Peculiarities of the degradation of benzoate and its chloro- and hydroxy-substituted analogs by actinobacteria

Solyanikova, Inna P.; Emelyanova, Elena V.; Шумкова, Е. С.; Егорова, Д. О.; Korsakova, E. S.; Плотникова, Е. Г.; Golovleva, Ludmila

doi:10.1016/j.ibiod.2015.02.028

Cited by 28 publications

(13 citation statements)

References 35 publications

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“…Actinomycetales’ significant impact was also simulated in various pathways associated with degradation of fluorobenzoate and compounds from the polychlorinated biphenyls (PCBs) pollutant family. This may stem from one of Actinomycetales high dominance enzyme, benzoate 1,2-dioxygenase (EC 1.14.12.10), which catalyzes a variety of ’first-step’ reactions toward the degradation of an array of benzoate analogs ( Solyanikova et al, 2015 ). In the root environment, pathways that were affected by the removal included lipids, terepnoids, and plant induced secondary metabolites categories ( Figure 3B ).…”

Section: Resultsmentioning

confidence: 99%

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

et al. 2017

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Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants – wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.

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Section: Resultsmentioning

confidence: 99%

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

et al. 2017

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“…( Actinobacteria ) are Gram-positive soil bacteria, appearing in a rod or coccoid shape ( 1 ), which grow under aerobic and anaerobic conditions ( 1 ). They are present in Antarctic ( 2 ) and desert ( 3 ) soils and in alkaline and subglacial lakes ( 4 , 5 ), and some species are known to promote plant growth ( 5 – 8 ), to inhibit plant-pathogenic bacteria and fungi or wood-decaying fungi ( 7 , 9 ), and to degrade a wide range of organic and polyaromatic pollutants ( 4 , 10 , 11 ).…”

Section: Announcementmentioning

confidence: 99%

Whole-Genome Sequences of Two Arthrobacter sp. Strains, 4041 and 4042, Potentially Usable in Agriculture and Environmental Depollution

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Grizard²,

Chablais

et al. 2018

Microbiol Resour Announc

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“…X80625]), physiological, and biochemical features analysis ( 1 ). Strain P25 was capable of utilizing a broad range of aromatic compounds (biphenyl, phenol, toluene, naphthalene, salicylate, gentisate, ortho -phthalate, benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, and 3,4-dihydroxybenzoate), as well as their substituted derivatives (chlorinated biphenyls and chlorobenzoates, para -methylbenzoate, and 2,4-dichlorophenoxyacetate) as a sole carbon and energy source ( 2 – 4 ). R. ruber P25 is an active destructor of polychlorinated biphenyls, which are toxic and persistent organic pollutants ( 5 ).…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated Biphenyl Degrader

et al. 2015

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Peculiarities of the degradation of benzoate and its chloro- and hydroxy-substituted analogs by actinobacteria

Cited by 28 publications

References 35 publications

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

Whole-Genome Sequences of Two Arthrobacter sp. Strains, 4041 and 4042, Potentially Usable in Agriculture and Environmental Depollution

Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated Biphenyl Degrader

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