Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum

Saito, A

doi:10.1016/s0168-6496(98)00009-9

Cited by 33 publications

(36 citation statements)

References 10 publications

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“…In support of this, Mitsui et al (25) and Klappenbach et al (21) found slow-growing oligotrophic ␣-Proteobacteria to be more dominant in soil. In the former study, many of these isolates were nonsymbiotic members of the Rhizobiaceae and Bradyrhizobiaceae (25,26), families that have genomes Ͼ6-8 Mb. Generation times in soil are thought to be low, with mean generations measured at three per year (27).…”

Section: Resultsmentioning

confidence: 99%

Trends between gene content and genome size in prokaryotic species with larger genomes

Konstantinidis

Tiedje

2004

Proc. Natl. Acad. Sci. U.S.A.

439

347

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Although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. We have compared 115 completed prokaryotic genomes by using the Clusters of Orthologous Groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategies associated with genome expansion. We found that large genomes are disproportionately enriched in regulation and secondary metabolism genes and depleted in protein translation, DNA replication, cell division, and nucleotide metabolism genes compared to mediumand small-sized genomes. Furthermore, large genomes do not accumulate noncoding DNA or hypothetical ORFs, because the portion of the genome devoted to these functions remained constant with genome size. Traits other than genome size or strain-specific processes are reflected by the dispersion around the mean for cell functions that showed no correlation with genome size. For example, Archaea had significantly more genes in energy production, coenzyme metabolism, and the poorly characterized category, and fewer in cell membrane biogenesis and carbohydrate metabolism than Bacteria. The trends we noted with genome size by using Clusters of Orthologous Groups were confirmed by our independent analysis with The Institute for Genomic Research's Comprehensive Microbial Resource and Kyoto Encyclopedia of Genes and Genomes' Orthology annotation databases. These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil.

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Section: Resultsmentioning

confidence: 99%

Trends between gene content and genome size in prokaryotic species with larger genomes

Konstantinidis

Tiedje

2004

Proc. Natl. Acad. Sci. U.S.A.

439

347

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“…Symbiosis loci required for host nodulation and nitrogen fixation are clustered onto large plasmids or genomic islands [15][16][17][18][19], that can be transferred among lineages, presumably via conjugation [20][21][22]. Non-nodulating rhizobia are also common [23,24], and these strains often lack some or all of the characterized symbiosis loci [23][24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

et al. 2015

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The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory Bsymbiosis island^loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypeswith a single Bepidemic^haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and nonsymbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.

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“…Members of Bradyrhizobiaceae include a number of nonsymbiotic bacteria with diverse biochemical functions such as photosynthesis (Molouba et al, 1999;Larimer et al, 2004;Giraud et al, 2007), oligotrophy (Saito et al, 1998;King, 2007), 2,4-dichlorophenoxyacetic acid degradation (Kamagata et al, 1997) and nitrification (Starkenburg et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

et al. 2008

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Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G þ C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.

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Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum

Cited by 33 publications

References 10 publications

Trends between gene content and genome size in prokaryotic species with larger genomes

Trends between gene content and genome size in prokaryotic species with larger genomes

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

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