Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons

Tikariha, Hitesh; Purohit, Hemant J.

doi:10.1016/j.ygeno.2018.12.005

Cited by 27 publications

(12 citation statements)

References 30 publications

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“…All the genera detected in both metagenomes are shown. *Significant differences between FN1 and FN4 microcosms as determined by STAMP (P < 0.05, difference between the proportions > 1% and twofold of ratio between the proportions, as determined by STAMP) condition in some hydrocarbon degraders [29]. The absence of the urtD and urtE genes in FN4 could only be attributed to the addition of CFMM, which provide the needed inorganic nitrogen, thus making it impracticable due to energy costs to use urea as nitrogen source.…”

Section: Discussionmentioning

confidence: 93%

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Salam¹,

Obayori

2020

Journal of Genetic Engineering and Biotechnology

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Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

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Section: Discussionmentioning

confidence: 93%

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Salam¹,

Obayori

2020

Journal of Genetic Engineering and Biotechnology

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“…Several cys enzymes were used to synthesize sulfites and convert sulfates into sulfides, and the existence of sulfate utilization enhanced the bacterial ability to produce amino acids, such as cysteine and methionine. 45 These processes provided biosulfur for the microbial communities in coals. Gene celF was another core gene linking the co-occurrence network of the C–N–S-related genes ( Figure 7 ), which was dominant in C degradation genes ( Figure 3 ).…”

Section: Discussionmentioning

confidence: 99%

Carbon–Nitrogen–Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals

Liu

Chen

et al. 2022

ACS Omega

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Coal microbes are the predominant form of life in the subsurface ecosystem, which play a vital role in biogeochemical cycles. However, the systematic information about carbon–nitrogen–sulfur (C–N–S)-related microbial communities in coal seams is limited. In this study, 16S rRNA gene data from a total of 93 microbial communities in coals were collected for meta-analysis. The results showed that 718 functional genera were related to the C–N–S cycle, wherein N 2 fixation, denitrification, and C degradation groups dominated in relative abundance, Chao1 richness, Shannon diversity, and niche width. Genus Pseudomonas having the most C–N–S-related functions showed the highest relative abundance, and genus Herbaspirillum with a higher abundance participated in C degradation, CH 4 oxidation, N 2 fixation, ammoxidation, and denitrification. Such Herbaspirillum was a core genus in the co-occurrence network of microbial prokaryotes and showed higher levels in weight degree, betweenness centrality, and eigenvector centrality. In addition, most of the methanogens could fix N 2 and dominated in the N 2 fixation groups. Among them, genera Methanoculleus and Methanosaeta showed higher levels in the betweenness centrality index. In addition, the genus Clostridium was linked to the methanogenesis co-occurrence network module. In parallel, the S reduction gene was present in the highest total relative abundance of genes, followed by the C degradation and the denitrification genes, and S genes (especially cys genes) were the main genes linked to the co-occurrence network of the C–N–S-related genes. In summary, this study strengthened our knowledge regarding the C–N–S-related coal microbial communities, which is of great significance in understanding the microbial ecology and geochemical cycle of coals.

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“…The denitri cation pathway was present in the RAST server (Supplementary Figure 4). nar, nir, nos and nor are the genes responsible for the conversion of nitrate to ammonia (Tikariha, H. and Purohit, H.J., 2019) were also present in the genome. Some previously published work has been shown how signi cant denitri cation is to control algal blooms (Jiang, X., et al, 2020).…”

Section: Polysaccharides Degradation Enzymesmentioning

confidence: 99%

Genomic insight for algicidal activity in Rhizobium strain AQ_MP

2021

Self Cite

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Occurrence of Harmful Algal Blooms (HABs) creates a threat to aquatic ecosystem affecting the existing ora and fauna. Hence, the mitigation of HABs through an eco-friendly approach remains a challenge for environmentalists. The present study provides the genomic insights of Rhizobium sp. (AQ_MP), an environmental isolate that showed the capability of degrading Microcystis aeruginosa (Cyanobacteria) at laboratory scale. Genome sequence analysis of Rhizobium sp. (AQ_MP) was performed to determine the algal lysis properties and toxin degradative pathway. It is envisaged that Rhizobium sp. (AQ_MP) secreted CAZymes like Glycosyltransferases (GT), Glycoside Hydrolases (GH), polysaccharide lyases (PL), which allowed algal polysaccharide degradation (lysis) and enabled nutrient release for the subsequent growth of Rhizobium sp. (AQ_MP) Genome analysis also showed the presence of the glutathione metabolic pathway, which is the biological detoxi cation pathway responsible for microcystin degradation. The conserved region mlrC, a microcystin toxin degrading responsible gene, was also annotated in Rhizobium sp. (AQ_MP). This study con rmed that Rhizobium sp. (AQ_MP) harbours a wide range of crucial enzymes released for lysis of Microcystis aeruginosa (M. aeruginosa) cells and also for degradation of microcystin toxin. This study thus nd promiscuity for scaling the lab based analysis to eld level in future.

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Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons

Cited by 27 publications

References 30 publications

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Carbon–Nitrogen–Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals

Genomic insight for algicidal activity in Rhizobium strain AQ_MP

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