Metagenomic Analysis for Taxonomic and Functional Potential of Polyaromatic Hydrocarbons (PAHs) and Polychlorinated Biphenyl (PCB) Degrading Bacterial Communities in Steel Industrial Soil

Abstract Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has potential to remediate these contaminants. The present study highlights the metabolic potential of resident microbial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. The sample MGB-3 was richer in terms of macronutrients (C, N, P) supporting high microbial diversity than MGB-2. Taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic together with physicochemical analysis of contaminated site which improves the understanding of metabolic potential and adaptation of bacteria growing under stressful environment.

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Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

mSystems ◽

10.1128/msystems.00517-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Nunzia Picone ◽

Carmen Hogendoorn ◽

Geert Cremers ◽

Lianna Poghosyan ◽

Arjan Pol ◽

...

Keyword(s):

Microbial Community ◽

Greenhouse Gas ◽

Relative Abundance ◽

Hot Spots ◽

Microbial Community Composition ◽

Metagenomic Analysis ◽

Volcanic Soil ◽

Metabolic Potential ◽

Gas Emissions ◽

Geothermal Activity

ABSTRACT Volcanic and geothermal environments are characterized by low pH, high temperatures, and gas emissions consisting of mainly CO2 and varied CH4, H2S, and H2 contents which allow the formation of chemolithoautotrophic microbial communities. To determine the link between the emitted gases and the microbial community composition, geochemical and metagenomic analysis were performed. Soil samples of the geothermic region Favara Grande (Pantelleria, Italy) were taken at various depths (1 to 50 cm). Analysis of the gas composition revealed that CH4 and H2 have the potential to serve as the driving forces for the microbial community. Our metagenomic analysis revealed a high relative abundance of Bacteria in the top layer (1 to 10 cm), but the relative abundance of Archaea increased with depth from 32% to 70%. In particular, a putative hydrogenotrophic methanogenic archaeon, related to Methanocella conradii, appeared to have a high relative abundance (63%) in deeper layers. A variety of [NiFe]-hydrogenase genes were detected, showing that H2 was an important electron donor for microaerobic microorganisms in the upper layers. Furthermore, the bacterial population included verrucomicrobial and proteobacterial methanotrophs, the former showing an up to 7.8 times higher relative abundance. Analysis of the metabolic potential of this microbial community showed a clear capacity to oxidize CH4 aerobically, as several genes for distinct particulate methane monooxygenases and lanthanide-dependent methanol dehydrogenases (XoxF-type) were retrieved. Analysis of the CO2 fixation pathways showed the presence of the Calvin-Benson-Bassham cycle, the Wood-Ljungdahl pathway, and the (reverse) tricarboxylic acid (TCA) cycle, the latter being the most represented carbon fixation pathway. This study indicates that the methane emissions in the Favara Grande might be a combination of geothermal activity and biological processes and further provides insights into the diversity of the microbial population thriving on CH4 and H2. IMPORTANCE The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that most of the microorganisms in this extreme environment are only distantly related to cultivated bacteria. The results obtained profoundly increased the understanding of these natural hot spots of greenhouse gas production/degradation and will help to enrich and isolate the microbial key players. After isolation, it will become possible to unravel the molecular mechanisms by which they adapt to extreme (thermo/acidophilic) conditions, and this may lead to new green enzymatic catalysts and technologies for industry.

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Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis

10.1101/760637 ◽

2019 ◽

Cited By ~ 1

Author(s):

Itzel Gaytán ◽

Ayixon Sánchez-Reyes ◽

Manuel Burelo ◽

Martín Vargas-Suárez ◽

Ivan Liachko ◽

...

Keyword(s):

Microbial Community ◽

Metagenomic Analysis ◽

Contaminated Sites ◽

Physical Analysis ◽

Glycol Ethers ◽

Metabolic Potential ◽

Proximity Ligation ◽

Polyurethane Acrylate ◽

Biodegradation Process ◽

Genes Encoding

ABSTRACTPolyurethanes (PU) are the sixth more produced plastics with around 19-million tons/year, but since they are not recyclable they are burned or landfilled, generating ecological damage. To elucidate the mechanisms that landfill microbial communities perform to attack recalcitrant PU plastic, we studied the BP8 community selected by its capability to grow in a water PU dispersion (WPUD) that contains a polyether-polyurethane-acrylate (PE-PU-A) copolymer and xenobiotic additives (N-methyl 2-pyrrolidone, isopropanol and glycol ethers), and performed a proximity ligation-based metagenomic analysis for revealing the community structure and potential biodegradative capacity. Additives were consumed early whereas the copolymer was cleaved throughout the 25-days incubation. BP8 metagenomic deconvolution reconstructed five genomes, three of them from novel species. Genes encoding enzymes for additives biodegradation were predicted. The chemical and physical analysis of the biodegradation process, and the identified biodegradation products show that BP8 cleaves esters, aromatic urethanes, C-C and ether groups by hydrolytic and oxidative mechanisms. The metagenomic analysis allowed to predicting comprehensive metabolic pathways and enzymes that explain the observed PU biodegradation. This is the first study revealing the metabolic potential of a landfill microbial community that thrives within a WPUD system and shows potential for bioremediation of polyurethane- and xenobiotic additives-contaminated sites.

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