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Aso RE, Obuekwe IS. Polycyclic aromatic hydrocarbon: underpinning the contribution of specialist microbial species to contaminant mitigation in the soil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:654. [PMID: 38913190 DOI: 10.1007/s10661-024-12778-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024]
Abstract
The persistence of PAHs poses a significant challenge for conventional remediation approaches, necessitating the exploration of alternative, sustainable strategies for their mitigation. This review underscores the vital role of specialized microbial species (nitrogen-fixing, phosphate-solubilizing, and biosurfactant-producing bacteria) in tackling the environmental impact of polycyclic aromatic hydrocarbons (PAHs). These resistant compounds demand innovative remediation strategies. The study explores microbial metabolic capabilities for converting complex PAHs into less harmful byproducts, ensuring sustainable mitigation. Synthesizing literature from 2016 to 2023, it covers PAH characteristics, sources, and associated risks. Degradation mechanisms by bacteria and fungi, key species, and enzymatic processes are examined. Nitrogen-fixing and phosphate-solubilizing bacteria contributions in symbiotic relationships with plants are highlighted. Biosurfactant-producing bacteria enhance PAH solubility, expanding microbial accessibility for degradation. Cutting-edge trends in omics technologies, synthetic biology, genetic engineering, and nano-remediation offer promising avenues. Recommendations emphasize genetic regulation, field-scale studies, sustainability assessments, interdisciplinary collaboration, and knowledge dissemination. These insights pave the way for innovative, sustainable PAH-contaminated environment restoration.
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Affiliation(s)
- Rufus Emamoge Aso
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin, Edo State, Nigeria
| | - Ifeyinwa Sarah Obuekwe
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin, Edo State, Nigeria.
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2
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Yang J, Jiang L, Guo Z, Sarkodie EK, Li K, Shi J, Peng Y, Liu H, Liu X. The Cd immobilization mechanisms in paddy soil through ureolysis-based microbial induced carbonate precipitation: Emphasis on the coexisting cations and metatranscriptome analysis. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133174. [PMID: 38086299 DOI: 10.1016/j.jhazmat.2023.133174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 02/08/2024]
Abstract
Microbial induced carbonate precipitation (MICP) can immobilize metals and reduce their bioavailability. However, little is known about the immobilization mechanism of Cd in the presence of soil cations and the triggered gene expression and metabolic pathways in paddy soil. Thus, microcosmic experiments were conducted to study the fractionation transformation of Cd and metatranscriptome analysis. Results showed that bioavailable Cd decreased from 0.62 to 0.29 mg/kg after 330 d due to the MICP immobilization. This was ascribed to the increase in carbonate bound, Fe-Mn oxides bound, and residual Cd. The underlying immobilization mechanisms could be attributed to the formation of insoluble Cd-containing precipitates, the complexation and lattice substitution with carbonate and Fe, Mn and Al (hydr)oxides, and the adsorption on functional group on extracellular polymers of cell. During the MICP immobilization process, up-regulated differential expression urease genes were significantly enriched in the paddy soil, corresponding to the arginine biosynthesis, purine metabolism and atrazine degradation. The metabolic pathway of bacterial chemotaxis, flagellum assembly, and peptidoglycan biosynthesis and the expression of cadA gene related to Cd excretion enhanced Cd resistance of soil microbiome. Therefore, this study provided new insights into the immobilization mechanisms of Cd in paddy soils through ureolysis-based MICP process.
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Affiliation(s)
- Jiejie Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
| | - Ziwen Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Emmanuel Konadu Sarkodie
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Kewei Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Jiaxin Shi
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Yulong Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
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3
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Gupta RK, Tikariha H, Purohit HJ, Khardenavis AA. Pangenome-driven insights into nitrogen metabolic characteristics of Citrobacter portucalensis strain AAK_AS5 associated with wastewater nitrogen removal. Arch Microbiol 2023; 205:270. [PMID: 37356030 DOI: 10.1007/s00203-023-03597-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/27/2023]
Abstract
Nitrogen metabolism in the genus Citrobacter is very poorly studied despite its several implications in wastewater treatment. In the current study, Citrobacter portucalensis strain AAK_AS5 was assessed for remediation of simulated wastewater supplemented with different inorganic nitrogen sources. Combination of (NH4)2SO4 with KNO3 was the most preferred for achieving high growth density followed by (NH4)2SO4 and KNO3 alone. This was in agreement with highest ammonical nitrogen removal of 92.9% in the presence of combined nitrogen sources and the corresponding nitrate nitrogen removal of 93% in the presence of KNO3. Furthermore, these removal capacities were validated by investigating the uniqueness and the spread of metabolic features through pan-genomic approach that revealed the largest number of unique genes (2097) and accessory genes (705) in strain AAK_AS5. Of the total 44 different types of nitrogen metabolism-related genes, 39 genes were associated with the core genome, while 5 genes such as gltI, nasA, nasR, nrtA, and ntrC uniquely belonged to the accessory genome. Strain AAK_AS5 possessed three major nitrate removal pathways viz., assimilatory and dissimilatory nitrate reduction to ammonia (ANRA & DNRA), and denitrification; however, the absence of nitrification was compensated by ammonia assimilation catalyzed by gene products of the GDH and GS-GOGAT pathways. narGHIJ encoding the respiratory nitrate reductase was commonly identified in all the studied genomes, while genes such as nirK, norB, and nosZ were uniquely present in the strain AAK_AS5 only. A markedly different genetic content and metabolic diversity between the strains reflected their adaptive evolution in the environment thus highlighting the significance of C. portucalensis AAK_AS5 for potential application in nitrogen removal from wastewater.
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Affiliation(s)
- Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hitesh Tikariha
- NUS Environmental Research Institute, National University of Singapore, Singapore, 117411, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
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Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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5
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Wang M, Ding M, Yuan Y. Bioengineering for the Microbial Degradation of Petroleum Hydrocarbon Contaminants. Bioengineering (Basel) 2023; 10:bioengineering10030347. [PMID: 36978738 PMCID: PMC10045523 DOI: 10.3390/bioengineering10030347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/18/2023] Open
Abstract
Petroleum hydrocarbons are relatively recalcitrant compounds, and as contaminants, they are one of the most serious environmental problems. n-Alkanes are important constituents of petroleum hydrocarbons. Advances in synthetic biology and metabolic engineering strategies have made n-alkane biodegradation more designable and maneuverable for solving environmental pollution problems. In the microbial degradation of n-alkanes, more and more degradation pathways, related genes, microbes, and alkane hydroxylases have been discovered, which provide a theoretical basis for the further construction of degrading strains and microbial communities. In this review, the current advances in the microbial degradation of n-alkanes under aerobic condition are summarized in four aspects, including the biodegradation pathways and related genes, alkane hydroxylases, engineered microbial chassis, and microbial community. Especially, the microbial communities of “Alkane-degrader and Alkane-degrader” and “Alkane-degrader and Helper” provide new ideas for the degradation of petroleum hydrocarbons. Surfactant producers and nitrogen providers as a “Helper” are discussed in depth. This review will be helpful to further achieve bioremediation of oil-polluted environments rapidly.
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Affiliation(s)
- Minzhen Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Correspondence:
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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6
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Oyetibo GO, Adebusoye SA, Ilori MO, Amund OO. Heavy metals assessment of ecosystem polluted with wastewaters and taxonomic profiling of multi-resistant bacteria with potential for petroleum hydrocarbon catabolism in nitrogen-limiting medium. World J Microbiol Biotechnol 2023; 39:84. [PMID: 36693977 DOI: 10.1007/s11274-023-03524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
The coexistence of heavy metals (HMs) and petroleum hydrocarbons (PHs) exacerbates ecotoxicity and impair the drivers of eco-functionalities that stimulate essential nutrients for the productivity of the impacted environment. Profiling the bacteria that stem the ecological impact via HMs sequestration and PHs catabolism with nitrogen fixation is imperative to bioremediation of the polluted sites. The sediment of site that was consistently contaminated with industrial wastewaters was analysed for ecological toxicants and the bacterial strains that combined HMs resistance with PHs catabolism in a nitrogen-limiting system were isolated from the sediment and characterized. The geochemistry of the samples revealed the co-occurrence of the above-benchmark concentrations of HMs with the derivatives of hydrocarbons. Notwithstanding, nickel and mercury (with 5% each of the total metal concentrations in the polluted site) exhibited probable effect concentrations on the biota and thus hazardous to the ecosystem. Approx. 31% of the bacterial community, comprising unclassified Planococcaceae, unclassified Bradyrhizobiaceae, Rhodococcus, and Bacillus species, resisted 160 µmol Hg2+ in the nitrogen-limiting system within 24 h post-inoculation. The bacterial strains adopt volatilization, and sometimes in combination with adsorption/bioaccumulation strategies to sequester Hg2+ toxicity while utilizing PHs as sources of carbon and energy. Efficient metabolism of petroleum biomarkers (> 87%) and Hg2+ sequestration (≥ 75% of 40 µmol Hg2+) displayed by the selected bacterial strains portend the potential applicability of the bacilli for biotechnological restoration of the polluted site.
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Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria. .,Institute of Maritime Studies, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.
| | - Sunday A Adebusoye
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria
| | - Matthew O Ilori
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.,Institute of Maritime Studies, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.,Office of the Vice Chancellor, Elizade University, Ilara-Mokin, Ondo State, Nigeria
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7
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Abstract
The detection and quantification of transposable elements (TE) are notoriously challenging despite their relevance in evolutionary genomics and molecular ecology. The main hurdle is caused by the dependence of numerous tools on genome assemblies, whose level of completion directly affects the comparability of the results across species or populations. dnaPipeTE, whose use is demonstrated here, tackles this issue by directly performing TE detection, classification, and quantification from unassembled short reads. This chapter details all the required steps to perform a comparative analysis of the TE content between two related species, starting from the installation of a recently containerized version of the program to the post-processing of the outputs.
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Affiliation(s)
- Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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8
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Jha V, Bombaywala S, Purohit H, Dafale NA. Differential colonization and functioning of microbial community in response to phosphate levels. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115856. [PMID: 35985261 DOI: 10.1016/j.jenvman.2022.115856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Microbes play a major role in phosphate cycling and regulate its availability in various environments. The metagenomic study highlights the microbial community divergence and interplay of phosphate metabolism functional genes in response to phosphate rich (100 mgL-1), limiting (25 mgL-1), and stressed (5 mgL-1) conditions at lab-scale bioreactor. Total five core phyla were found responsive toward different phosphate (Pi) levels. However, major variations were observed in Proteobacteria and Actinobacteria with 33-81% and 5-56% relative abundance, respectively. Canonical correspondence analysis reflects the colonization of Sinorhizobium (0.8-4%), Mesorhizobium (1-4%), Rhizobium (0.5-3%) in rich condition whereas, Pseudomonas (1-2%), Rhodococcus (0.2-2%), Flavobacterium (0.2-1%) and Streptomyces (0.3-4%) colonized in limiting and stress condition. The functional profiling demonstrates that Pi limiting and stress condition subjected biomass were characterized by abundant PQQ-Glucose dehydrogenase, alkaline phosphatase, 5'-nucleotidase, and phospholipases C genes. The finding implies that the major abundant genera belonging to phosphate solubilization enriched in limiting/stressed conditions decide the functional turnover by modulating the metabolic flexibility for Pi cycling. The study gives a better insight into intrinsic ecological responsiveness mediated by microbial communities in different Pi conditions that would help to design the microbiome according to the soil phosphate condition. Furthermore, this information assists in sustainably maintaining the ecological balance by omitting excessive chemical fertilizers and eutrophication.
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Affiliation(s)
- Varsha Jha
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sakina Bombaywala
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemant Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Li Y, Zhang Y, Xue S. pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs. Front Microbiol 2022; 13:952285. [PMID: 36187958 PMCID: PMC9515653 DOI: 10.3389/fmicb.2022.952285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5–6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5–6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines, Anhui University of Science and Technology, Huainan, China
- *Correspondence: Yang Li, ; ; orcid.org/0000-0002-8946-3962
| | - Yuanyuan Zhang
- School of Safety Science and Engineering, Anhui University of Science and Technology, Huainan, China
| | - Sheng Xue
- School of Safety Science and Engineering, Anhui University of Science and Technology, Huainan, China
- Joint National-Local Engineering Research Centre for Safe and Precise Coal Mining, Anhui University of Science and Technology, Huainan, China
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10
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Li Y, Liu B, Chen J, Yue X. Carbon-Nitrogen-Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals. ACS OMEGA 2022; 7:22671-22681. [PMID: 35811862 PMCID: PMC9260939 DOI: 10.1021/acsomega.2c02126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 06/03/2023]
Abstract
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 N2 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, CH4 oxidation, N2 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 N2 and dominated in the N2 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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Affiliation(s)
- Yang Li
- State
Key Laboratory of Mining Response and Disaster Prevention and Control
in Deep Coal Mines, Anhui University of
Science & Technology, Huainan, Anhui 232001, China
- Institute
of Energy, Hefei Comprehensive National Science Center, Hefei, Anhui 230031, China
| | - Bingjun Liu
- State
Key Laboratory of Mining Response and Disaster Prevention and Control
in Deep Coal Mines, Anhui University of
Science & Technology, Huainan, Anhui 232001, China
- Institute
of Energy, Hefei Comprehensive National Science Center, Hefei, Anhui 230031, China
| | - Jian Chen
- Coal
Mining National Engineering and Technology Research Institute, Huainan, Anhui 232001, China
| | - Xuelian Yue
- Jinneng
Holding Shanxi Science and Technology Research Institute Co. LTD., Taiyuan, Shanxi 030600, China
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11
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Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes. Appl Microbiol Biotechnol 2022; 106:4643-4654. [PMID: 35699736 DOI: 10.1007/s00253-022-12020-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Reconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms resilient to isolation in laboratory conditions. Here, we assembled 12 high-quality metagenome-assembled genomes (MAGs) with an estimated completion of ≥ 90% from cow and buffalo rumen metagenomes. Average nucleotide identity (ANI) score-based screening with an existing database suggests the novelty of these genomes. Gene prediction led to the identification of 30,359 protein-encoding genes (PEGs) across 12 genomes, of which only 44.8% were annotated against a specific functional attribute. Further analysis revealed the presence of 985 carbohydrate-active enzymes (CAZymes) from more than 50 glycoside hydrolase families, of which 90% do not have a proper match in the CAZy database. Genome mining revealed the presence of a high frequency of plant biomass deconstructing genes in Bacteroidetes MAGs compared to Firmicutes. The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries. KEY POINTS: • Genome binning plays a crucial role in revealing the metabolic potential of uncultivable microbes. • Assembled 12 novel genomes from cow and buffalo rumen metagenome datasets. • High frequency of plant biomass deconstructing genes identified in Bacteroidetes MAGs.
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12
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Li Y, Liu B, Tu Q, Xue S, Liu X, Wu Z, An S, Chen J, Wang Z. The ecological roles of assembling genomes for Bacillales and Clostridiales in coal seams. FEMS Microbiol Lett 2022; 369:6605329. [PMID: 35687414 DOI: 10.1093/femsle/fnac053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/11/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Biogenic coalbed methane is produced by biological processes mediated by synergistic interactions of microbial complexes in coal seams. However, the ecological role of functional bacteria in biogenic coalbed methane remains poorly understood. Here, we studied the metagenome assembled genomes (MAGs) of Bacillales and Clostridiales from coal seams, revealing further expansion of hydrogen and acetogen producers involved in organic matter decomposition. In this study, Bacillales and Clostridiales were dominant orders (91.85 ± 0.94%) in cultured coal seams, and a total of 16 MAGs from 6 families, including Bacillus, Paenibacillus, Staphylococcus, Anaerosalibacter, Hungatella and Paeniclostridium, were reconstructed. These microbial groups possessed multiple metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate, β-oxidation, TCA cycle, assimilatory sulfate reduction, nitrogen metabolism and encoding hydrogenase) that provided metabolic substrates (acetate and/or H2) for the methanogenic processes. Therein, the hydrogenase-encoding gene and hydrogenase maturation factors were merely found in all the Clostridiales MAGs. β-oxidation was the main metabolic pathway involved in short-chain fatty acid degradation and acetate production, and most of these pathways were detected and exhibited different operon structures in Bacillales MAGs. In addition, assimilatory sulfate reduction and nitrogen metabolism processes were also detected in some MAGs, and these processes were also closely related to acetate production and/or organic matter degradation according to their operon structures and metabolic pathways. In summary, this study enabled a better understanding of the ecological roles of Bacillales and Clostridiales in biogenic methane in coal seams based on a combination of bioinformatic techniques.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines, Anhui University of Science & Technology, Huainan, Anhui province, China
| | - Bingjun Liu
- Institute of Energy, Hefei Comprehensive National Science Center, Anhui, Hefei, 230031, China
| | - Qingyi Tu
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines, Anhui University of Science & Technology, Huainan, Anhui province, China
| | - Sheng Xue
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines, Anhui University of Science & Technology, Huainan, Anhui province, China
| | - Xiaozhou Liu
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines, Anhui University of Science & Technology, Huainan, Anhui province, China
| | - Zhijian Wu
- Coal Mining National Engineering and Technology Research Institute, Huainan, Anhui Province, China
| | - Shikai An
- Coal Mining National Engineering and Technology Research Institute, Huainan, Anhui Province, China
| | - Jian Chen
- Coal Mining National Engineering and Technology Research Institute, Huainan, Anhui Province, China
| | - Zhigen Wang
- China National Coal Xinji Group Corporation, Huainan, Anhui Province, China
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Pal M, Purohit HJ, Qureshi A. Genomic insight for algicidal activity in Rhizobium strain AQ_MP. Arch Microbiol 2021; 203:5193-5203. [PMID: 34341843 DOI: 10.1007/s00203-021-02496-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/28/2022]
Abstract
Occurrence of Harmful Algal Blooms (HABs) creates a threat to aquatic ecosystem affecting the existing flora 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 strain AQ_MP, an environmental isolate that showed the capability of degrading Microcystis aeruginosa (Cyanobacteria) through lytic mechanisms. Genome sequence analysis of Rhizobium strain AQ_MP unraveled the algal lytic features and toxin degradative pathways in it. Functional genes of CAZymes such as glycosyltransferases (GT), glycoside hydrolases (GH), polysaccharide lyases (PL) which supports algal polysaccharide degradation (lysis) were present in Rhizobium strain AQ_MP. Genome analysis also clarified the presence of the glutathione metabolic pathway, which is the biological detoxification pathway responsible for toxin degradation. The conserved region mlrC, a microcystin toxin-degrading gene was also annotated in the genome. The study illustrated that Rhizobium strain AQ_MP harbored a wide range of mechanisms for the lysis of Microcystis aeruginosa cells and its toxin degradation. In future, this study finds promiscuity for employing Rhizobium strain AQ_MP species for bioremediation, based on its physiological and genomic analysis.
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Affiliation(s)
- Mili Pal
- Environmental Biotechnology and Genomics Division, CSIR- National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR- National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR- National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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14
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Egbe CC, Oyetibo GO, Ilori MO. Ecological impact of organochlorine pesticides consortium on autochthonous microbial community in agricultural soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111319. [PMID: 32947214 DOI: 10.1016/j.ecoenv.2020.111319] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Organochlorine pesticides (OCPs) used in agricultural practices are of global concern due to their toxicological hazards on biomes of the impacted soil. Geochemistry and microbiome of OCPs-impacted (OW) soil was determined and compared with those of pristine (L1) soils. Microbiome of OW was based on sequencing total 16S rRNA genes of prokaryotes and Internal Transcribed Spacer (ITS2) regions between 5.8S and 28S rRNA genes of eukaryotes using Illumina MiSeq platform for bacterial and fungal communities, respectively. Geochemical properties of OW were assessed for ecological risks of OCPs on biota via risk quotient (RQ) and maximum cumulative ratio (MCR). It was established OW was polluted with 15 OCPs, along with consequential nitrate and phosphorous deficiencies. Ten of the 15 OCPs exerted severe ecological risk (RQ > 1: 4-992), of which endosulfan contributed 76% of the ecotoxicity (MCR = 1.3) on OW. The key players in OW were observed to be Enterobacteriaceae and Mortierellaceae represented by Escherichia and Mortierella taxa, respectively. Low abundance of Nitrospirae species and extinction of Glomeromycota in OW connoted serious toxicological consequences of the OCPs. Taxon XOR (Taxon Exclusive Or) analysis revealed 38,212 and 63,474 counts of bacterial and fungal species, respectively, were exclusively found in the impacted OW and possibly contributed to natural attenuation of the OCPs in the impacted agricultural soil. Conversely, 61,005 (bacteria) and 33,397 (fungi) species counts that were missing in OCPs-impacted OW, but present in pristine L1, opined the species as bio-indicators of OCPs ecotoxicity in agricultural soils. While the species tagged as bio-indicators would be valuable in monitoring OCPs pollution, those suggested to be players in self-recovery process will be invaluable to designing bioremediation strategies for OCPs-impacted agricultural soil.
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Affiliation(s)
- Chinyere Christiana Egbe
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
| | - Ganiyu Oladunjoye Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
| | - Matthew Olusoji Ilori
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria; Institute of Maritime Studies, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
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15
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Salam LB, Obayori OS. Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment. J Genet Eng Biotechnol 2020; 18:70. [PMID: 33175233 PMCID: PMC7658278 DOI: 10.1186/s43141-020-00089-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
Abstract
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. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-020-00089-9.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Summit University, Offa, Kwara, Nigeria.
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Agrahari RK, Singh P, Koyama H, Panda SK. Plant-microbe Interactions for Sustainable Agriculture in the Post-genomic Era. Curr Genomics 2020; 21:168-178. [PMID: 33071611 PMCID: PMC7521031 DOI: 10.2174/1389202921999200505082116] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022] Open
Abstract
Plant-microbe interactions are both symbiotic and antagonistic, and the knowledge of both these interactions is equally important for the progress of agricultural practice and produce. This review gives an insight into the recent advances that have been made in the plant-microbe interaction study in the post-genomic era and the application of those for enhancing agricultural production. Adoption of next-generation sequencing (NGS) and marker assisted selection of resistant genes in plants, equipped with cloning and recombination techniques, has progressed the techniques for the development of resistant plant varieties by leaps and bounds. Genome-wide association studies (GWAS) of both plants and microbes have made the selection of desirable traits in plants and manipulation of the genomes of both plants and microbes effortless and less time-consuming. Stress tolerance in plants has been shown to be accentuated by association of certain microorganisms with the plant, the study and application of the same have helped develop stress-resistant varieties of crops. Beneficial microbes associated with plants are being extensively used for the development of microbial consortia that can be applied directly to the plants or the soil. Next-generation sequencing approaches have made it possible to identify the function of microbes associated in the plant microbiome that are both culturable and non-culturable, thus opening up new doors and possibilities for the use of these huge resources of microbes that can have a potential impact on agriculture.
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Affiliation(s)
- Raj Kishan Agrahari
- 1Faculty of Applied Biological Sciences, Gifu University, Gifu501-1193, Japan; 2Lab of Plant-Microbe Interactions, Centre for DNA Fingerprinting and Diagnostics, Graduate studies: Manipal Academy of Higher Education, Manipal, Karnataka, India; 3Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan 305817, India
| | - Prashantee Singh
- 1Faculty of Applied Biological Sciences, Gifu University, Gifu501-1193, Japan; 2Lab of Plant-Microbe Interactions, Centre for DNA Fingerprinting and Diagnostics, Graduate studies: Manipal Academy of Higher Education, Manipal, Karnataka, India; 3Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan 305817, India
| | - Hiroyuki Koyama
- 1Faculty of Applied Biological Sciences, Gifu University, Gifu501-1193, Japan; 2Lab of Plant-Microbe Interactions, Centre for DNA Fingerprinting and Diagnostics, Graduate studies: Manipal Academy of Higher Education, Manipal, Karnataka, India; 3Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan 305817, India
| | - Sanjib Kumar Panda
- 1Faculty of Applied Biological Sciences, Gifu University, Gifu501-1193, Japan; 2Lab of Plant-Microbe Interactions, Centre for DNA Fingerprinting and Diagnostics, Graduate studies: Manipal Academy of Higher Education, Manipal, Karnataka, India; 3Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan 305817, India
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Tikariha H, Purohit HJ. Unfolding microbial community intelligence in aerobic and anaerobic biodegradation processes using metagenomics. Arch Microbiol 2020; 202:1269-1274. [PMID: 32130435 DOI: 10.1007/s00203-020-01839-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/25/2022]
Abstract
Environmental factors and available nutrients influence microbial communities, and with that, there exists a dynamic shift in community structure and hierarchy in wastewater treatment systems. Of the various factors, the availability and gradient of oxygen selectively enrich a typical microbial community and also form the community stratification which could be established through metagenomics studies. In recent years, metagenomics with various sets of bioinformatics tools has assisted in exploration and better insight into the organization and relation of the taxonomical and functional composition and associate physiological intelligence of the microbial communities. The microbial communities, under defined conditions acquire a typical hierarchy with flexible but active network of the metabolic route, which ensures the survival needs of every member residing in that community and their abundance. This knowledge of community functional organization defines the rule in designing and improving biodegradation processes in case of both aerobic and anaerobic systems.
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Affiliation(s)
- Hitesh Tikariha
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India.
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18
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Mapping Microbial Capacities for Bioremediation: Genes to Genomics. Indian J Microbiol 2019; 60:45-53. [PMID: 32089573 DOI: 10.1007/s12088-019-00842-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
Bioremediation is a process wherein the decontamination strategies are designed so that a site could achieve the environmental abiotic and biotic parameters close to its baseline. In the process, the driving force is the available microbial genetic degradative capabilities, which are supported by required nutrients so that the desired expression of these capabilities could be exploited in favour of removal of pollutants. With genomics tools not only the available abilities could be estimated but their dynamic performance could also be established. These tools are now playing important role in bioprocess optimization, which not only derive the bio-stimulation plans but also could suggest possible genetic bio-augmentation options.
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