Comamonas

Willems, Anne; Vos, Paul De

doi:10.1007/0-387-30745-1_31

Cited by 31 publications

(31 citation statements)

References 99 publications

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“…Wakelin et al (56) reported that Gammaproteobacteria were correlated with DOC concentrations in stream sediments. Langenheder and Prosser (34) also demonstrated that Betaproteobacteria and Gammaproteobacteria were the major degraders of organic pollutants in sediments, and these classes are well-known for their ability to degrade diverse organic compounds that include some persistent organic chemicals (40,57). Environments with proximal unsaturated conditions exhibited the emergence of Bacilli and Actinobacteria.…”

Section: Discussionmentioning

confidence: 97%

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

Liu

Sharp

Saikaly

et al. 2012

Appl Environ Microbiol

120

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ABSTRACTThis study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classesBetaproteobacteriaandGammaproteobacteriaare positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

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Section: Discussionmentioning

confidence: 97%

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

Liu

Sharp

Saikaly

et al. 2012

Appl Environ Microbiol

120

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“…Comamonas spp. are aerobic proteobacteria (Willems & De Vos, ), and thus are likely involved in oxygen scavenging. Desulfovibrio spp.…”

Section: Discussionmentioning

confidence: 99%

Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen

Ren

Yan

et al. 2019

MicrobiologyOpen

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Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai-Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp.,Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota. K E Y W O R D SBos grunniens, Campylobacter spp., dorsal and ventral epithelium, ecology niches, Howardella spp, rumen, solid and liquid

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“…omamonas species are ubiquitous in the environment and have been isolated from soil, mud, water, activated sludge, clinical samples, and organic pollutant-and heavy metal-contaminated environments (1). Comamonas species play an important role in matter cycling in nature and have been noted for their capabilities to degrade various aromatics (1)(2)(3)(4)(5).…”

mentioning

confidence: 99%

“…Comamonas species play an important role in matter cycling in nature and have been noted for their capabilities to degrade various aromatics (1)(2)(3)(4)(5). Interestingly, many Comamonas strains have been found to harbor plasmids, most of which have been confirmed to be related to the catabolism of xenobiotic aromatics (4,(6)(7)(8).…”

mentioning

confidence: 99%

Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics

Chen

Zhang

et al. 2016

Appl Environ Microbiol

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bComamonas plasmids play important roles in shaping the phenotypes of their hosts and the adaptation of these hosts to changing environments, and understanding the evolutionary strategy of these plasmids is thus of great concern. In this study, the sequence of the 119-kb 3,5-dibromo-4-hydroxybenzonitrile-catabolizing plasmid pBHB from Comamonas sp. strain 7D-2 was studied and compared with those of three other Comamonas haloaromatic catabolic plasmids. Incompatibility group determination based on a phylogenetic analysis of 24 backbone gene proteins, as well as TrfA, revealed that these four plasmids all belong to the IncP-1␤ subgroup. Comparison of the four plasmids revealed a conserved backbone region and diverse genetic-load regions. The four plasmids share a core genome consisting of 40 genes (>50% similarities) and contain 12 to 50 unique genes each, most of which are xenobiotic-catabolic genes. Two functional reductive dehalogenase gene clusters are specifically located on pBHB, showing distinctive evolution of pBHB for haloaromatics. The higher catabolic ability of the bhbA2B2 cluster than the bhbAB cluster may be due to the transcription levels and the character of the dehalogenase gene itself rather than that of its extracytoplasmic binding receptor gene. The plasmid pBHB is riddled with transposons and insertion sequence (IS) elements, and ISs play important roles in the evolution of pBHB. The analysis of the origin of the bhb genes on pBHB suggested that these accessory genes evolved independently. Our work provides insights into the evolutionary strategies of Comamonas plasmids, especially into the adaptation mechanism employed by pBHB for haloaromatics. Comamonas species are ubiquitous in the environment and have been isolated from soil, mud, water, activated sludge, clinical samples, and organic pollutant-and heavy metal-contaminated environments (1). Comamonas species play an important role in matter cycling in nature and have been noted for their capabilities to degrade various aromatics (1-5). Interestingly, many Comamonas strains have been found to harbor plasmids, most of which have been confirmed to be related to the catabolism of xenobiotic aromatics (4, 6-8). For example, the plasmid pI2, responsible for the degradation of aniline/3-chloroaniline, was isolated from Comamonas testosteroni I2 (4, 9, 10). Another transferable plasmid, pTB30, which is involved in the mineralization of 3-chloroaniline, was isolated from C. testosteroni TB30 (9, 11). In addition, the plasmid pCNB1, encoding the catabolic pathway to convert 4-chloronitrobenzene to 5-chloro-4-hydroxy-2-oxovalerate, was sequenced in Comamonas sp. strain CNB-1 (12, 13). Recently, the plasmid pBHB was characterized in Comamonas sp. strain 7D-2. This plasmid is involved in the mineralization of the herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile), which includes the reductive dehalogenation of the bromoxynil nitrile hydrolyte 3,5-dibromo-4-hydroxybenzoate (DBHB) (14).Plasmids are among the most important elements in the evolutio...

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Comamonas

Cited by 31 publications

References 99 publications

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen

Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics

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