Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge

Devpura, Neelam; Jain, Kunal; Patel, Anand; Joshi, Chaitanya G.; Madamwar, Datta

doi:10.1016/j.ibiod.2017.06.011

Cited by 40 publications

(5 citation statements)

References 42 publications

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“…The Pseudomonadales group is predicted to have a central role in terpenoid biosynthesis in the organic samples and fluorobenzoate degradation in the conventional site (Figure 7C). Both functions are consistent with reports from previous studies (Devpura et al, 2017; McDonald et al, 2019). The involvement of Pseudomonadales in terpenoid biosynthesis in the organic samples is consistent with the importance of this pathway as inferred across the analysis.…”

Section: Discussionsupporting

confidence: 93%

Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples

Bartuv

Vetcos

Medina

et al. 2023

Environmental Microbiology

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Fruits harbour abundant and diverse microbial communities that protect them from post‐harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of ‘Golden Delicious’ apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high‐quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.

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Section: Discussionsupporting

confidence: 93%

Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples

Bartuv

Vetcos

Medina

et al. 2023

Environmental Microbiology

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“…The genome of the microbial communities also showed potential for the biological nitrogen xation process which was evident from the presence of genes encoding the enzyme (nifB, nifE nifK, nifN) responsible for nitrogen xation to ammonia. Bacteria playing a dominant role in N metabolism at genus level in this study are similar to that of industrial polluted sites reported by Devpura et al 2017. The absence of nitrogen-xing reads can also be related to the high nitrogen (biologically available) and presence of aerobic conditions in MGB-3.…”

Section: General Metabolism Of Microbial Communitysupporting

confidence: 87%

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

Sandhu

Paul

Jha³

2021

Preprint

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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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“…Alicyclobacillus (Firmicutes) was generally capable of degrading polycyclic aromatic hydrocarbons (PAHs) in crude-oil contaminated soil (Yang et al, 2014). A higher abundance of Firmicutes after forest fire has been previously reported (Ferrenberg et al, 2013), and these microorganisms might dominate post-fire forest ecosystems through different succession stages: i) survive after the fire and out-compete the majority of copiotrophs in stressed condition via spores (Yeager et al, 2005;Galperin et al, 2012), ii) take advantage of labile C to maintain their fast growth and metabolisms (Verastegui et al, 2014;Bonanomi et al, 2019), while additional C/nutrients are offered by recovering plants, and iii) degrade complex C, such as chitin, for survival when available labile resources are depleted (Ng et al, 2014;Devpura et al, 2017;Bonanomi et al, 2019).…”

Section: Som and Microbiome Interactions In S2 Soilmentioning

confidence: 97%

Organic matter chemistry and bacterial community structure regulate decomposition processes in post-fire forest soils

Jeewani

et al. 2021

Soil Biology and Biochemistry

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Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge

Cited by 40 publications

References 42 publications

Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples

Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples

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

Organic matter chemistry and bacterial community structure regulate decomposition processes in post-fire forest soils

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