Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions.

The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.

Aerobic denitration of 2,4,6-trinitrotoluene in the presence of phenazine compounds and reduced pyridine nucleotides.

Phenazine-containing spent culture supernatants of Pseudomonas aeruginosa concentrated with a C18 solid-phase extraction cartridge initiate NAD(P)H-dependent denitration of 2,4,6-trinitrotoluene (TNT). In this study, TNT denitration was investigated under aerobic conditions using two phenazine secondary metabolites excreted by P. aeruginosa, pyocyanin (Py) and its precursor phenazine-1- carboxylic acid (PCA), and two chemically synthesized pyocyanin analogs, phenazine methosulfate (PMS+) and phenazine ethosulfate (PES+). The biomimetic Py/NAD(P)H/O2 system was characterized and found to extensively denitrate TNT in unbuffered aqueous solution with minor production of toxic amino aromatic derivatives. To a much lesser extent, TNT denitration was also observed with PMS+ and PES+ in the presence of NAD(P)H. No TNT denitration was detected with the biomimetic PCA/NAD(P)H/O2 system. Electron paramagnetic resonance (EPR) spectroscopy analysis of the biomimetic Py/NAD(P)H/O2 system revealed the generation of superoxide radical anions (O2 •−). In vitro TNT degradation experiments in the presence of specific inhibitors of reactive oxygen species suggest a nucleophilic attack of superoxide radical anion followed by TNT denitration through an as yet unknown mechanism. The results of this research confirm the high functional versatility of the redox-active metabolite pyocyanin and the susceptibility of aromatic compounds bearing electron withdrawing substituents, such as nitro groups, to superoxide-driven nucleophilic attack.

Microbial 2,4,6-trinitrotoluene degradation: could we learn from (bio)chemistry for bioremediation and vice versa?

2,4,6-Trinitrotoluene (TNT) is released in nature from manufacturing or demilitarization facilities but also after munitions firing/detonation or leakage from explosive remnants of war. Due to its toxicity and recalcitrance, life cycle of TNT-containing products and bioremediation are critical issues. As TNT is a strongly electron-deficient aromatic with a positive molecular quadrupole moment and three electrophilic nitro groups, its environmental fate is contingent upon specific sorptive electron donor-acceptor interactions and nucleophilic, reductive (bio)transformations. The microbial degradation of TNT is governed by cometabolism and therefore depends on the growth substrate(s) available in contaminated environments. Long considered an ecotoxicological safety endpoint, the immobilization of TNT metabolites derived from nitro moiety reduction in soil is controversial because they preferentially bind to the dissolved soil organic matter which can be released into surface and groundwaters. The ever-growing biochemical knowledge of TNT degradation has made bioaugmentation and phytoremediation attractive alternatives. While the discovery and engineering of microorganisms with novel/improved degradative abilities are very challenging, the deciphering of the physiological roles of promiscuous enzymes involved in TNT biodegradation, such as type II hydride transferases of the Old Yellow Enzyme family, opens new perspectives for bioremediation. Finally, transgenic plants have enabled effective phytoremediation at the field scale, which is emerging as the preferable in situ option to rehabilitate TNT-contaminated sites.

Draft Whole-Genome Sequence of the Anthracene-Degrading Strain Mycolicibacterium frederiksbergense LB501T, Isolated from a Polycyclic Aromatic Hydrocarbon-Contaminated Soil.

Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion pathways with promiscuous activities.

Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil.

We report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium sp. strain LB126. The genes involved in the upper biodegradation pathway of fluorene are located on a plasmid, and the lower pathway that generates tricarboxylic acid cycle intermediates is initiated by the meta-cleavage of protocatechuic acid that is chromosomally encoded.

Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments.

It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota.

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology.

Microbial ecosystems exhibit specific robustness attributes arising from the assembly and interaction networks of diverse, heterogeneous communities challenged by fluctuating environmental conditions. Synthetic ecology provides new insights into key biodiversity-stability relationships and robustness determinants of host-associated or environmental microbiomes. Driven by the advances of meta-omics technologies and bioinformatics, community-centered approaches (defined as molecular systems synecology) combined with the development of dynamic and mechanistic mathematical models make it possible to decipher and predict the outcomes of microbial ecosystems under disturbances. Beyond discriminating the normal operating range and natural, intrinsic dynamics of microbial processes from systems-level responses to environmental forcing, predictive modeling is poised to be integrated within prescriptive analytical frameworks and thus provide guidance in decision-making and proactive microbial resource management.

Denitration of 2,4,6-trinitrotoluene in aqueous solutions using small-molecular-weight catalyst(s) secreted by Pseudomonas aeruginosa ESA-5.

The denitration of 2,4,6-trinitrotoluene (TNT) can produce mono- or dinitro aromatic compounds susceptible to microbial mineralization. In the present study, denitration of TNT and other nitro aromatic compounds was investigated with a solid-phase extract obtained from the culture supernatant of Pseudomonas aeruginosa ESA-5 grown on a chemically defined aerobic medium. When the C18 solid-phase extract containing extracellular catalysts (EC) was incubated with TNT and NAD(P)H, we observed a significant release of nitrite. The concentration of nitrite released in the reaction medium was strongly dependent on the concentration of NAD(P)H and EC. Denitration also occurred with two TNT-related molecules, 2,4,6-trinitrobenzaldehyde, and 2,4,6-trinitrobenzyl alcohol. The release of nitrite was coupled with the formation of two polar metabolites, and mass spectrometry analyses indicated that each of these compounds had lost two nitro groups from the trinitro aromatic parent molecule. During this process, the production of toxic reduced TNT metabolites was minimal. The incubation of EC with TNT, NAD(P)H, and specific scavengers of reactive oxygen species suggested the involvement of superoxide radicals (O2*-) and hydrogen peroxide in the denitration process. Results obtained in this study reveal for the first time that extracellular small-molecular-weight substance(s) of bacterial origin can serve as green catalyst(s) to initiate TNT denitration. In addition, this study gives clear evidence for the production of a TNT metabolite bearing a single nitro groupfollowing a denitration reaction with catalyst(s) of biotic origin.

Denitration of 2,4,6-trinitrotoluene by Pseudomonas aeruginosa ESA-5 in the presence of ferrihydrite.

Denitration of 2,4,6-trinitrotoluene (TNT) was evaluated in oxygen-depleted enrichment cultures. These cultures were established starting with an uncontaminated or a TNT-contaminated soil inoculum and contained TNT as sole nitrogen source. Incubations were carried out in the presence or absence of ferrihydrite. A significant release of nitrite was observed in the liquid culture containing TNT, ferrihydrite, and inoculum from a TNT-contaminated soil. Under these conditions, Pseudomonas aeruginosa was the predominant bacterium in the enrichment, leading to the isolation of P. aeruginosa ESA-5 as a pure strain. The isolate had TNT denitration capabilities as confirmed by nitrite release in oxygen-depleted cultures containing TNT and ferrihydrite. In addition to reduced derivatives of TNT, several unidentified metabolites were detected. Concomitant to a decrease of TNT concentration, a release of nitrite was observed. The concentration of nitrite peaked and then it slowly decreased. In the absence of TNT, the drop in the concentration of nitrite in oxygen-depleted cultures was lower when ferrihydrite was provided, suggesting that ferrihydrite inhibited the utilization of nitrite by P. aeruginosa ESA-5.

Emerging high-throughput approaches to analyze bioremediation of sites contaminated with hazardous and/or recalcitrant wastes.

Sustainable development requires the promotion of environmental management and a constant search for new technologies to treat a wide range of aquatic and terrestrial habitats contaminated by increasing anthropogenic activities. Bioremediation, i.e. the elimination of natural or xenobiotic pollutants by living organisms, is an environmentally friendly and cost-effective alternative to physico-chemical cleanup options. However, the strategy and outcome of bioremediation in open systems or confined environments depend on a variety of physico-chemical and biological factors that need to be assessed and monitored. In particular, microorganisms are key players in bioremediation applications, yet their catabolic potential and their dynamics in situ remain poorly characterized. To perform a comprehensive assessment of the biodegradative potential of a contaminated site and efficiently monitor changes in the structure and activities of microbial communities involved in bioremediation processes, sensitive, fast and large-scale methods are needed. Over the last few years, the scientific literature has revealed the progressive emergence of genomic high-throughput technologies in environmental microbiology and biotechnology. In this review, we discuss various high--throughput techniques and their possible--or already demonstrated-application to assess biotreatment of contaminated environments.

Aerobic growth of Escherichia coli with 2,4,6-trinitrotoluene (TNT) as the sole nitrogen source and evidence of TNT denitration by whole cells and cell-free extracts.

Escherichia coli grew aerobically with 2,4,6-trinitrotoluene (TNT) as sole nitrogen source and caused TNT's partial denitration. This reaction was enhanced in nongrowing cell suspensions with 0.516 mol nitrite released per mol TNT. Cell extracts denitrated TNT in the presence of NAD(P)H. Isomers of amino-dimethyl-tetranitrobiphenyl were detected and confirmed with U-15N-labeled TNT.