Skip to main content
SpringerLink
Log in

Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal

  • Research
  • Published:
World Journal of Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

Data availability

The data of metagenome sequences, used in this study has been uploaded on MG-RAST server, which can be available from the corresponding author on reasonable request.

References

  • Adetutu EM, Smith RJ, Weber J, Aleer S, Mitchell JG, Ball AS, Juhasz AL (2013) A polyphasic approach for assessing the suitability of bioremediation for the treatment of hydrocarbon-impacted soil. Sci Total Environ 450:51–58

    Article  PubMed  Google Scholar 

  • Alcalde M, Ferrer M, Plou FJ, Ballesteros A (2006) Environmental biocatalysis: from remediation with enzymes to novel green processes. Trends Biotechnol 24(6):281–287

    Article  CAS  PubMed  Google Scholar 

  • Alekshun MN, Levy SB (2007) Molecular mechanisms of antibacterial multidrug resistance. Cell 128(6):1037–1050

    Article  CAS  PubMed  Google Scholar 

  • American Public Health Association (APHA), W.E.F. (2017) Standard methods for the examination of water and wastewater, 23rd edn. American Water Works Association, AWWA, Washington DC

    Google Scholar 

  • Amos GC, Zhang L, Hawkey PM, Gaze WH, Wellington EM (2014) Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes. Vet Microbiol 171(3):441–447

    Article  CAS  PubMed  Google Scholar 

  • Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA, Goodwin LA, Woyke T, Currie CR, Suen G, Poulsen M (2013) Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol 79(12):3724–3733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Badalamenti JP, Krajmalnik-Brown R, Torres CI, Bond DR (2015) Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, two haloalkaliphilic metal-reducing Deltaproteobacteria. Genome Announc 3(2):e00039-e115

    Article  PubMed  PubMed Central  Google Scholar 

  • Baraniecki CA, Aislabie J, Foght JM (2002) Characterization of Sphingomonas sp. Ant 17, an aromatic hydrocarbon-degrading bacterium isolated from Antarctic soil. Microb Ecol 43(1):44–54

    Article  CAS  PubMed  Google Scholar 

  • Bell TH, Yergeau E, Martineau C, Juck D, Whyte LG, Greer CW (2011) Identification of nitrogen-incorporating bacteria in petroleum-contaminated arctic soils by using [15N] DNA-based stable isotope probing and pyrosequencing. Appl Environ Microbiol 77(12):4163–4171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buckley DH, Schmidt TM (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5(6):441–452

    Article  PubMed  Google Scholar 

  • Cabral L, Júnior GV, de Sousa ST, Dias AC, Cadete LL, Andreote FD, Hess M, de Oliveira VM (2016) Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities. Environ Pollut 216:460–469

    Article  CAS  PubMed  Google Scholar 

  • Chougule AS, Jadhav SB, Jadhav JP (2014) Microbial degradation and detoxification of synthetic dye mixture by Pseudomonas sp. SUK 1. Proc Natl Acad Sci, India Sect B Biol Sci 84(4):1059–1068

    Article  CAS  Google Scholar 

  • CPCB (2010) Annual water quality statistics of India. Central Pollution Control Board, Governmnet of India

    Google Scholar 

  • Czekalski N, Berthold T, Caucci S, Egli A, Bürgmann H (2012) Increased levels of multiresistant bacteria and resistance genes after wastewater treatment and their dissemination into Lake Geneva, Switzerland. Front Microbiol. https://doi.org/10.3389/fmicb.2012.00106

    Article  PubMed  PubMed Central  Google Scholar 

  • de Menezes A, Clipson N, Doyle E (2012) Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environ Microbiol 14(9):2577–2588

    Article  PubMed  Google Scholar 

  • Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D (2012) Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6(9):1677–1687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Desai C, Madamwar D (2007) Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments. Biores Technol 98(4):761–768

    Article  CAS  Google Scholar 

  • Desai C, Pathak H, Madamwar D (2010) Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Biores Technol 101(6):1558–1569

    Article  CAS  Google Scholar 

  • dos Santos DF, Istvan P, Noronha EF, Quirino BF, Krüger RH (2015) New dioxygenase from metagenomic library from Brazilian soil: insights into antibiotic resistance and bioremediation. Biotech Lett 37(9):1809–1817

    Article  Google Scholar 

  • Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML, Jauregui R, Pieper DH (2017) Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ Microbiol 19:2992

    Article  CAS  PubMed  Google Scholar 

  • Ercal N, Gurer-Orhan H, Aykin-Burns N (2001) Toxic metals and oxidative stress part I: mechanisms involved in metal-induced oxidative damage. Curr Top Med Chem 1(6):529–539

    Article  CAS  PubMed  Google Scholar 

  • Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73(21):7059–7066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fortin D, Davis B, Beveridge TJ (1996) Role of Thiobacillus and sulfate-reducing bacteria in iron biocycling in oxic and acidic mine tailings. FEMS Microbiol Ecol 21(1):11–24

    Article  CAS  Google Scholar 

  • Garg SK, Tripathi M, Lal N (2015) Response surface methodology for optimization of process variable for reactive orange 4 dye discoloration by Pseudomonas putida SKG-1 strain and bioreactor trial for its possible use in large-scale bioremediation. Desalin Water Treat 54(11):3122–3133

    Article  CAS  Google Scholar 

  • Gaston KJ (2010) Valuing common species. Science 327(5962):154–155

    Article  CAS  PubMed  Google Scholar 

  • Gerdes S, El Yacoubi B, Bailly M, Blaby IK, Blaby-Haas CE, Jeanguenin L, Lara-Núñez A, Pribat A, Waller JC, Wilke A, Overbeek R (2011) Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics 12(1):S2

    Article  PubMed  PubMed Central  Google Scholar 

  • Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P (2009) Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci 106(5):1374–1379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gillan DC, Roosa S, Kunath B, Billon G, Wattiez R (2015) The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study. Environ Microbiol 17(6):1991–2005

    Article  CAS  PubMed  Google Scholar 

  • Gołębiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B (2014) 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb Ecol 67(3):635–647

    Article  PubMed  PubMed Central  Google Scholar 

  • Gomez-Alvarez V, Teal TK, Schmidt TM (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J 3(11):1314–1317

    Article  PubMed  Google Scholar 

  • Goñi-Urriza M, Corsellis Y, Lanceleur L, Tessier E, Gury J, Monperrus M, Guyoneaud R (2015) Relationships between bacterial energetic metabolism, mercury methylation potential, and hgcA/hgcB gene expression in Desulfovibrio dechloroacetivorans BerOc1. Environ Sci Pollut Res 22(18):13764–13771

    Article  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haq I, Kumar S, Kumari V, Singh SK, Raj A (2016) Evaluation of bioremediation potentiality of ligninolytic Serratia liquefaciens for detoxification of pulp and paper mill effluent. J Hazard Mater 305:190–199

    Article  CAS  PubMed  Google Scholar 

  • Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331(6016):463–467

    Article  CAS  PubMed  Google Scholar 

  • Hooper DU, Chapin FS, Ewel JJ, Hector A, Inchausti P, Lavorel S, Lawton JH, Lodge DM, Loreau M, Naeem S, Schmid B (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monogr 75(1):3–5

    Article  Google Scholar 

  • Isaac P, Martínez FL, Bourguignon N, Sánchez LA, Ferrero MA (2015) Improved PAHs removal performance by a defined bacterial consortium of indigenous Pseudomonas and actinobacteria from Patagonia, Argentina. Int Biodeterior Biodegradation 101:23–31

    Article  CAS  Google Scholar 

  • Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335(6068):587–590

    Article  CAS  PubMed  Google Scholar 

  • Joutey NT, Bahafid W, Sayel H, Ananou S, El Ghachtouli N (2014) Hexavalent chromium removal by a novel Serratia proteamaculans isolated from the bank of Sebou River (Morocco). Environ Sci Pollut Res 21(4):3060–3072

    Article  Google Scholar 

  • Jozefczak M, Remans T, Vangronsveld J, Cuypers A (2012) Glutathione is a key player in metal-induced oxidative stress defenses. Int J Mol Sci 13(3):3145–3175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428(4):726–731

    Article  CAS  PubMed  Google Scholar 

  • Karnachuk OV, Mardanov AV, Avakyan MR, Kadnikov VV, Vlasova M, Beletsky AV, Gerasimchuk AL, Ravin NV (2015) Draft genome sequence of the first acid-tolerant sulfate-reducing deltaproteobacterium Desulfovibrio sp. TomC having potential for minewater treatment. FEMS Microbiol Lett 362(4):1–3

    Article  Google Scholar 

  • Korlević M, Zucko J, Dragić MN, Blažina M, Pustijanac E, Zeljko TV, Gacesa R, Baranasic D, Starcevic A, Diminic J, Long PF (2015) Bacterial diversity of polluted surface sediments in the northern Adriatic sea. Syst Appl Microbiol 38(3):189–197

    Article  PubMed  Google Scholar 

  • Labbé D, Margesin R, Schinner F, Whyte LG, Greer CW (2007) Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils. FEMS Microbiol Ecol 59(2):466–475

    Article  PubMed  Google Scholar 

  • Lavery TJ, Roudnew B, Seymour J, Mitchell JG, Jeffries T (2012) High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces. PLoS ONE 7(5):e36478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442(7104):806–809

    Article  CAS  PubMed  Google Scholar 

  • Lesser MP (2006) Oxidative stress in marine environments: biochemistry and physiological ecology. Annu Rev Physiol 68:253–278

    Article  CAS  PubMed  Google Scholar 

  • Li YQ, Xin Y, Li C, Liu J, Huang T (2023) Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil. Braz J Microbiol 54:935–947

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu J, Jin Q, He Y, He X, Zhao J (2014) Simultaneous removal of phenol and ammonium using Serratia sp. LJ-1 capable of heterotrophic nitrification-aerobic denitrification. Water Air Soil Pollut 225(9):2125

    Article  Google Scholar 

  • Lumppio HL, Shenvi NV, Summers AO, Voordouw G, Kurtz DM (2001) Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection System. J Bacteriol 183(1):101–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lyons KG, Brigham CA, Traut BH, Schwartz MW (2005) Rare species and ecosystem functioning. Conserv Biol 9(4):1019–1024

    Article  Google Scholar 

  • MacDougall AS, McCann KS, Gellner G, Turkington R (2013) Diversity loss with persistent human disturbance increases vulnerability to ecosystem collapse. Nature 494(7435):86–89

    Article  CAS  PubMed  Google Scholar 

  • Martinez JL (2009) Environmental pollution by antibiotics and by antibiotic resistance determinants. Environ Pollut 157(11):2893–2902

    Article  CAS  PubMed  Google Scholar 

  • May RM (1975) Patterns of species abundance and diversity. In: Cody ML, Diamond JM (eds) Ecology and evolution of communities. Belnap/Harvard University Press, pp 81–120

    Google Scholar 

  • Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinf 9(1):386

    Article  CAS  Google Scholar 

  • Mouillot D, Bellwood DR, Baraloto C, Chave J, Galzin R, Harmelin-Vivien M, Kulbicki M, Lavergne S, Lavorel S, Mouquet N, Paine CT (2013) Rare species support vulnerable functions in high-diversity ecosystems. PLoS Biol 11(5):e1001569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagayama H, Sugawara T, Endo R, Ono A, Kato H, Ohtsubo Y, Nagata Y, Tsuda M (2015) Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts. Appl Microbiol Biotechnol 99(10):4453–4470

    Article  CAS  PubMed  Google Scholar 

  • Nathani NM, Mootapally C, Sharma P, Solomon S, Kumar R, Fulke AB, Kumar M (2023) Microbial machinery dealing diverse aromatic compounds: decoded from pelagic sediment ecogenomics in the gulfs of Kathiawar Peninsula and Arabian Sea. Environ Res 225:115603

    Article  CAS  PubMed  Google Scholar 

  • Ntougias S, Lapidus A, Han J, Mavromatis K, Pati A, Chen A, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI (2014) High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6 T), a diphenol degrader with genes involved in the catechol pathway. Stand Genomic Sci 9(3):783

    Article  PubMed  PubMed Central  Google Scholar 

  • Olivera ER, Carnicero D, Jodra R, Miñambres B, García B, Abraham GA, Gallardo A, Román JS, García JL, Naharro G, Luengo JM (2001) Genetically engineered Pseudomonas: a factory of new bioplastics with broad applications. Environ Microbiol 3(10):612–618

    Article  CAS  PubMed  Google Scholar 

  • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Acids Res 33(17):5691–5702

    Article  CAS  Google Scholar 

  • Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30(21):3123–3124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patel V, Munot H, Shouche YS, Madamwar D (2014) Response of bacterial community structure to seasonal fluctuation and anthropogenic pollution on coastal water of Alang-Sosiya ship breaking yard, Bhavnagar, India. Biores Technol 161:362–370

    Article  CAS  Google Scholar 

  • Pat-Espadas AM, Razo-Flores E, Rangel-Mendez JR, Cervantes FJ (2013) Reduction of palladium and production of nano-catalyst by Geobacter sulfurreducens. Appl Microbiol Biotechnol 97(21):9553–9560

    Article  CAS  PubMed  Google Scholar 

  • Payne RB, Gentry DM, Rapp-Giles BJ, Casalot L, Wall JD (2002) Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c3 mutant. Appl Environ Microbiol 68(6):3129–3132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pieper DH, Reineke W (2000) Engineering bacteria for bioremediation. Curr Opin Biotechnol 11(3):262–270

    Article  CAS  PubMed  Google Scholar 

  • Poyntner C, Kutzner A, Margesin R (2021) Biodegradation potential and putative catabolic genes of culturable bacteria from an Alpine deciduous forest site. Microorganisms 9:1920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prakash OM, Gihring TM, Dalton DD, Chin KJ, Green SJ, Akob DM, Wanger G, Kostka JE (2010) Geobacter daltonii sp. Nov., an Fe (III)-and uranium (VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. Int J System Evol Microbiol 60(3):546–553

    Article  CAS  Google Scholar 

  • Preston EW (1962) The canonical distribution of commonness and rarity. Part I Ecol 43:185–215

    Google Scholar 

  • Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38(20):e191

    Article  PubMed  PubMed Central  Google Scholar 

  • Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, Anand S, Malhotra J, Jindal S, Nigam A, Lal R (2012) Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS ONE 7(9):e46219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6):863–864

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shah V, Zakrzewski M, Wibberg D, Eikmeyer F, Schlüter A, Madamwar D (2013) Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. Microb Ecol 66(3):533–550

    Article  PubMed  Google Scholar 

  • Sharaff M, Kamat S, Archana G (2017) Analysis of copper tolerant rhizobacteria from the industrial belt of Gujarat, western India for plant growth promotion in metal polluted agriculture soils. Ecotoxicol Environ Saf 138:113–121

    Article  CAS  PubMed  Google Scholar 

  • Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21(8):1794–1805

    Article  CAS  PubMed  Google Scholar 

  • Singh A, Chauhan NS, Thulasiram HV, Taneja V, Sharma R (2010) Identification of two flavin monooxygenases from an effluent treatment plant sludge metagenomic library. Biores Technol 101(21):8481–8484

    Article  CAS  Google Scholar 

  • Singleton DR, Ramirez LG, Aitken MD (2009) Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain. Appl Environ Microbiol 75(9):2613–2620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith MD, Knapp AK (2003) Dominant species maintain ecosystem function with non-random species loss. Ecol Lett 6(6):509–517

    Article  Google Scholar 

  • Sukul P, Spiteller M (2007) Fluoroquinolone antibiotics in the environment. Reviews of environmental contamination and toxicology. Springer, pp 131–162

    Chapter  Google Scholar 

  • Sutton NB, Maphosa F, Morillo JA, Al-Soud WA, Langenhoff AA, Grotenhuis T, Rijnaarts HH, Smidt H (2013) Impact of long-term diesel contamination on soil microbial community structure. Appl Environ Microbiol 79(2):619–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tokeshi M (1993) Species abundance patterns and community structure. Adv Ecol Res 24:111–186

    Article  Google Scholar 

  • Torrentó C, Cama J, Urmeneta J, Otero N, Soler A (2010) Denitrification of groundwater with pyrite and Thiobacillus denitrificans. Chem Geol 278(1):80–91

    Article  Google Scholar 

  • Ufarté L, Laville É, Duquesne S, Potocki-Veronese G (2015) Metagenomics for the discovery of pollutant degrading enzymes. Biotechnol Adv 33(8):1845–1854

    Article  PubMed  Google Scholar 

  • Varin T, Lovejoy C, Jungblut AD, Vincent WF, Corbeil J (2012) Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the high Arctic. Appl Environ Microbiol 78(2):549–559

    Article  PubMed  PubMed Central  Google Scholar 

  • Webber MA, Piddock LJ (2003) The importance of efflux pumps in bacterial antibiotic resistance. J Antimicrob Chemother 51(1):9–11

    Article  CAS  PubMed  Google Scholar 

  • Wickramasekara S, Neilson J, Patel N, Breci L, Hilderbrand A, Maier RM, Wysocki V (2011) Proteomics analyses of the opportunistic pathogen Burkholderia vietnamiensis using protein fractionations and mass spectrometry. BioMed Res Int. https://doi.org/10.1155/2011/701928

    Article  Google Scholar 

  • Yang S, Wen X, Jin H, Wu Q (2012) Pyrosequencing investigation into the bacterial community in permafrost soils along the China–Russia Crude Oil Pipeline (CRCOP). PLoS ONE 7(12):e52730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang T, Shao MF, Ye L (2012) 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6(6):1137–1147

    Article  CAS  PubMed  Google Scholar 

  • Zhou S, Xu J, Yang G, Zhuang L (2014) Methanogenesis affected by the co-occurrence of iron (III) oxides and humic substances. FEMS Microbiol Ecol 88(1):107–120

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors acknowledge Department of Biotechnology, Ministry of Science and Technology, New Delhi, India for financial support. JJ acknowledges Department of Science and Technology (DST), New Delhi for INSPIRE fellowship. The sequencing of metagenome using the Ion Torrent Platform sequencing facility was performed at Anand Agricultural University, Anand (Gujarat).

Funding

This work was supported by the Department of Biotechnology (DBT) grant (BT/1/CEIB/09/V/05) from the Ministry of Science and Technology, New Delhi, India. Jenny Johnson acknowledges Department of Science and Technology (DST), New Delhi for INSPIRE fellowship.

Author information

Authors and Affiliations

  1. Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India

    Jenny Johnson & Kunal R. Jain

  2. Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India

    Anand Patel & Nidhi Parmar

  3. P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa (Anand), Gujarat, 388 421, India

    Datta Madamwar

  4. Gujarat Biotechnology Research Centre, 6th Floor, M. S. Building, Sector 11, Gandhinagar, Gujarat, 382011, India

    Chaitanya Joshi

Authors
  1. Jenny Johnson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kunal R. Jain
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anand Patel
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nidhi Parmar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chaitanya Joshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Datta Madamwar
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

KRJ and DM conceived the concept of the study. JJ and KRJ performed the sampling. JJ preformed the experiments and drafted initial manuscript. JJ, KRJ, AP and NP performed the sequencing. KRJ, CJ and DM supervised the study, refined and edited the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Datta Madamwar.

Ethics declarations

Competing interest

The authors have no relevant financial or non-financial interests to disclose.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 3176 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Johnson, J., Jain, K.R., Patel, A. et al. Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal. World J Microbiol Biotechnol 40, 52 (2024). https://doi.org/10.1007/s11274-023-03848-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11274-023-03848-1

Keywords

Search

Navigation