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.
Amplicon sequencing
Coastal marine microbiome
Metagenomics
Microbial composition and function
Operational taxonomic unit
Supervised machine learning
Journal
BMC microbiology
ISSN: 1471-2180
Titre abrégé: BMC Microbiol
Pays: England
ID NLM: 100966981
Informations de publication
Date de publication:
10 May 2024
10 May 2024
Historique:
received:
03
09
2023
accepted:
04
04
2024
medline:
11
5
2024
pubmed:
11
5
2024
entrez:
10
5
2024
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
BACKGROUND
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
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
CONCLUSIONS
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.
Identifiants
pubmed: 38730339
doi: 10.1186/s12866-024-03295-4
pii: 10.1186/s12866-024-03295-4
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
DNA, Bacterial
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
162Subventions
Organisme : University Grants Commission
ID : PDFSS-2013-14-ST-MAH-4350
Informations de copyright
© 2024. The Author(s).
Références
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.
pubmed: 23844080
pmcid: 3701056
doi: 10.1371/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.
pubmed: 28752603
doi: 10.1111/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.
pubmed: 26323861
doi: 10.1016/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.
pubmed: 20411108
pmcid: 2857370
doi: 10.3390/md8030438
Kraemer SA, Ramachandran A, Perron GG. Antibiotic pollution in the environment: from microbial ecology to public policy. Microorganisms. 2019;7(6):180.
pubmed: 31234491
pmcid: 6616856
doi: 10.3390/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.
pubmed: 31636428
doi: 10.1038/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.
pubmed: 31710600
pmcid: 6874084
doi: 10.1371/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.
pubmed: 36030922
doi: 10.1016/j.envres.2022.114202
Cabral JP. Water microbiology bacterial pathogens and water. Int J Environ Res Public Health. 2010;7(10):3657–703.
pubmed: 21139855
pmcid: 2996186
doi: 10.3390/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.
doi: 10.1038/s41579-019-0222-5
Stewart EJ. Growing unculturable bacteria. J Bacteriol. 2012;194(16):4151–60.
pubmed: 22661685
pmcid: 3416243
doi: 10.1128/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.
pubmed: 33665032
pmcid: 7916533
doi: 10.7717/peerj.10911
Neu AT, Allen EE, Roy K. Defining and quantifying the core microbiome: challenges and prospects. PNAS. 2021;118(51):e2104429118.
pubmed: 34862327
pmcid: 8713806
doi: 10.1073/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.
pubmed: 33077589
pmcid: 7959581
doi: 10.1073/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.
pubmed: 32598345
pmcid: 7323985
doi: 10.1371/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.
pubmed: 21640949
doi: 10.1016/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.
doi: 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.
doi: 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.
pubmed: 34526853
pmcid: 8437043
doi: 10.1016/j.rser.2021.111181
Mehdizadeh Allaf M, Peerhossaini H. Cyanobacteria: model microorganisms and beyond. Microorganisms. 2022;10(4):696.
pubmed: 35456747
pmcid: 9025173
doi: 10.3390/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.
doi: 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.
pubmed: 27720011
doi: 10.1016/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.
pubmed: 28878754
pmcid: 5572232
doi: 10.3389/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.
pubmed: 31866976
pmcid: 6906166
doi: 10.3389/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.
pubmed: 33354517
pmcid: 7731724
doi: 10.5334/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.
doi: 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.
doi: 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.
doi: 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.
pubmed: 30800106
pmcid: 6376745
doi: 10.3389/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.
pubmed: 32234773
pmcid: 7112960
doi: 10.1128/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.
pubmed: 36379333
doi: 10.1016/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.
doi: 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.
pubmed: 31341288
pmcid: 7015180
doi: 10.1038/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.
pubmed: 32343490
pmcid: 9285460
doi: 10.1002/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.
pubmed: 33885785
pmcid: 8265157
doi: 10.1093/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.
pubmed: 33216126
doi: 10.1093/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.
pubmed: 30801021
pmcid: 6372836
doi: 10.1128/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.
pubmed: 33986544
pmcid: 8184642
doi: 10.1038/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.
pubmed: 31552137
pmcid: 6759219
doi: 10.21105/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.
pubmed: 3781942
doi: 10.1111/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.
doi: 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.
pubmed: 20518792
doi: 10.1111/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.
pubmed: 10461381
doi: 10.1111/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.
doi: 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.
doi: 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.
doi: 10.1016/j.jmarsys.2008.12.010
Pauly D, Christensen V. Primary production required to sustain global fisheries. Nat. 1995;374:255–7.
doi: 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.
pubmed: 32275514
doi: 10.1016/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.
pubmed: 22053120
pmcid: 3205352
doi: 10.1016/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.
doi: 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.
doi: 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.
pubmed: 18250305
pmcid: 2538866
doi: 10.1073/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.
pubmed: 36894593
pmcid: 9998654
doi: 10.1038/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.
doi: 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.
doi: 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 .
doi: 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.
pubmed: 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 .
doi: 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.
pubmed: 20738403
doi: 10.1111/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 .
doi: 10.3389/fmicb.2023.1163896
pubmed: 37333635
pmcid: 10272453
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 .
doi: 10.1016/j.scitotenv.2018.01.288
pubmed: 29426121
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.
doi: 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.
pubmed: 36344551
pmcid: 9640712
doi: 10.1038/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.
pubmed: 36060757
pmcid: 9432862
doi: 10.3389/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.
pubmed: 30733732
pmcid: 6353758
doi: 10.1016/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.
pubmed: 37481658
pmcid: 10363106
doi: 10.1038/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.
pubmed: 37806325
doi: 10.1016/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.
pubmed: 20375359
pmcid: 2863362
doi: 10.1128/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.
doi: 10.1111/1541-4337.13283
Wydro U. Soil microbiome study based on DNA extraction: a review. Water. 2022;14(24):3999.
doi: 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.
doi: 10.3390/microbiolres12040063
Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules. 2014;4(1):117–39.
pubmed: 24970208
pmcid: 4030981
doi: 10.3390/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.
pubmed: 37491583
pmcid: 10368615
doi: 10.1038/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.
pubmed: 31614851
pmcid: 6843647
doi: 10.3390/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.
pubmed: 34539610
pmcid: 8440912
doi: 10.3389/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.
pubmed: 37508415
pmcid: 10375983
doi: 10.3390/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.
pubmed: 32499497
pmcid: 7610499
doi: 10.1038/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.
pubmed: 35797741
pmcid: 10321321
doi: 10.1016/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.
pubmed: 25350160
doi: 10.1038/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.
pubmed: 34445742
pmcid: 8396473
doi: 10.3390/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.
pubmed: 37520347
pmcid: 10374199
doi: 10.3389/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.
pubmed: 34775906
pmcid: 8810056
doi: 10.1080/21655979.2021.2004645