High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

Liu, Lin; Zhu, Wentao; Cao, Zhan; Xu, Bin; Wang, Gejiao; Luo, Meizhong

doi:10.1186/s12864-015-1314-x

Cited by 39 publications

(38 citation statements)

References 67 publications

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“…However, exceptions to this trend are the genus Comamonas , in which all four species with sequenced genomes have the pathway, and the SAR86 cluster, in which all three strains with sequenced draft genomes have the pathway. Recently, genotypic analysis of 14 Comamonas testosteroni strains revealed that the testosterone/cholate degradation pathway is part of the core genome of this species ( 31 ). Unfortunately, most of these genomes were not available at the time of our analysis.…”

Section: Discussionmentioning

confidence: 99%

Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

Bergstrand

Cardenas

Holert

et al. 2016

mBio

106

135

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Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria.

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Section: Discussionmentioning

confidence: 99%

Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

Bergstrand

Cardenas

Holert

et al. 2016

mBio

106

135

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“…Previous studies found that the Comamonas strains could only oxidize Sb(III) but not As(III) (114,119,124,125). Furthermore, Hydrogenophaga taeniospiralis IDSBO-1, isolated by Terry et al (115), was shown to possess the aioA gene and oxidized As(III), but not Sb(III), under aerobic conditions.…”

Section: Microbial Antimony Cyclementioning

confidence: 99%

Microbial Antimony Biogeochemistry: Enzymes, Regulation, and Related Metabolic Pathways

Wang

Oremland

et al. 2016

Appl Environ Microbiol

Self Cite

163

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e Antimony (Sb) is a toxic metalloid that occurs widely at trace concentrations in soil, aquatic systems, and the atmosphere. Nowadays, with the development of its new industrial applications and the corresponding expansion of antimony mining activities, the phenomenon of antimony pollution has become an increasingly serious concern. In recent years, research interest in Sb has been growing and reflects a fundamental scientific concern regarding Sb in the environment. In this review, we summarize the recent research on bacterial antimony transformations, especially those regarding antimony uptake, efflux, antimonite oxidation, and antimonate reduction. We conclude that our current understanding of antimony biochemistry and biogeochemistry is roughly equivalent to where that of arsenic was some 20 years ago. This portends the possibility of future discoveries with regard to the ability of microorganisms to conserve energy for their growth from antimony redox reactions and the isolation of new species of "antimonotrophs."

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“…testosteroni [49][50][51], S. xenophaga [52,53] and N. oligotropha [54,55] were identified. These bacteria would be the indigenous bacteria in irrigation water and then colonized in the nutrient solution, and would aid in the self-purification of the recirculating nutrient solution.…”

Section: Discussionmentioning

confidence: 99%

Microbial community dynamics in the recirculating nutrient solution of tomato plug seedlings cultivated under ebb-and-flow system

Chen¹,

Li²,

Wang³

et al. 2019

Preprint

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Background: The ebb-and-flow system has ability to recirculate water and nutrients, and offers a good method to control nutrient leaching from greenhouses into the environment. However, the potential for the rapid spread of bacterial and fungal pathogens is the main hindrance for its adoption in vegetable seedlings production. Natural microflora has often shown a certain ability to suppress diseases.Results: Here, through 16S rRNA- and ITS1-targeted Illumina sequencing, the dynamic changes in bacterial and fungal communities in the recirculating nutrient solution were characterized for tomato plug seedlings cultivated in an ebb-and-flow system in summer and winter. Both bacterial number and microbial diversity in the nutrient solution increased with recirculating irrigation, and these changes differed between summer and winter. Pseudomonas was among the most predominant bacterial genera in the nutrient solution; its relative abundance gradually increased with recycling in summer but decreased dramatically in winter. In summer, the predominant bacteria also included Comamonas and Sediminibacterium , whose relative abundances in the nutrient solution decreased and increased, respectively. In winter, the nutrient solution was also colonized by Sphingomonas , predominantly at the late stage of irrigation. Among fungi, Amanita and Trichoderma were predominant in both summer and winter. Amanita gradually increased in summer but decreased rapidly after the first irrigation cycle in winter, whereas Trichoderma accumulated rapidly at the late stage of irrigation in both summer and winter. Alternaria and Fusarium were predominant in the nutrient solution only in summer, with the former decreased and the latter increased with recirculating irrigation. Moreover, Pseudomonas mediterranea , a potentially pathogenic bacterium, and Fusarium oxysporum , a fungal pathogen were present predominantly in winter and summer, respectively. Some potentially beneficial microbes functioning in plant-growth promotion and water self-purification, such as Sphingobium xenophagum , Trichoderma harzianum , and T. virens , were identified to be increased in the recirculating nutrient solution.Conclusions: The present data elucidate the bacterial and fungal dynamics in an ebb-and-flow system and provide useful information for pathogen control during tomato seedling production.

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High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

Cited by 39 publications

References 67 publications

Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

Microbial Antimony Biogeochemistry: Enzymes, Regulation, and Related Metabolic Pathways

Microbial community dynamics in the recirculating nutrient solution of tomato plug seedlings cultivated under ebb-and-flow system

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