction assay is generally performed under the following conditions: precultured bacterial cells are suspended into N-free or -deficient liquid medium containing a carbon source, usually D-glucose or D-mannitol (35) at 0.5 to 2.0%, and exposed for 24 h or less at a representative room temperature, e.g., 25°C (2). However, this method is not applicable to free-living, microaerobic N 2 -fixing bacteria, which have been regarded as notoriously difficult to culture. To solve this problem, Döbereiner and her group developed a soft g...

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 52%

High Rate of N ₂ Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

Hara

Hashidoko

Desyatkin

et al. 2009

Appl Environ Microbiol

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“…The next largest group, Myco-NIII, containing seven clones, clustered with Sphingomonas sp. strain EC-K085, which was recently reported (25) to promote the growth of rhizosphere-inhabiting Frateuria spp. Strikingly, sequences of bands from bulk soil and most clones from the G-soil and N-soil (bulk soil) clone libraries all cluster with sequences from the same German forest, hinting that Sphingomonadaceae communities from bulk soils might be similar in different locations.…”

Section: Discussionmentioning

confidence: 99%

Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies

Boersma

Warmink

Andreote

et al. 2009

Appl Environ Microbiol

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The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the Sphingomonadaceae family at the bases of the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans in comparison to the adjacent bulk soil. To do so, we used a previously designed Sphingomonadaceae-specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a Sphingomonadaceae-specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the Sphingomonadaceae community structures. The effect was especially prevalent with R. exalbicans. Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of L. proxima and R. exalbicans still revealed divergent community structures, indicating that different fungi select for different members of the Sphingomonadaceae family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific Sphingomonadaceae types. It further showed that major groups from the mycospheres of R. exalbicans and L. proxima did not cluster with known bacteria from the database, indicating new groups within the family of Sphingomonadaceae present in these environments.

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“…No information on the degradation of 2,4-D by this genus has been published up to now. Recently, Ogita et al 18) found that some Sphingomonas spp. displayed helperlike behaviors for Frauteuria sp., and that the linear 3-hydrobutyrate tetramer produced by Sphingomonas sp.…”

Section: Diversity Of Isolated 24-d-and 245-t-degrading Bacteriamentioning

confidence: 99%

2,4-Dichlorophenoxyacetic Acid (2,4-D)- and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacterial Community in Soil-Water Suspension during the Enrichment Process

2008

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Changes in the bacterial community in soil-water suspensions during the enrichment period of 2,4-D and 2,4,5-T degraders were examined using denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The nucleotide sequences of almost all major bands at the degradation of 2,4-D and 2,4,5-T corresponded to those of 2,4-Dand 2,4,5-T-degrading isolates, and successions of diverse 2,4-D-and 2,4,5-T-degrading bacterial communities were demonstrated in the DGGE profile. These results suggested that 2,4-D-and 2,4,5-T-degrading isolates were responsible for the degradation of 2,4-D and 2,4,5-T in soil-water suspensions; however, one major band of a non-degrader was found in some cases. Therefore, to elucidate the relationship between the structures and functions of bacterial communities, the importance of a combined approach using both culture-dependent and -independent methods was demonstrated.

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Linear 3-Hydroxybutyrate Tetramer (HB4) Produced bySphingomonassp. Is Characterized as a Growth Promoting Factor for Some Rhizomicrofloral Composers

Cited by 17 publications

References 13 publications

High Rate of N ₂ Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

High Rate of N ₂ Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies

2,4-Dichlorophenoxyacetic Acid (2,4-D)- and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacterial Community in Soil-Water Suspension during the Enrichment Process

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Linear 3-Hydroxybutyrate Tetramer (HB4) Produced bySphingomonassp. Is Characterized as a Growth Promoting Factor for Some Rhizomicrofloral Composers

Cited by 17 publications

References 13 publications

High Rate of N 2 Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

High Rate of N 2 Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies

2,4-Dichlorophenoxyacetic Acid (2,4-D)- and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacterial Community in Soil-Water Suspension during the Enrichment Process

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High Rate of N ₂ Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum

High Rate of N ₂ Fixation by East Siberian Cryophilic Soil Bacteria as Determined by Measuring Acetylene Reduction in Nitrogen-Poor Medium Solidified with Gellan Gum