A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

Anaerobic degradation processes are very important to attenuate polycyclic aromatic hydrocarbons (PAHs) in saturated, anoxic sediments. However, PAHs are poorly degradable, leading to very slow microbial growth and thus resulting in only a few cultures that have been enriched and studied so far. Here, we report on a new phenanthrene-degrading, sulfate-reducing enrichment culture, TRIP1. Genome-resolved metagenomics and strain specific cell counting with FISH and flow cytometry indicated that the culture is dominated by a microorganism belonging to the Desulfobacteraceae family (60% of the community) and sharing 93% 16S rRNA sequence similarity to the naphthalene-degrading, sulfate-reducing strain NaphS2. The anaerobic degradation pathway was studied by metabolite analyses and revealed phenanthroic acid as the major intermediate consistent with carboxylation as the initial activation reaction. Further reduced metabolites were indicative of a stepwise reduction of the ring system. We were able to measure the presumed second enzyme reaction in the pathway, phenanthroate-CoA ligase, in crude cell extracts. The reaction was specific for 2-phenanthroic acid and did not transform other isomers. The present study provides first insights into the anaerobic degradation pathways of three-ringed PAHs. The biochemical strategy follows principles known from anaerobic naphthalene degradation, including carboxylation and reduction of the aromatic ring system.

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“…() to reconstruct nearly complete genomes using the pre‐assembly approach described in Gkanogiannis et al . ().…”

Section: Methodsmentioning

confidence: 97%

“…Processing of metagenomics shotgun reads. The raw reads were processed as in Adam et al (2017) to reconstruct nearly complete genomes using the pre-assembly approach described in Gkanogiannis et al (2016).…”

Section: Metagenome Sequencingmentioning

confidence: 99%

Anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture

Himmelberg

Brüls

Farmani

et al. 2018

Environmental Microbiology

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“…GapCloser (http://soap.genomics.org.cn/soapdenovo.html) was run successively with the PE and MP data to reduce the number of undetermined bases (Supplementary Table 1). Completeness and representativeness of the assembly was assessed using sequence clustering (binning) software described in Gkanogiannis et al, (2016). The assembly data were integrated for automatic annotation into the Microscope platform (Vallenet et al, 2013), http://www.genoscope.cns.fr/agc/microscope/home.…”

Section: Methodsmentioning

confidence: 99%

Microbial Degradation of a Recalcitrant Pesticide: Chlordecone

et al. 2016

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Chlordecone (Kepone®) is a synthetic organochlorine insecticide (C10Cl10O) used worldwide mostly during the 1970 and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 μg/mL) in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C9Cl5H3 (named B1) as well as two minor metabolites C10Cl9HO (named A1) and C9Cl4H4 (named B3). Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus, and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process.

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“…The metagenome of the TRIP culture was sequenced, and genome-resolved analyses (Gkanogiannis et al, 2016) led to the reconstruction of five nearly-complete genomes that were annotated using the MicroScope microbial genome annotation and analysis platform (Médigue et al, 2017;Himmelberg et al, 2018). A general overview of the main genomic features of these organisms is presented in Table 1.…”

Section: Resultsmentioning

confidence: 99%

Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation

Kraiselburd

Brüls

Heilmann

et al. 2019

Environmental Microbiology

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SummaryPolycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As oxygen is rapidly depleted in water‐saturated PAH‐contaminated sites, anaerobic microorganisms are crucial for their consumption. Here, we report the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of Deltaproteobacteria and genome‐resolved metagenomics led to the reconstruction of its genome along with a handful of genomes from lower abundance bacteria. Proteogenomic analyses confirmed metabolic capabilities for dissimilatory sulfate reduction and indicated the presence of the Embden‐Meyerhof‐Parnas pathway, a complete tricarboxylic acid cycle as well as a complete Wood‐Ljungdahl pathway. Genes encoding enzymes putatively involved in the degradation of phenanthrene were identified. This includes two gene clusters encoding a multisubunit carboxylase complex likely involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses, and provide the first insights into the metabolic pathway responsible for the anaerobic degradation of three‐ringed PAHs.

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A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

Cited by 10 publications

References 18 publications

Anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture

Anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture

Microbial Degradation of a Recalcitrant Pesticide: Chlordecone

Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation

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