The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1

Rabus, Ralf; Kube, Michael; Heider, Johann; Beck, Alfred; Heitmann, Katja; Widdel, Friedrich; Reinhardt, Richard

doi:10.1007/s00203-004-0742-9

Cited by 254 publications

(311 citation statements)

References 48 publications

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“…The periplasmic localization of the nitrate reductase components (duplicated nap operon) and detoxification of NO 2 -via an NO 3 -/NO 2 -antiporter (NarK) might decrease toxicity of nitrite. In contrast, the denitrification pathway is complete in strain EbN1 for which denitrification appears to be a typical feature 10 .…”

Section: Pseudomonas Aeruginosa Pa01 (Pa0074 -Pa0101)mentioning

confidence: 93%

“…There are three genes encoding flagellins (fliC1, fliC2, fliC3) and two encoding flagellar motor proteins, suggesting an important role for motility in the plant-associated lifestyle. In contrast, the nonmotile strain EbN1 does not possess a complete flagellar regulon 10 .…”

Section: Plant-associated Lifestylementioning

confidence: 95%

“…1b, circle 3). In contrast, the genome of the Azoarcus-related soil isolate strain EbN1 contains 237 transposon-related genes 10 . Also rhizobial genomes harbor 4100 transposases or phage-related genes (http://www.kazusa.or.jp/rhizobase/).…”

mentioning

confidence: 99%

“…Although the genome of a related species, strain EbN1, belonging to a branch of Azoarcus species that typically occurs in soils and sediments but not in association with plants 9 , is available 10 , phenotypic differences and phylogenetic distances of 5-6% suggest they might deserve the rank of a separate genus in future 9 . The plant-associated strain BH72-like many N 2 -fixing endophytes grass endophytes-has not been detected in root-free soil 11 .…”

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confidence: 99%

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Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

et al. 2006

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Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.Endophytic bacteria reside within the living tissue of plants without substantively harming them. They are of high interest for agrobiotechnological applications, such as the improvement of plant growth and health, phytoremediation 1 or even as biofertilizer 2 . Supply of nitrogen derived from fixation of atmospheric N 2 by grass endophytes, such as Gluconacetobacter diazotrophicus and Azoarcus sp. strain BH72, which has been shown to occur in sugarcane 3 and Kallar grass 2 , is a process of potential agronomical and ecological importance.Although the lifestyle of these endophytes is relatively well documented, the molecular mechanisms by which they interact beneficially with plants have only been poorly elucidated. A combination of features makes Azoarcus sp. strain BH72 an excellent model grassendophyte 4 . (i) It supplies nitrogen derived from N 2 fixation to its host, Kallar grass (Leptochloa fusca (L.) Kunth); in planta it is usually not culturable, but can be detected by culture-independent methods based on nifH-encoding nitrogenase reductase, the key enzyme for N 2 fixation 2 . (ii) It colonizes nondiseased plants in remarkably high numbers: estimates range from 10 8 cells (culturable cells per gram root dry weight (RDW) of field-grown Kallar grass 5 ) to 10 10 cells (estimated on the basis of abundance of bacterial nifH-mRNA in roots) 2 . (iii) It is the only cultured grass endophyte shown by molecular methods to be the most actively N 2 -fixing bacterium of the natural population in roots 2 . (iv) It also colonizes the roots of rice, a cereal of global importance, in high numbers (10 9 cells per g RDW) in the laboratory, and spreads systemically into shoots 6 . Plant stress response is only very limited in a compatible, that is, well-colonized rice cultivar 7 . Notably, Azoarcus sp. strain BH72 is capable of endophytic N 2 -fixation inside the roots of rice 8 .For a wider application in agriculture, more knowledge is required on mechanisms o...

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Section: Pseudomonas Aeruginosa Pa01 (Pa0074 -Pa0101)mentioning

confidence: 93%

Section: Plant-associated Lifestylementioning

confidence: 95%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

et al. 2006

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“…In addition, predicted ORFs were screened against the database of Clusters of Orthologous Groups of proteins (COGs 27 ). These methods were implemented in the web-based platform HTGA (High-Throughput Genome Annotation 29 ) and used for annotation. The annotated genome of D. ethenogenes strain 195 (NCBI accession number CP000027) was used for comparison and refinement of the annotation of strain CBDB1.…”

Section: Methodsmentioning

confidence: 99%

Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

et al. 2005

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Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.In the past century, human activities have released large amounts of chlorinated organic compounds into the environment, and these compounds are among the most pervasive groundwater pollutants. Chloroorganics with fewer chlorines can usually be biodegraded by aerobic microorganisms, whereas more highly chlorinated ones can be reductively dechlorinated by organisms using them as electron acceptors for anaerobic respiration. Several microbial groups carry out respiratory reductive dechlorination 1 , but one genus, Dehalococcoides, seems particularly adapted to a unique niche, and the bacteria are only known to use chloroorganics as electron acceptors and hydrogen as an electron donor for growth. Several studies have now shown successful application of Dehalococcoides-containing cultures for in situ remediation of contaminated sites 2,3 . The recently described genome sequence of D. ethenogenes, strain 195 (ref. 4), an organism that reductively dechlorinates the solvents tetrachloroethene and trichloroethene to vinyl chloride and ethene 5 , reflects this specialization: although only 1.47-megabases (Mb) long, the genome possesses 17 rdhAB pairs potentially encoding reductive dehalogenases and genes predicted to encode five different hydrogenase complexes. We describe here the genome sequence of Dehalococcoides sp. strain CBDB1, a bacterium that has in many ways a different dechlorination spectrum from strain 195. For instance, strain CBDB1 (refs. 6,7) dechlorinated 1,2,3-trichlorobenzene, 1,2,4-trichlorobenzene, 2,3-dichloro-p-dibenzodioxin and the 'Seveso dioxin ' 2,3,7,8-tetrachloro-p-dibenzodioxin, but strain 195 (ref. 8) did not. In contrast to strain 195, strain CBDB1 did not dechlorinate tetrachloroethene past dichloroethene 6 . By sequencing a second Dehalococcoides genome, we can now show that strain CBDB1 has an even greater potential as a reductive dechlorinator than strain 195 and, in addition, the comparison of the two genomes with each other provides insights into the evolution of reductive dechlori...

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Biodegradation of Residua and Asphalt

Speight¹,

Arjoon²

2012

Bioremediation of Petroleum and Petroleum Products

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The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1

Cited by 254 publications

References 48 publications

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

Biodegradation of Residua and Asphalt

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