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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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Sumranwanich T, Amosu E, Chankhamhaengdecha S, Phetruen T, Loktumraks W, Ounjai P, Harnvoravongchai P. Evaluating lignin degradation under limited oxygen conditions by bacterial isolates from forest soil. Sci Rep 2024; 14:13350. [PMID: 38858437 PMCID: PMC11164938 DOI: 10.1038/s41598-024-64237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
Lignin, a heterogeneous aromatic polymer present in plant biomass, is intertwined with cellulose and hemicellulose fibrils, posing challenges to its effective utilization due to its phenolic nature and recalcitrance to degradation. In this study, three lignin utilizing bacteria, Klebsiella sp. LEA1, Pseudomonas sp. LEA2, and Burkholderia sp. LEA3, were isolated from deciduous forest soil samples in Nan province, Thailand. These isolates were capable of growing on alkali lignin and various lignin-associated monomers at 40 °C under microaerobic conditions. The presence of Cu2+ significantly enhanced guaiacol oxidation in Klebsiella sp. LEA1 and Pseudomonas sp. LEA2. Lignin-related monomers and intermediates such as 2,6-dimethoxyphenol, 4-vinyl guaiacol, 4-hydroxybenzoic acid, benzoic acid, catechol, and succinic acid were detected mostly during the late stage of incubation of Klebsiella sp. LEA1 and Pseudomonas sp. LEA2 in lignin minimal salt media via GC-MS analysis. The intermediates identified from Klebsiella sp. LEA1 degradation suggested that conversion and utilization occurred through the β-ketoadipate (ortho-cleavage) pathway under limited oxygen conditions. The ability of these bacteria to thrive on alkaline lignin and produce various lignin-related intermediates under limited oxygen conditions suggests their potential utility in oxygen-limited processes and the production of renewable chemicals from plant biomass.
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Affiliation(s)
- Thitinun Sumranwanich
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Esther Amosu
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Wethaka Loktumraks
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand.
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3
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Ilyas M, Purkait D, Atmakuri K. Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens. Brief Funct Genomics 2024; 23:55-68. [PMID: 36528816 DOI: 10.1093/bfgp/elac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 01/21/2024] Open
Abstract
To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.
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Affiliation(s)
- Mohd Ilyas
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Dyuti Purkait
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Krishnamohan Atmakuri
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
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4
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de Pedro-Jové R, Corral J, Rocafort M, Puigvert M, Azam FL, Vandecaveye A, Macho AP, Balsalobre C, Coll NS, Orellano E, Valls M. Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats. PLoS Pathog 2023; 19:e1011888. [PMID: 38113281 PMCID: PMC10763947 DOI: 10.1371/journal.ppat.1011888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/03/2024] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between habitats is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate pathogen adaptation to water and soil, two environments that act as bacterial reservoirs, and compare this information with gene expression in planta. Gene expression in water resembled that observed during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). Alkaline pH and nutrient scarcity-conditions also encountered during late infection stages-were identified as the triggers for this T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and genes for the use of alternate carbon sources, such as phenylacetate catabolism and the glyoxylate cycle, and downregulated virulence-associated genes. We proved through gain- and loss-of-function experiments that genes associated with the oxidative stress response, such as the regulator OxyR and the catalase KatG, are key for bacterial survival in soil, as their deletion cause a decrease in culturability associated with a premature induction of the viable but non culturable state (VBNC). This work identifies essential factors necessary for R. solanacearum to complete its life cycle and is the first comprehensive gene expression analysis in all environments occupied by a bacterial plant pathogen, providing valuable insights into its biology and adaptation to unexplored habitats.
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Affiliation(s)
- Roger de Pedro-Jové
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Jordi Corral
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Mercedes Rocafort
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Marina Puigvert
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Fàtima Latif Azam
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Agustina Vandecaveye
- Área Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-UNR-CONICET), Rosario, Santa Fe, Argentina
| | - Alberto P. Macho
- Shanghai Centre for Plant Stress Biology, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Carlos Balsalobre
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Elena Orellano
- Área Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-UNR-CONICET), Rosario, Santa Fe, Argentina
| | - Marc Valls
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
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5
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Lou F, Okoye CO, Gao L, Jiang H, Wu Y, Wang Y, Li X, Jiang J. Whole-genome sequence analysis reveals phenanthrene and pyrene degradation pathways in newly isolated bacteria Klebsiella michiganensis EF4 and Klebsiella oxytoca ETN19. Microbiol Res 2023; 273:127410. [PMID: 37178499 DOI: 10.1016/j.micres.2023.127410] [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: 04/05/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are diverse pollutants of significant environmental concerns, requiring effective biodegradation. This study used different bioinformatics tools to conduct whole-genome sequencing of two novel bacterial strains, Klebsiella michiganensis EF4 and K. oxytoca ETN19, to improve our understanding of their many genomic functions and degradation pathways of phenanthrene and pyrene. After 28 days of cultivation, strain EF4 degraded approximately 80% and 60% of phenanthrene and pyrene, respectively. However, their combinations (EF4 +ETN19) showed tremendous phenanthrene degradation efficiency, supposed to be at the first-level kinetic model with a t1/2 value of approximately 6 days. In addition, the two bacterial genomes contained carbohydrate-active enzymes and secondary metabolites biosynthetic gene clusters associated with PAHs degradation. The two genomes contained the bZIP superfamily of transcription factors, primarily the cAMP-response element-binding protein (CREB), which could regulate the expression of several PAHs degradation genes and enzymes. Interestingly, the two genomes were found to uniquely degrade phenanthrene through a putative pathway that catabolizes 2-carboxybenzalpyruvate into the TCA cycle. An operon containing multicomponent proteins, including a novel gene (JYK05_14550) that could initiate the beginning step of phenanthrene and pyrene degradation, was found in the EF4 genome. However, the degradation pathway of ETN19 showed that the yhfP gene encoding putative quinone oxidoreductase was associated with phenanthrene and pyrene catabolic processes. Furthermore, the significant expression of catechol 1,2-dioxygenase and quinone oxidoreductase genes in EF4 +ETN19 and ETN19 following the quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis confirmed the ability of the bacteria combination to degrade pyrene and phenanthrene effectively. These findings present new insight into the possible co-metabolism of the two bacterial species in the rapid biodegradation of phenanthrene and pyrene in soil environments.
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Affiliation(s)
- Feiyue Lou
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Charles Obinwanne Okoye
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Lu Gao
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Huifang Jiang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yanfang Wu
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongli Wang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xia Li
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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6
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Tan Z, Yang X, Liu Y, Chen L, Xu H, Li Y, Gong B. The capability of chloramphenicol biotransformation of Klebsiella sp. YB1 under cadmium stress and its genome analysis. CHEMOSPHERE 2023; 313:137375. [PMID: 36435315 DOI: 10.1016/j.chemosphere.2022.137375] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/30/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
Co-contamination by antibiotics and heavy metal is common in the environment, however, there is scarce information about antibiotics biodegradation under heavy metals stress. In this study, Klebsiella sp. Strain YB1 was isolated which is capable of biodegrading chloramphenicol (CAP) with a biodegradation efficiency of 22.41% at an initial CAP of 10 mg L-1 within 2 days. CAP biodegradation which fitted well with the first-order kinetics. YB1 still degrades CAP under Cd stress, however 10 mg L-1 Cd inhibited CAP biodegradation by 15.1%. Biotransformation pathways remained the same under Cd stress, but two new products (Cmpd 19 and Cmpd 20) were identified. Five parallel metabolism pathways of CAP were proposed with/without Cd stress, including one novel pathway (pathway 5) that has not been reported before. In pathway 5, the initial reaction was oxidation of CAP by disruption of C-C bond at the side chain of C1 and C2 with the formation of 4-nitrobenzyl alcohol and CY7, then these intermediates were oxidized into p-nitrobenzoic acid and CY1, respectively. CAP acetyltransferase and nitroreductase and 2,3/4,5-dioxygenase may play an important role in CAP biodegradation through genome analysis and prediction. This study deepens our understanding of mechanism of antibiotic degradation under heavy metal stress in the environment.
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Affiliation(s)
- Zewen Tan
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xiuyue Yang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yiling Liu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China
| | - Lian Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China
| | - Huijuan Xu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China
| | - Beini Gong
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou, 510642, PR China.
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7
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Xiang L, Harindintwali JD, Wang F, Redmile-Gordon M, Chang SX, Fu Y, He C, Muhoza B, Brahushi F, Bolan N, Jiang X, Ok YS, Rinklebe J, Schaeffer A, Zhu YG, Tiedje JM, Xing B. Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16546-16566. [PMID: 36301703 PMCID: PMC9730858 DOI: 10.1021/acs.est.2c02976] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.
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Affiliation(s)
- Leilei Xiang
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jean Damascene Harindintwali
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- Institute
for Environmental Research, RWTH Aachen
University, 52074 Aachen, Germany
- or
| | - Marc Redmile-Gordon
- Department
of Environmental Horticulture, Royal Horticultural
Society, Wisley, Surrey GU23 6QB, U.K.
| | - Scott X. Chang
- Department
of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yuhao Fu
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao He
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zhejiang University, Hangzhou 310058, China
| | - Bertrand Muhoza
- College
of Food Science, Northeast Agricultural
University, Harbin, Heilongjiang 150030, China
| | - Ferdi Brahushi
- Department
of Agroenvironment and Ecology, Agricultural
University of Tirana, Tirana 1029, Albania
| | - Nanthi Bolan
- School of
Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6001, Australia
| | - Xin Jiang
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Sik Ok
- Korea
Biochar Research Center, APRU Sustainable Waste Management Program
& Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic
of Korea
| | - Jörg Rinklebe
- Department
of Soil and Groundwater Management, Bergische
Universität, 42285 Wuppertal, Germany
| | - Andreas Schaeffer
- Institute
for Environmental Research, RWTH Aachen
University, 52074 Aachen, Germany
- School
of the Environment, State Key Laboratory of Pollution Control and
Resource Reuse, Nanjing University, 210023 Nanjing, China
- Key
Laboratory of the Three Gorges Reservoir Region’s Eco-Environment, Chongqing University, 400045 Chongqing, China
| | - Yong-guan Zhu
- University
of Chinese Academy of Sciences, Beijing 100049, China
- Key
Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State
Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of
Sciences, Beijing 100085, China
| | - James M. Tiedje
- Center
for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| | - Baoshan Xing
- Stockbridge
School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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8
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Hentati D, Abed RMM, Abotalib N, El Nayal AM, Ashraf I, Ismail W. Biotreatment of oily sludge by a bacterial consortium: Effect of bioprocess conditions on biodegradation efficiency and bacterial community structure. Front Microbiol 2022; 13:998076. [PMID: 36212842 PMCID: PMC9532598 DOI: 10.3389/fmicb.2022.998076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
We studied the biodegradation of oily sludge generated by a petroleum plant in Bahrain by a bacterial consortium (termed as AK6) under different bioprocess conditions. Biodegradation of petroleum hydrocarbons in oily sludge (C11-C29) increased from 24% after two days to 99% after 9 days of incubation in cultures containing 5% (w/v) of oily sludge at 40°C. When the nitrogen source was excluded from the batch cultures, hydrocarbon biodegradation dropped to 45% within 7 days. The hydrocarbon biodegradation decreased also by increasing the salinity to 3% and the temperature above 40°C. AK6 tolerated up to 50% (w/v) oily sludge and degraded 60% of the dichloromethane-extractable oil fraction. Illumina-MiSeq analyses revealed that the AK6 consortium was mainly composed of Gammaproteobacteria (ca. 98% of total sequences), with most sequences belonging to Klebsiella (77.6% of total sequences), Enterobacter (16.7%) and Salmonella (5%). Prominent shifts in the bacterial composition of the consortium were observed when the temperature and initial sludge concentration increased, and the nitrogen source was excluded, favoring sequences belonging to Pseudomonas and Stenotrophomonas. The AK6 consortium is endowed with a strong oily sludge tolerance and biodegradation capability under different bioprocess conditions, where Pseudomonas spp. appear to be crucial for hydrocarbon biodegradation.
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Affiliation(s)
- Dorra Hentati
- Environmental Biotechnology Program, Department of Life Sciences, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Raeid M. M. Abed
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Nasser Abotalib
- Environmental Biotechnology Program, Department of Life Sciences, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ashraf M. El Nayal
- Environmental Biotechnology Program, Department of Life Sciences, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | | | - Wael Ismail
- Environmental Biotechnology Program, Department of Life Sciences, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
- *Correspondence: Wael Ismail,
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9
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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10
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Njoku KL, Ude EO, Jegede TO, Adeyanju OZ, Iheme PO. Characterization of hydrocarbon degrading microorganisms from Glycine max and Zea mays phytoremediated crude oil contaminated soil. Environ Anal Health Toxicol 2022; 37:e2022008-0. [PMID: 35878916 PMCID: PMC9314210 DOI: 10.5620/eaht.2022008] [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: 02/16/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Microbe-plant partnership in phytoremediation involves a synergistic interaction that leads to degradation of contaminants. The identification and characterization of these microorganisms is fundamental in environmental management. This study is aimed at investigating the influence of Glycine max and Zea mays on microbial make-up and differentiation of soil bacterial and fungal isolates in crude oil contaminated soil. We employed conventional technique of microbial isolation and gene sequencing to evaluate the microbial composition in crude oil contaminated soil. The microorganisms were isolated from crude oil contaminated soil (0%, 4%, 8%) and were identified using 16S rRNA gene (for bacteria) and Internal Transcribed Spacer (ITS) gene (for fungi). We observed a change in the microbial cell density with respect to treatment conditions implying a shift in microbial dynamics to total hydrocarbon utilizing bacteria as the dominant microbes. The sequence data revealed five bacteria strain; Klebsiella aerogenes strain 77, Klebsiella aerogenes strain UISO178, Salmonella enterica strain ABUH7, Klebsiella aerogenes strain M242 and Enterobacter sp. NCCP-607 and three fungi strains; Galactomyces geotrichum strain CBS, Aspergillus niger strain YMCHA73 and Trichoderma virens isolate A701. Annotation analysis using FGENESB and gene scan revealed proteins involved in various metabolic processes and hydrocarbon utilization. GHOSTKOLA output revealed several genetic elements and pathways such as DnaA, PYG, mrcA, environmental, cellular and genetic information processing and degradation enhancers. Our findings show that G. max and Z. mays in association with bacteria can enhance ecosystem restoration of crude oil contaminated soil.
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Affiliation(s)
- Kelechi L Njoku
- Environmental Biology Research Unit, Cell Biology and Genetics Department, University of Lagos, Akoka, Lagos,
Nigeria
- Correspondence:
| | - Eme O Ude
- Environmental Biology Research Unit, Cell Biology and Genetics Department, University of Lagos, Akoka, Lagos,
Nigeria
- Helmholtz Zentrum UFZ, Department of Environmental Biotechnology, Leipzig,
Germany
| | - Temitope O Jegede
- Environmental Biology Research Unit, Cell Biology and Genetics Department, University of Lagos, Akoka, Lagos,
Nigeria
| | - Omotoyosi Z Adeyanju
- Environmental Biology Research Unit, Cell Biology and Genetics Department, University of Lagos, Akoka, Lagos,
Nigeria
| | - Patricia O Iheme
- Environmental Biology Research Unit, Cell Biology and Genetics Department, University of Lagos, Akoka, Lagos,
Nigeria
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11
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Alfaify AM, Mir MA, Alrumman SA. Klebsiella oxytoca: an efficient pyrene-degrading bacterial strain isolated from petroleum-contaminated soil. Arch Microbiol 2022; 204:248. [PMID: 35397012 DOI: 10.1007/s00203-022-02850-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are the hazardous xenobiotic agents of oil production. One of the methods to eliminate hazardous compounds is bioremediation, which is the most efficient and cost-effective method to eliminate the harmful byproducts of crude petroleum processing. In this study, five pure bacterial isolates were isolated from petroleum-contaminated soil, four of which showed a robust growth on the PAH pyrene, as a sole carbon source. Various methods viz mass spectroscopy, biochemical assays, and 16S RNA sequencing employed to identify the isolates ascertained the consistent identification of Klebsiella oxytoca by all three methods. Scanning electron microscopy and Gram staining further demonstrated the characterization of the K. oxytoca. High-performance liquid chromatography of the culture supernatant of K. oxytoca grown in pyrene containing media showed that the cells started utilizing pyrene from the 6th day onwards and by the 12th day of growth, 70% of the pyrene was completely degraded. A genome search for the genes predicted to be involved in pyrene degradation using Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their presence in the genome of K. oxytoca. These results suggest that K. oxytoca would be a suitable candidate for removing soil aromatic hydrocarbons.
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Affiliation(s)
- Abdulkhaleg M Alfaify
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Mushtaq Ahmad Mir
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P. O. Box 3665, Abha, 61421, Saudi Arabia.
| | - Sulaiman A Alrumman
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
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12
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Alves NSF, Kaory Inoue SG, Carneiro AR, Albino UB, Setzer WN, Maia JG, Andrade EH, da Silva JKR. Variation in Peperomia pellucida growth and secondary metabolism after rhizobacteria inoculation. PLoS One 2022; 17:e0262794. [PMID: 35061852 PMCID: PMC8785609 DOI: 10.1371/journal.pone.0262794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/05/2022] [Indexed: 01/31/2023] Open
Abstract
Peperomia pellucida L. Kunth is a herb well-known for its secondary metabolites (SM) with biological potential. In this study, the variations in the SM of P. pellucida during association with rhizobacteria were evaluated. Plants were inoculated with Enterobacter asburiae and Klebsiella variicola, which were identified by sequencing of the 16S rRNA gene. The data were evaluated at 7, 21, and 30-day post inoculation (dpi). Plant-bacteria symbiosis improved plant growth and weight. Total phenolic content and phenylalanine ammonia lyase enzyme activity had a significant increase mainly at 30 dpi. P. pellucida was mainly composed of phenylpropanoids (37.30-52.28%) and sesquiterpene hydrocarbons (39.28-49.42%). The phenylpropanoid derivative 2,4,5-trimethoxy-styrene (ArC2), the sesquiterpene hydrocarbon ishwarane, and the phenylpropanoid dillapiole were the major compounds. Principal component analysis (PCA) of the classes and compounds ≥ 2.0% indicated that plants colonized by E. asburiae had a reduction in the content of sesquiterpene hydrocarbons and an increase in phenylpropanoids and derivatives. Plants treated with this bacterium also had an increase in the content of 2,4,5-trimethoxystyrene at 30 dpi. Plants inoculated with K. variicola had significant increases only in the content of the classes monoterpene hydrocarbons and 'other compounds' (hydrocarbons, esters, ketones, etc.). These data suggest that the production of plant secondary metabolites can be modified depending on the type of rhizobacteria inoculated.
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Affiliation(s)
| | | | - Adriana Ribeiro Carneiro
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Pará,
Belém, Brazil
- Faculdade de Biotecnologia, Universidade Federal do Pará, Belém,
Brazil
| | | | - William N. Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville,
AL, United States of America
- Aromatic Plant Research Center, Lehi, UT, United States of
America
| | - José Guilherme Maia
- Programa de Pós-Graduação em Química, Universidade Federal do Pará,
Belém, Brazil
| | | | - Joyce Kelly R. da Silva
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Pará,
Belém, Brazil
- Faculdade de Biotecnologia, Universidade Federal do Pará, Belém,
Brazil
- Programa de Pós-Graduação em Química, Universidade Federal do Pará,
Belém, Brazil
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13
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Kumar G, Lal S, Maurya SK, Bhattacherjee AK, Chaudhary P, Gangola S, Rajan S. Exploration of Klebsiella pneumoniae M6 for paclobutrazol degradation, plant growth attributes, and biocontrol action under subtropical ecosystem. PLoS One 2021; 16:e0261338. [PMID: 34914805 PMCID: PMC8675670 DOI: 10.1371/journal.pone.0261338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/30/2021] [Indexed: 01/31/2023] Open
Abstract
In recent times, injudicious use of paclobutrazol (PBZ) in mango orchards deteriorates the soil quality and fertility by persistence nature and causes a serious ecosystem imbalance. In this study, a new Klebsiella pneumoniae strain M6 (MW228061) was isolated from mango rhizosphere and characterized as a potent plant growth promoter, biocontrol, and PBZ degrading agent. The strain M6 efficiently utilizes PBZ as carbon, energy and nitrogen source and degrades up to 98.28% (50 mgL-1 initial conc.) of PBZ at 15th day of incubation in MS medium. In the soil system first order degradation kinetics and linear model suggested 4.5 days was the theoretical half-life (t1/2 value) of PBZ with strain M6. Box Behnken design (BBD) model of Response surface methodology (RSM) showed pH 7.0, 31°C temperature, and 2.0 ml inoculum size (8 x 109 CFU mL-1) was optimized condition for maximum PBZ degradation with strain M6. Plant growth promoting attributes such as Zn, K, PO4 solubilization IAA, HCN and NH3 production of strain M6 showed positive results and were assessed quantitatively. The relation between plant growth promotion and PBZ degradation was analyzed by heat map, principal component analysis (PCA) and, clustal correlation analysis (CCA). Strain M6 was also showing a significant biocontrol activity against pathogenic fungi such as Fusarium oxysporum (MTCC–284), Colletotrichum gloeosporioides (MTCC– 2190), Pythium aphanidermatum (MTCC– 1024), Tropical race 1 (TR -1), and Tropical race 4 (TR -4). Hence, results of the study suggested that strain M6 can be utilized as an effective bio-agent to restore degraded land affected by persistent use of paclobutrazol.
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Affiliation(s)
- Govind Kumar
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
- * E-mail:
| | - Shatrohan Lal
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | | | | | - Parul Chaudhary
- Department of Animal Biotechnology, NDRI, Karnal, Haryana, India
| | | | - Shailendra Rajan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
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14
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Jha V, Purohit H, Dafale NA. Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis. 3 Biotech 2021; 11:473. [PMID: 34777930 DOI: 10.1007/s13205-021-03020-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/05/2021] [Indexed: 12/28/2022] Open
Abstract
Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5'-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index-3.47), and protease activity (proteolytic index-2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03020-2.
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15
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Remediation of Petroleum-Contaminated Soils with Microbial and Microbial Combined Methods: Advances, Mechanisms, and Challenges. SUSTAINABILITY 2021. [DOI: 10.3390/su13169267] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The petroleum industry’s development has been supported by the demand for petroleum and its by-products. During extraction and transportation, however, oil will leak into the soil, destroying the structure and quality of the soil and even harming the health of plants and humans. Scientists are researching and developing remediation techniques to repair and re-control the afflicted environment due to the health risks and social implications of petroleum hydrocarbon contamination. Remediation of soil contamination produced by petroleum hydrocarbons, on the other hand, is a difficult and time-consuming job. Microbial remediation is a focus for soil remediation because of its convenience of use, lack of secondary contamination, and low cost. This review lists the types and capacities of microorganisms that have been investigated to degrade petroleum hydrocarbons. However, investigations have revealed that a single microbial remediation faces difficulties, such as inconsistent remediation effects and substantial environmental consequences. It is necessary to understand the composition and source of pollutants, the metabolic genes and pathways of microbial degradation of petroleum pollutants, and the internal and external aspects that influence remediation in order to select the optimal remediation treatment strategy. This review compares the degradation abilities of microbial–physical, chemical, and other combination remediation methods, and highlights the degradation capabilities and processes of the greatest microbe-biochar, microbe–nutrition, and microbe–plant technologies. This helps in evaluating and forecasting the chemical behavior of contaminants with both short- and long-term consequences. Although there are integrated remediation strategies for the removal of petroleum hydrocarbons, practical remediation remains difficult. The sources and quantities of petroleum pollutants, as well as their impacts on soil, plants, and humans, are discussed in this article. Following that, the focus shifted to the microbiological technique of degrading petroleum pollutants and the mechanism of the combined microbial method. Finally, the limitations of existing integrated microbiological techniques are highlighted.
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16
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Dell’ Anno F, Rastelli E, Sansone C, Brunet C, Ianora A, Dell’ Anno A. Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era. Microorganisms 2021; 9:1695. [PMID: 34442774 PMCID: PMC8400010 DOI: 10.3390/microorganisms9081695] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022] Open
Abstract
Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.
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Affiliation(s)
- Filippo Dell’ Anno
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Antonio Dell’ Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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17
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Premnath N, Mohanrasu K, Guru Raj Rao R, Dinesh GH, Siva Prakash G, Pugazhendhi A, Jeyakanthan J, Govarthanan M, Kumar P, Arun A. Effect of C/N substrates for enhanced extracellular polymeric substances (EPS) production and Poly Cyclic Aromatic Hydrocarbons (PAHs) degradation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116035. [PMID: 33581631 DOI: 10.1016/j.envpol.2020.116035] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 05/22/2023]
Abstract
Extracellular Polymeric Substances (EPS) influenced Poly Cyclic Aromatic Hydrocarbons (PAHs) degrading Klebsiella pneumoniae was isolated from the marine environment. To increase the EPS production by Klebsiella pneumoniae, several physicochemical parameters were tweaked such as different carbon sources (arabinose, glucose, glycerol, lactose, lactic acid, mannitol, sodium acetate, starch, and sucrose at 20 g/L), nitrogen sources (ammonium chloride, ammonium sulphate, glycine, potassium nitrate, protease peptone and urea at 2 g/L), different pH, carbon/nitrogen ratio, temperature, and salt concentration were examined. Maximum EPS growth and biodegradation of Anthracene (74.31%), Acenaphthene (67.28%), Fluorene (62.48%), Naphthalene (57.84%), and mixed PAHs (55.85%) were obtained using optimized conditions such as glucose (10 g/L) as carbon source, potassium nitrate (2 g/L) as the nitrogen source at pH 8, growth temperature of 37 °C, 3% NaCl concentration and 72 h incubation period. The Klebsiella pneumoniae biofilm architecture was studied by confocal laser scanning microscopy (CLSM) and scanning electron microscope (SEM). The present study demonstrates the EPS influenced PAHs degradation of Klebsiella pneumoniae.
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Affiliation(s)
- N Premnath
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India; Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - K Mohanrasu
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India; Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - R Guru Raj Rao
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - G H Dinesh
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India; Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - G Siva Prakash
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho, Chi Minh City, Viet Nam.
| | - J Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ponnuchamy Kumar
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - A Arun
- Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India.
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18
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Rajkumari J, Choudhury Y, Bhattacharjee K, Pandey P. Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community. Front Microbiol 2021; 12:593023. [PMID: 33708179 PMCID: PMC7940843 DOI: 10.3389/fmicb.2021.593023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/18/2021] [Indexed: 11/27/2022] Open
Abstract
The non-clinical Klebsiella pneumoniae variants, isolated from different environments, are now well acknowledged for their role in plant-growth promotion and biodegradation of pollutants. In the present study, a non-clinical environmental isolate K. pneumoniae AWD5 is being described for rhizoremediation of pyrene, applied through the rhizosphere of an ornamental plant, Tagetes erecta L (marigold). The non-pathogenic nature of AWD5 was established using an in vivo mouse model experiment, where AWD5 was unable to cause lung infection in tested mice. Degradation of pyrene, in the presence of succinate as co-substrate, was observed to be 87.5% by AWD5, after 21 days of incubation in minimal (Bushnell–Hass) medium in vitro conditions. Consequently, the bacterial inoculation through the rhizosphere of T. erecta L. plants resulted in 68.61% degradation of pyrene, which was significantly higher than control soil. Inoculation of AWD5 also improved plant growth and exhibited an increase in root length (14.64%), dry root weight (80.56%), shoot length (3.26%), and dry shoot weight (45.35%) after 60 days of incubation. T. erecta L., an ornamental plant, was also found to be suitable for bioremediation of pyrene. The effect of AWD5 application, and rhizoremediation process, on rhizosphere bacterial diversity and community structure has been studied using the metagenomic analysis of the 16S (V3–V4) region of rRNA. 37 bacterial phyla constituted the core microbiome, which was dominated by Proteobacteria followed by Actinobacteria, Actinobacteria, and Planctomycetes for all the treatments. AWD5 inoculation enhanced the relative abundance of Firmicutes and Acidobacteria as compared with other treatments. Genus Kaistobacter and Verrucomicrobia were found to be an abundant indigenous population in pyrene-spiked soils. Bacterial richness and diversity were analyzed using the Shannon–Wiener (H) index. A lower diversity index was observed in pyrene-spiked soils. Canonical correspondence analysis (CCA) showed a possible linkage with plant growth attributes and available nitrogen content that influences diversity and abundance of the bacterial community.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, India
| | | | | | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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19
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Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
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20
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José S, Jordao L. Exploring the Interaction between Microplastics, Polycyclic Aromatic Hydrocarbons and Biofilms in Freshwater. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1830809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sílvia José
- Department of Environmental Health, National Institute of Health Dr Ricardo Jorge, Lisboa, Portugal
| | - Luisa Jordao
- Department of Environmental Health, National Institute of Health Dr Ricardo Jorge, Lisboa, Portugal
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21
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Muccee F, Ejaz S. Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil. Microbiol Res 2020; 238:126504. [PMID: 32534383 DOI: 10.1016/j.micres.2020.126504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/28/2020] [Accepted: 05/01/2020] [Indexed: 10/24/2022]
Abstract
The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of β-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.
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Affiliation(s)
- Fatima Muccee
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
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22
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Multicolor emitting N/S-doped carbon dots as a fluorescent probe for imaging pathogenic bacteria and human buccal epithelial cells. Mikrochim Acta 2019; 186:157. [DOI: 10.1007/s00604-019-3270-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/20/2019] [Indexed: 12/20/2022]
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23
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Optimization Kerosene Bio-degradation by a Local Soil Bacterium Isolate Klebsiella pneumoniae Sp. pneumonia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.41] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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