Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere

Matilla, Miguel A.; Espinosa‐Urgel, Manuel; Rodríguez‐Herva, José J.; Ramos, Juan L.; Ramos-González, Marı́a Isabel

doi:10.1186/gb-2007-8-9-r179

Cited by 192 publications

(175 citation statements)

References 47 publications

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“…This might be due to reductive evolution and could reflect a more stringent association with its plant host, although smaller size is not specific to A1501 and was reported for other P. stutzeri strains that do not necessarily have the same lifestyle (38). In addition, P. putida KT2440, which is also a rhizospheric strain, has a much larger genome (3,39) (Table 1). We identified a set of 487 genes common to other Pseudomonas and absent in the A1501 genome, suggesting loss of functions in A1501, as noted for the alginate biosynthesis gene cluster and for fluorescent siderophore production.…”

Section: Discussionmentioning

confidence: 99%

“…12 and 14, their actual involvement in colonization remains to be established. Recent work in the rhizospheric P. pudtia KT2440 identified 91 genes up-regulated in the presence of maize exudates (39), and 31 of them are conserved in A1501 (including regulators, transport systems, stress response, and chemotaxis) (data not shown). Present knowledge of the genome should help in elucidating regulatory mechanisms that control the association with the host plant, thus enabling better comprehension of mechanisms of nitrogen transfer.…”

Section: Discussionmentioning

confidence: 99%

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Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Yan

Yang

et al. 2008

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

329

263

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The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give A1501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.genome sequencing ͉ root-associated diazotroph

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Yan

Yang

et al. 2008

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

329

263

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“…Activation of the stress response genes in PGPR organisms by the root exudates was reported in a previous study (Matilla et al, 2007). Through the observed up-regulation of the SasA alarmone biosynthesis pathway it was hypothesized that the level of (p)ppGpp might be increased in bacteria treated with the root exudates.…”

Section: Gene Expression Profilingmentioning

confidence: 94%

Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates

Mwita

Chan

Pretorius

et al. 2016

Gene

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Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during plant colonization. Active PGPR strain B. atrophaeus UCMB-5137 was studied in this research. RNA sequencing profiles were generated in experiments where root exudate stimulations were used to mimic interactions between bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42, which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49 putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general regulatory network of B. atrophaeus UCMB-5137 genome was designed.1 Highlights  Plant colonizing PGPR Bacillus responded differently to the root exudate stimuli;  In UCMB-5137 the CcpA-CodY-AbrB regulation caused fast cell immobilization;  DegU regulon is important for plant colonization behavior in PGPR Bacillus;  ncRNA involved in regulation of plant colonization were identified;  A comprehensive model of gene regulation in UCMB-5137 was developed;

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“…The phenols might end up in the rhizosphere from decaying roots or as root exudates and sustain the detected diverse ring-cleavage community including endophytic bacteria in the root. Very recently, it has been shown that Pseudomonas type aromatic degrading genes are upregulated in corn rhizosphere indicating that corn root exudates contain aromatic compounds (Matilla et al, 2007). Simultaneous assay of 16S rRNA and ring-cleavage marker genes illustrated contrasting rhizosphere effects at different bacterial community levels.…”

Section: Discussionmentioning

confidence: 99%

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Sipilä

Keskinen²,

Akerman³

et al. 2008

The ISME Journal

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Genes encoding key enzymes of catabolic pathways can be targeted by DNA fingerprinting to explore genetic degradation potential in pristine and polluted soils. We performed a greenhouse microcosm experiment to elucidate structural and functional bacterial diversity in polyaromatic hydrocarbon (PAH)-polluted soil and to test the suitability of birch (Betula pendula) for remediation. Degradation of PAHs was analysed by high-performance liquid chromatography, DNA isolated from soil amplified and fingerprinted by restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP). Bacterial 16S rRNA T-RFLP fingerprinting revealed a high structural bacterial diversity in soil where PAH amendment altered the general community structure as well as the rhizosphere community. Birch augmented extradiol dioxygenase diversity in rhizosphere showing a rhizosphere effect, and further pyrene was more efficiently degraded in planted pots. Degraders of aromatic compounds upon PAH amendment were shown by the changed extradiol ring-cleavage community structure in soil. The RFLP analysis grouped extradiol dioxygenase marker genes into 17 distinct operational taxonomic units displaying novel phylogenetic clusters of ring-cleavage dioxygenases representing putative catabolic pathways, and the peptide sequences contained conserved amino-acid signatures of extradiol dioxygenases. A branch of major environmental TS cluster was identified as being related to Parvibaculum lavantivorans ring-cleavage dioxygenase. The described structural and functional diversity demonstrated a complex interplay of bacteria in PAH pollution. The findings improve our understanding of rhizoremediation and unveil the extent of uncharacterized enzymes and may benefit bioremediation research by facilitating the development of molecular tools to detect and monitor populations involved in degradative processes.

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Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere

Cited by 192 publications

References 47 publications

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

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