A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.

Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE

Original Publication: London : BioMed Central, [2001-

RNA, Ribosomal, 16S*/genetics ; Bacteria*/classification ; Bacteria*/genetics ; Bacteria*/isolation & purification ; Microbiota*/genetics ; Seawater*/microbiology ; Phylogeny* ; Supervised Machine Learning* ; Bays*/microbiology; India ; Biodiversity ; DNA, Bacterial/genetics ; Salinity ; Sequence Analysis, DNA/methods

Background: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.
Results: The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.
Conclusion: Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.
(© 2024. The Author(s).)

Erratum in: BMC Microbiol. 2024 Jun 22;24(1):220. doi: 10.1186/s12866-024-03382-6. (PMID: 38909193)

Liquete C, Piroddi C, Drakou EG, Gurney L, Katsanevakis S, Charef A, Egoh B. Current status and future prospects for the assessment of marine and coastal ecosystem services: a systematic review. PLoS One. 2013;8(7):e67737. (PMID: 23844080370105610.1371/journal.pone.0067737)
Pausch J, Kuzyakov Y. Carbon input by roots into the soil: Quantification of rhizodeposition from root to ecosystem scale. Glob Chang Biol. 2018;24(1):1–12. (PMID: 2875260310.1111/gcb.13850)
Slingenberg A, Braat L, van der Windt H, Eichler L, Turner K. Study on understanding the causes of biodiversity loss and the policy assessment framework. Contract no. DG.ENV.G.1/FRA/2006/0073. Rotterdam: European Commission Directorate-General for Environment; 2009. p. 1–199.
Rekadwad BN, Khobragade CN. A case study on effects of oil spills and tar-ball pollution on beaches of Goa (India). Mar Pollut Bull. 2015;100(1):567–70. (PMID: 2632386110.1016/j.marpolbul.2015.08.019)
Penesyan A, Kjelleberg S, Egan S. Development of novel drugs from marine surface associated microorganisms. Mar Drugs. 2010;8:438–59. (PMID: 20411108285737010.3390/md8030438)
Kraemer SA, Ramachandran A, Perron GG. Antibiotic pollution in the environment: from microbial ecology to public policy. Microorganisms. 2019;7(6):180. (PMID: 31234491661685610.3390/microorganisms7060180)
Trevathan-Tackett SM, Sherman CD, Huggett MJ, Campbell AH, Laverock B, Hurtado-McCormick V, Seymour JR, Firl A, Messer LF, Ainsworth TD, Negandhi KL, Daffonchio D, Egan S, Engelen AH, Fusi M, Thomas T, Vann L, Hernandez-Agreda A, Gan HM, Marzinelli EM, Steinberg PD, Hardtke L, Macreadie PI. A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol. 2019;3:1509–20. (PMID: 3163642810.1038/s41559-019-0999-7)
Wilkins LGE, Leray M, O’Dea A, Yuen B, Peixoto RS, Pereira TJ, Bik HM, Coil DA, Duffy JE, Herre EA, Lessios HA, Lucey NM, Mejia LC, Rasher DB, Sharp KH, Sogin EM, Thacker RW, Vega Thurber R, Wcislo WT, Wilbanks EG, Eisen JA. Host-associated microbiomes drive structure and function of marine ecosystems. PLoS Biol. 2019;17(11):e3000533. (PMID: 31710600687408410.1371/journal.pbio.3000533)
Chen CZ, Li P, Liu L, Li ZH. Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: a review. Environ Res. 2022;214(Pt 4):114202. (PMID: 3603092210.1016/j.envres.2022.114202)
Cabral JP. Water microbiology bacterial pathogens and water. Int J Environ Res Public Health. 2010;7(10):3657–703. (PMID: 21139855299618610.3390/ijerph7103657)
Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists’ warning to humanity: microorganisms and climate change. Nature Rev Microbiol. 2019;17(9):569–86. (PMID: 10.1038/s41579-019-0222-5)
Stewart EJ. Growing unculturable bacteria. J Bacteriol. 2012;194(16):4151–60. (PMID: 22661685341624310.1128/JB.00345-12)
Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ. 2021;9:e10911. (PMID: 33665032791653310.7717/peerj.10911)
Neu AT, Allen EE, Roy K. Defining and quantifying the core microbiome: challenges and prospects. PNAS. 2021;118(51):e2104429118. (PMID: 34862327871380610.1073/pnas.2104429118)
Pierre JF. Chapter 1: introduction and background to microbiome research. In: Metabolism of nutrients by gut microbiota. 2022. p. 1–17.
Hoshino T, Doi H, Uramoto GI, Inagaki F. Global diversity of microbial communities in marine sediment. PNAS. 2020;117(44):27587–97. (PMID: 33077589795958110.1073/pnas.1919139117)
Adyasari D, Hassenrück C, Montiel D, Dimova N. Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD). PLoS One. 2020;15(6):e0235235. (PMID: 32598345732398510.1371/journal.pone.0235235)
Maron PA, Mougel C, Ranjard L. Soil microbial diversity: Methodological strategy, spatial overview and functional interest. C R Biol. 2011;334(5–6):403–11. (PMID: 2164094910.1016/j.crvi.2010.12.003)
Murillo AA, Molina V, Salcedo-Castro J, Harrod C. Editorial: marine microbiome and biogeochemical cycles in marine productive areas. Front Mar Sci. 2019;6:657. (PMID: 10.3389/fmars.2019.00657)
Henley SF, Cavan EL, Fawcett SE, Kerr R, Monteiro T, Sherrell RM, Bowie AR, Boyd PW, Barnes DKA, Schloss IR, Marshall T, Flynn R, Smith S. Changing biogeochemistry of the Southern Ocean and its ecosystem implications. Front Mar Sci. 2020;7:581. (PMID: 10.3389/fmars.2020.00581)
Tanvir RU, Zhang J, Canter T, Chen D, Lu J, Hu Z. Harnessing solar energy using phototrophic microorganisms: a sustainable pathway to bioenergy, biomaterials, and environmental solutions. Renew Sustain Energy Rev. 2021;146:1–111181. (PMID: 34526853843704310.1016/j.rser.2021.111181)
Mehdizadeh Allaf M, Peerhossaini H. Cyanobacteria: model microorganisms and beyond. Microorganisms. 2022;10(4):696. (PMID: 35456747902517310.3390/microorganisms10040696)
He Z, Lin L, Wang X, Qin W, Zhang C. Editorial: carbon storage by marine microorganisms for carbon neutrality. Front Mar Sci. 2022;9:1018397. (PMID: 10.3389/fmars.2022.1018397)
Verde C, Giordano D, Bellas CM, di Prisco G, Anesio AM. Polar marine microorganisms and climate change. Adv Microb Physiol. 2016;69:187–215. (PMID: 2772001110.1016/bs.ampbs.2016.07.002)
Currie AR, Tait K, Parry H, de Francisco-Mora B, Hicks N, Osborn AM, Widdicombe S, Stahl H. Marine microbial gene abundance and community composition in response to ocean acidification and elevated temperature in two contrasting coastal marine sediments. Front Microbiol. 2017;8:1599. (PMID: 28878754557223210.3389/fmicb.2017.01599)
Lønborg C, Baltar F, Carreira C, Morán XAG. Dissolved organic carbon source influences tropical coastal heterotrophic bacterioplankton response to experimental warming. Front Microbiol. 2019;10:2807. (PMID: 31866976690616610.3389/fmicb.2019.02807)
Landrigan PJ, Stegeman JJ, Fleming LE, Allemand D, Anderson DM, Backer LC, Brucker-Davis F, Chevalier N, Corra L, Czerucka D, Bottein MD, Demeneix B, Depledge M, Deheyn DD, Dorman CJ, Fénichel P, Fisher S, Gaill F, Galgani F, Gaze WH, Giuliano L, Grandjean P, Hahn ME, Hamdoun A, Hess P, Judson B, Laborde A, McGlade J, Mu J, Mustapha A, Neira M, Noble RT, Pedrotti ML, Reddy C, Rocklöv J, Scharler UM, Shanmugam H, Taghian G, van de Water JAJM, Vezzulli L, Weihe P, Zeka A, Raps H, Rampal P. Human health and ocean pollution. Ann Glob Health. 2020;86(1):151. (PMID: 33354517773172410.5334/aogh.2831)
Hilmi N, Chami R, Sutherland MD, Hall-Spencer JM, Lebleu L, Benitez MB, Levin LA. The role of blue carbon in climate change mitigation and carbon stock conservation. Front Climate. 2021;3:710546. (PMID: 10.3389/fclim.2021.710546)
Estes M Jr, Anderson C, Appeltans W, Bax N, Bednaršek N, Canonico G, Djavidnia S, Escobar E, Fietzek P, Gregoire M, Hazen E, Kavanaugh M, Lejzerowicz F, Lombard F, Miloslavich P, Möller KO, Monk J, Montes E, Moustahfid H, Muelbert MCC, Muller-Karger F, Reeves LEP, Satterthwaite EV, Schmidt JO, Sequeira AMM, Turner W, Weatherdon LV. Enhanced monitoring of life in the sea is a critical component of conservation management and sustainable economic growth. Mar Pol. 2021;132:104699. (PMID: 10.1016/j.marpol.2021.104699)
Abbass K, Qasim MZ, Song H, Murshed M, Mahmood H, Younis I. A review of the global climate change impacts, adaptation, and sustainable mitigation measures. Environ Sci Pollut Res. 2022;29:42539–59. (PMID: 10.1007/s11356-022-19718-6)
Rekadwad BN. Composite sampling method for soil microbiome and microbial abundance analysis. 2023. Zenodo. https://doi.org/10.5281/zenodo.8073695 .
Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS, Makharia GK. Comparison of small gut and whole gut microbiota of first-degree relatives with adult celiac disease patients and controls. Front Microbiol. 2019;10:164. (PMID: 30800106637674510.3389/fmicb.2019.00164)
Gaike AH, Paul D, Bhute S, Dhotre DP, Pande P, Upadhyaya S, Reddy Y, Sampath R, Ghosh D, Chandraprabha D, Acharya J, Banerjee G, Sinkar VP, Ghaskadbi SS, Shouche YS. The gut microbial diversity of newly diagnosed diabetics but not of prediabetics is significantly different from that of healthy nondiabetics. mSystems. 2020;5(2):e00578-19. (PMID: 32234773711296010.1128/mSystems.00578-19)
Singh KS, Paul D, Gupta A, Dhotre D, Klawonn F, Shouche Y. Indian sewage microbiome has unique community characteristics and potential for population-level disease predictions. Sci Total Environ. 2023;858:160178. (PMID: 3637933310.1016/j.scitotenv.2022.160178)
Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. Available online at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc .
Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG. Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. Giga Sci. 2016;5(1):s13742-016-0133–6. (PMID: 10.1186/s13742-016-0133-6)
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7. (PMID: 31341288701518010.1038/s41587-019-0209-9)
Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr Protoc Bioinformatics. 2020;70(1):e100. (PMID: 32343490928546010.1002/cpbi.100)
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293–6. (PMID: 33885785826515710.1093/nar/gkab301)
Santichaivekin S, Yang Q, Liu J, Mawhorter R, Jiang J, Wesley T, Wu YC, Libeskind-Hadas R. eMPRess: a systematic cophylogeny reconciliation tool. Bioinformatics. 2021;37(16):2481–2. (PMID: 3321612610.1093/bioinformatics/btaa978)
Martino C, Morton JT, Marotz CA, Thompson LR, Tripathi A, Knight R, Zengler K. A novel sparse compositional technique reveals microbial perturbations. mSystems. 2019;4:e00016-19. (PMID: 30801021637283610.1128/mSystems.00016-19)
Sun Z, Huang S, Zhang M, Zhu Q, Haiminen N, Carrieri AP, Vázquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YY. Challenges in benchmarking metagenomic profilers. Nat Methods. 2021;18(6):618–26. (PMID: 33986544818464210.1038/s41592-021-01141-3)
Bokulich NA, Dillon MR, Bolyen E, Kaehler BD, Huttley GA, Caporaso JG. q2-sample-classifier: machine-learning tools for microbiome classification and regression. J Open Res Softw. 2018;3(30):934. (PMID: 31552137675921910.21105/joss.00934)
Quevedo-Sarmiento J, Ramos-Cormenzana A, Gonzalez-Lopez J. Isolation and characterization of aerobic heterotrophic bacteria from natural spring waters in the Lanjaron area (Spain). J Appl Bacteriol. 1986;61(4):365–72. (PMID: 378194210.1111/j.1365-2672.1986.tb04298.x)
Bock M, Bosecker K, Kämpfer P, Dott W. Isolation and characterization of heterotrophic, aerobic bacteria from oil storage caverns in northern Germany. Appl Microbiol Biotechnol. 1994;42:463–8. (PMID: 10.1007/BF00902758)
Bessède E, Angla-Gre M, Delagarde Y, Sep Hieng S, Ménard A, Mégraud F. Matrix-assisted laser-desorption/ionization biotyper: experience in the routine of a University hospital. Clin Microbiol Infect. 2011;17(4):533–8. (PMID: 2051879210.1111/j.1469-0691.2010.03274.x)
Turner S, Pryer KM, Miao VPW, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol. 1999;46:327–38. (PMID: 1046138110.1111/j.1550-7408.1999.tb04612.x)
IILSS. International Institute for Law of the Sea Studies. https://iilss.net/ . Accessed 24 July 2023.
Sigman DM, Hain MP. The biological productivity of the ocean. Nat Educ Knowl. 2012;3(10):21.
Jensen TG. Arabian Sea and Bay of Bengal exchange of salt and tracers in an ocean model. Geophy Res Lett. 2011;28(20):3967–70. (PMID: 10.1029/2001GL013422)
Gordon AL. Bay of Bengal surface and thermocline and the Arabian Sea. New York: Ocean and Climate Physics, Lamont-Doherty Earth Observatory (LDEO), Columbia Climate School, Columbia University. https://people.climate.columbia.edu/projects/view/165 . Accessed 14 Aug 2023.
Rengarajan R, Sarin MM, Somayajulu BLK, Suhasini. Mixing in the surface waters of the western Bay of Bengal using 228Ra and 226Ra. J Mar Res. 2002;60:255–79. (PMID: 10.1357/00222400260497480)
Prasanna Kumar S, Madhupratap M, Dileep Kumar M, Muraleedharan PM, de Souza SN, Gauns M, Sarma VVSS. High biological productivity in the central Arabian Sea during the summer monsoon driven by Ekman pumping and lateral advection. Curr Sci. 2001;81(12):1633–8.
Cipollini P. Proceedings of the symposium on 15 years of progress in radar altimetry, by Danesy, D. ISBN:92-9092-925-1. Noordwijk: European Space Agency; 2006. id.112.
Lowe, Totdal range. ArcGIS StoryMaps. https://storymaps.arcgis.com/ . Accessed 22 Mar 2020.
Finney BP, Alheit J, Emeis KC, Field DB, Gutiérrez D, Struck U. Paleoecological studies on variability in marine fish populations: a long-term perspective on the impacts of climatic change on marine ecosystems. J Mar Syst. 2010;79:316–26. (PMID: 10.1016/j.jmarsys.2008.12.010)
Pauly D, Christensen V. Primary production required to sustain global fisheries. Nat. 1995;374:255–7. (PMID: 10.1038/374255a0)
Dang X, Chen X, Bai Y, He X, Chen CTA, Li T, Pan D, Zhang Z. Impact of ENSO events on phytoplankton over the Sulu Ridge. Mar Environ Res. 2020;157:104934. (PMID: 3227551410.1016/j.marenvres.2020.104934)
Pitcher GC, Figueiras FG, Hickey BM, Moita MT. The physical oceanography of upwelling systems and the development of harmful algal blooms. Prog Oceanogr. 2010;85(1–2):5–32. (PMID: 22053120320535210.1016/j.pocean.2010.02.002)
Vinayachandran PNM, Masumoto Y, Roberts MJ, Huggett JA, Halo I, Chatterjee A, Amol P, Gupta GVM, Singh A, Mukherjee A, Prakash S, Beckley LE, Raes EJ, Hood R. Reviews and syntheses: physical and biogeochemical processes associated with upwelling in the Indian Ocean. Biogeosci. 2021;18:5967–6029. (PMID: 10.5194/bg-18-5967-2021)
Harvey JBJ, Ryan JP, Zhang Y. Influences of extreme upwelling on a coastal retention zone. Front Mar Sci. 2021;8:648944. (PMID: 10.3389/fmars.2021.648944)
Rykaczewski RR, Checkley DM Jr. Influence of ocean winds on the pelagic ecosystem in upwelling regions. Proc Natl Acad Sci USA. 2008;105(6):1965–70. (PMID: 18250305253886610.1073/pnas.0711777105)
Moreau S, Hattermann T, de Steur L, Kauko HM, Ahonen H, Ardelan M, Assmy P, Chierici M, Descamps S, Dinter T, Falkenhaug T, Fransson A, Grønningsæter E, Hallfredsson EH, Huhn O, Lebrun A, Lowther A, Lübcker N, Monteiro P, Peeken I, Roychoudhury A, Różańska M, Ryan-Keogh T, Sanchez N, Singh A, Simonsen JH, Steiger N, Thomalla SJ, van Tonder A, Wiktor JM, Steen H. Wind-driven upwelling of iron sustains dense blooms and food webs in the eastern Weddell Gyre. Nat Commun. 2023;14(1):1303. (PMID: 36894593999865410.1038/s41467-023-36992-1)
García-Seoane R, Viana IG, Bode A. Seasonal upwelling influence on trophic indices of mesozooplankton in a coastal food web estimated from δ15N in amino acids. Prog Oceanogr. 2023;2(219):103149. (PMID: 10.1016/j.pocean.2023.103149)
Butler JN, Wells PG, Johnson S, Manock JJ. Beach tar on Bermuda: recent observations and implications for global monitoring. Mar Poll Bull. 1998;36(6):458–63. (PMID: 10.1016/S0025-326X(98)00005-8)
Taucher J, Bach LT, Boxhammer T, Nauendorf A, The Gran Canaria KOSMOS Consortium, Achterberg EP, Algueró-Muñiz M, Arístegui J, Czerny J, Esposito M, Guan W, Haunost M, Horn HG, Ludwig A, Meyer J, Spisla C, Sswat M, Stange P, Riebesell U. Influence of ocean acidification and deep water upwelling on oligotrophic plankton communities in the subtropical North Atlantic: insights from an in situ mesocosm study. Front Mar Sci. 2017;4:85. https://doi.org/10.3389/fmars.2017.00085 . (PMID: 10.3389/fmars.2017.00085)
Snively G. High tide, low tide. 1881. p. 1–141.
Selvaraj GSD. An approach to differentiate high and low tide data in the diurnal hydrobiological studies of estuaries. J Mar Biol Ass India. 2006;48(1):01–5.
Morris RL, Graham TDJ, Kelvin J, Ghisalberti M, Swearer SE. Kelp beds as coastal protection: wave attenuation of Ecklonia radiata in a shallow coastal bay. Ann Bot. 2020;125(2):235–46. (PMID: 31424534)
van Sebille E, Aliani S, Law KL, Maximenko N, Alsina JM, Bagaev A, Bergmann M, Chapron B, Chubarenko I, Cózar A, Delandmeter P, Egger M, Fox-Kemper B, Garaba SP, Goddijn-Murphy L, Hardesty BD, Hoffman MJ, Isobe A, Jongedijk CE, Kaandorp MLA, Khatmullina L, Koelmans AA, Kukulka T, Laufkötter C, Lebreton L, Lobelle D, Maes C, Martinez-Vicente V, Maqueda MAM, Poulain-Zarcos M, Rodríguez E, Ryan PG, Shanks AL, Shim WJ, Suaria G, Thiel M, van den Bremer TS, Wichmann D. The physical oceanography of the transport of floating marine debris. Environ Res Lett. 2020;15:023003. https://doi.org/10.1088/1748-9326/ab6d7d . (PMID: 10.1088/1748-9326/ab6d7d)
Nogales B, Lanfranconi MP, Piña-Villalonga JM, Bosch R. Anthropogenic perturbations in marine microbial communities. FEMS Microbiol Rev. 2011;35(2):275–98. (PMID: 2073840310.1111/j.1574-6976.2010.00248.x)
Liang S, Li H, Wu H, Yan B, Song A. Microorganisms in coastal wetland sediments: a review on microbial community structure, functional gene, and environmental potential. Front Microbiol. 2023;14:1163896. https://doi.org/10.3389/fmicb.2023.1163896 . (PMID: 10.3389/fmicb.2023.11638963733363510272453)
Louca S, Mazel F, Doebeli M, Parfrey LW. A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol. 2019;17(2):e3000106. https://doi.org/10.1371/journal.pbio.3000106 .
Chu EW, Karr JR. Environmental Impact: Concept, Consequences, Measurement. Ref Module Life Sci. 2017;B978-0-12-809633-8.02380-3. https://doi.org/10.1016/B978-0-12-809633-8.02380-3 .
Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci Total Environ. 2018;627:1018–38. https://doi.org/10.1016/j.scitotenv.2018.01.288 . (PMID: 10.1016/j.scitotenv.2018.01.28829426121)
Brown JK, Manz WL, Konstantinidis KT, Ward NR, Tiedje JM. A new view of the tree of life based on nearly complete genomes from archaea and bacteria. Nature. 2015;526(7571):585–90.
Xu Y, Jeanne T, Hogue R, Shi Y, Ziadi N, Parent LE. Soil bacterial diversity related to soil compaction and aggregates sizes in potato cropping systems. Appl Soil Ecol. 2021;168:104147. (PMID: 10.1016/j.apsoil.2021.104147)
Zakavi M, Askari H, Shahrooei M. Characterization of bacterial diversity between two coastal regions with heterogeneous soil texture. Sci Rep. 2022;12(1):18901. (PMID: 36344551964071210.1038/s41598-022-23487-0)
Jia M, Sun X, Chen M, Liu S, Zhou J, Peng X. Deciphering the microbial diversity associated with healthy and wilted Paeonia suffruticosa rhizosphere soil. Front Microbiol. 2022;13:967601. (PMID: 36060757943286210.3389/fmicb.2022.967601)
Farha AK, Tr T, Purushothaman A, Salam JA, Hatha AM. Phylogenetic diversity and biotechnological potentials of marine bacteria from continental slope of eastern Arabian Sea. J Genet Eng Biotechnol. 2018;16(2):253–8. (PMID: 30733732635375810.1016/j.jgeb.2018.06.002)
Petrosyan K, Thijs S, Piwowarczyk R, Ruraż K, Kaca W, Vangronsveld J. Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae). Sci Rep. 2023;13:11835. (PMID: 374816581036310610.1038/s41598-023-38899-9)
Elgendy MY, Ali SE, Abbas WT, Algammal AM, Abdelsalam M. The role of marine pollution on the emergence of fish bacterial diseases. Chemosphere. 2023;344:140366. (PMID: 3780632510.1016/j.chemosphere.2023.140366)
Iwamoto M, Ayers T, Mahon BE, Swerdlow DL. Epidemiology of seafood-associated infections in the United States. Clin Microbiol Rev. 2010;23(2):399–411. (PMID: 20375359286336210.1128/CMR.00059-09)
Brauge T, Mougin J, Ells T, Midelet G. Sources and contamination routes of seafood with human pathogenic Vibrio spp.: A Farm-to-Fork approach. Compr Rev Food Sci Food Saf. 2024;23:1–18. (PMID: 10.1111/1541-4337.13283)
Wydro U. Soil microbiome study based on DNA extraction: a review. Water. 2022;14(24):3999. (PMID: 10.3390/w14243999)
Castronovo LM, Del Duca S, Chioccioli S, Vassallo A, Fibbi D, Coppini E, Chioccioli P, Santini G, Zaccaroni M, Fani R. Biodiversity of soil bacterial communities from the Sasso Fratino integral nature reserve. Microbiol Res. 2021;12(4):862–77. (PMID: 10.3390/microbiolres12040063)
Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules. 2014;4(1):117–39. (PMID: 24970208403098110.3390/biom4010117)
Rehman A, Saeed A, Asad W, Khan I, Hayat A, Rehman MU, Shah TA, Sitotaw B, Sawoud TM, Bourhia M. Eco-friendly textile desizing with indigenously produced amylase from Bacillus cereus AS2. Sci Rep. 2023;13:11991. (PMID: 374915831036861510.1038/s41598-023-38956-3)
Odelade KA, Babalola OO. Bacteria, fungi and archaea domains in rhizospheric soil and their effects in enhancing agricultural productivity. Int J Environ Res Public Health. 2019;16(20):3873. (PMID: 31614851684364710.3390/ijerph16203873)
Kim H, Jeon J, Lee KK, Lee YH. Compositional shift of bacterial, archaeal, and fungal communities is dependent on trophic lifestyles in rice paddy soil. Front Microbiol. 2021;12:719486. (PMID: 34539610844091210.3389/fmicb.2021.719486)
Zambrano-Romero A, Ramirez-Villacis DX, Barriga-Medina N, Sierra-Alvarez R, Trueba G, Ochoa-Herrera V, Leon-Reyes A. Comparative methods for quantification of sulfate-reducing bacteria in environmental and engineered sludge samples. Biology. 2023;12(7):985. (PMID: 375084151037598310.3390/biology12070985)
van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol. 2020;18(9):491–506. (PMID: 32499497761049910.1038/s41579-020-0368-1)
Brettner L, Ho WC, Schmidlin K, Apodaca S, Eder R, Geiler-Samerotte K. Challenges and potential solutions for studying the genetic and phenotypic architecture of adaptation in microbes. Curr Opin Genet Dev. 2022;75:101951. (PMID: 357977411032132110.1016/j.gde.2022.101951)
Hartmann M, Frey B, Mayer J, Mäder P, Widmer F. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 2015;9(5):1177–94. (PMID: 2535016010.1038/ismej.2014.210)
Mhete M, Eze PN, Rahube TO, Akinyemi FO. Soil properties influence bacterial abundance and diversity under different land-use regimes in semi-arid environments. Sci Afr. 2020;7:e00246.
Abdul Rahman NSN, Abdul Hamid NW, Nadarajah K. Effects of abiotic stress on soil microbiome. Int J Mol Sci. 2021;22(16):9036. (PMID: 34445742839647310.3390/ijms22169036)
Park DG, Kwon J-G, Ha E-S, Kang B, Choi I, Kwak J-E, Choi J, Lee W, Kim SH, Kim SH, Park J, Lee J-H. Novel next generation sequencing panel method for the multiple detection and identification of foodborne pathogens in agricultural wastewater. Front Microbiol. 2023;14:1179934. (PMID: 375203471037419910.3389/fmicb.2023.1179934)
Rebello S, Nathan VK, Sindhu R, Binod P, Awasthi MK, Pandey A. Bioengineered microbes for soil health restoration: present status and future. Bioengineered. 2021;12(2):12839–53. (PMID: 34775906881005610.1080/21655979.2021.2004645)

PDFSS-2013-14-ST-MAH-4350 University Grants Commission

Keywords: Amplicon sequencing; Coastal marine microbiome; Metagenomics; Microbial composition and function; Operational taxonomic unit; Supervised machine learning

0 (RNA, Ribosomal, 16S)
0 (DNA, Bacterial)

Date Created: 20240510 Date Completed: 20240511 Latest Revision: 20240622

20240623

PMC11084130

10.1186/s12866-024-03295-4

38730339