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Yadav P, Das J, Sundharam SS, Krishnamurthi S. Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach. Microorganisms 2024; 12:397. [PMID: 38399801 PMCID: PMC10892101 DOI: 10.3390/microorganisms12020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.
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Affiliation(s)
- Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
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Zhang NC, A D, Chao YQ, Li HY, Li C, Lin QQ, Li YY, Qiu RL. Mechanism of polycyclic aromatic hydrocarbons degradation in the rhizosphere of Phragmites australis: Organic acid co-metabolism, iron-driven, and microbial response. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121608. [PMID: 37044257 DOI: 10.1016/j.envpol.2023.121608] [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: 11/02/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 06/19/2023]
Abstract
Microbial co-metabolism is crucial for the efficient biodegradation of polycyclic aromatic hydrocarbons (PAHs); however, their intrinsic mechanisms remain unclear. To explore the co-metabolic degradation of PAHs, root organic acids (ROAs) (phenolic ROAs: caffeic acid [CA] and ferulic acid [FA]; non-phenolic ROAs: oxalic acid [OA]) were exogenously added as co-metabolic substrates under high (HFe) and low (LFe) iron levels in this study. The results demonstrated that more than 90% of PAHs were eliminated from the rhizosphere of Phragmites australis. OA can promote the enrichment of unrelated degrading bacteria and non-specific dioxygenases. FA with a monohydroxy structure can activate hydroxylase; however, it relies on phytosiderophores released by plants (such as OA) to adapt to stress. Therefore, non-specific co-metabolism occurred in these units. The best performance for PAH removal was observed in the HFe-CA unit because: (a) HFe concentrations enriched the Fe-reducing and denitrifying bacteria and promoted the rate-limiting degradation for PAHs as the enzyme cofactor; (b) CA with a dihydroxyl structure enriched the related degrading bacteria, stimulated specific dioxygenase, and activated Fe to concentrate around the rhizosphere simultaneously to perform the specific co-metabolism. Understanding the co-metabolic degradation of PAHs will help improve the efficacy of rhizosphere-mediated remediation.
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Affiliation(s)
- Ni-Chen Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Dan A
- Engineering and Technology Research Center for Agricultural Land Pollution Integrated Prevention and Control of Guangdong Higher Education Institute, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yuan-Qing Chao
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hai-Yan Li
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs & Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Charles Li
- Department of Public Health, California State University, East Bay, CA, 94542, USA
| | - Qing-Qi Lin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ya-Ying Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Rong-Liang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
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Banerjee S, Bedics A, Tóth E, Kriszt B, Soares AR, Bóka K, Táncsics A. Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions. Front Microbiol 2022; 13:929128. [PMID: 36204622 PMCID: PMC9530055 DOI: 10.3389/fmicb.2022.929128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12T was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12T belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7T (98.42%), followed by Pseudomonas sagittaria JCM 18195T (98.29%) and Pseudomonas alcaliphila JCM 10630T (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12T is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12T is 4.36 Mb long, and the G+C content of MAP12T genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed that strain MAP12T is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12T from metagenomics sequence data and showed that strain MAP12T was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12T contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12T are summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The results of this polyphasic study support that strain MAP12T represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12T (=LMG 32466, =NCAIM B.02668).
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Affiliation(s)
- Sinchan Banerjee
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Anna Bedics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - André R. Soares
- Group for Aquatic Microbial Ecology, Institute for Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- *Correspondence: András Táncsics,
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Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions. Antonie Van Leeuwenhoek 2022; 115:1113-1128. [PMID: 35841500 PMCID: PMC9363352 DOI: 10.1007/s10482-022-01759-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022]
Abstract
In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C16:0 and summed feature 3 (C16:1ω7c/iso-C15:0 2-OH). The DNA G + C content of the type strain is 68.8 mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7T and closest relatives were below the threshold values for species demarcation. The genome of strain B7T, which is approximately 4.5 Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7T (= LMG 32,345T = NCAIM B.02664T).
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Hydrogenophaga crocea sp. nov. associated with cyanobacterial mat isolated from farmland mud. Arch Microbiol 2022; 204:265. [PMID: 35435503 DOI: 10.1007/s00203-022-02865-2] [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: 12/14/2021] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 11/02/2022]
Abstract
A catalase and oxidase-positive strain BA0156T was isolated from a cyanobacterial mat collected from the farmland mud cultivated with sugarcane from Ahmednagar, India. The 16S rRNA gene of strain BA0156T showed the highest percent sequence similarity with Hydrogenophaga borbori LMG 30805T (98.5%), followed by H. flava DSM 619T (98.3%) and H. intermedia DSM 5680T (98.2%). The strain BA0156T contained the major fatty acids, C16:0 (25.1%) and C17:0 cyclo (3.9%), whereas phosphatidylethanolamine and diphosphatidylglycerol were the major polar lipids. The OrthoANI and dDDH values between strain BA0156T and its closest relative H. borbori LMG 30805T were 84.6% and 28.3%, respectively. The DNA G+C content of strain BA0156T was 69.4 mol %. Furthermore, the biochemical and physiological features of strain BA0156T showed a distinct pattern from their closest phylogenetic neighbours. The phenotypic, genotypic and chemotaxonomic characteristics indicated that the strain BA0156T represents a new species for which the name Hydrogenophaga crocea (type strain BA0156T = MCC 3062T = KCTC 72452T = JCM 34507T) is proposed.
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Banerjee S, Bedics A, Harkai P, Kriszt B, Alpula N, Táncsics A. Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:28431-28445. [PMID: 34989990 PMCID: PMC8993774 DOI: 10.1007/s11356-021-18300-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.
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Affiliation(s)
- Sinchan Banerjee
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Anna Bedics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Péter Harkai
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Nagaraju Alpula
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Department of Biotechnology, Microbial Biotechnology Research Unit, Kakatiya University, Warangal, India
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary.
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