Abstract
Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.
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Data Availability
Raw sequencing data was deposited as FASTQ files in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under the primary accession number PRJEB38775.
References
Luck MA, Jenerette GD, Wu J, Grimm NB (2001) The urban funnel model and the spatially heterogeneous ecological footprint. Ecosystems 4:782–796. https://doi.org/10.1007/s10021-001-0046-8
Shuster WD, Bonta J, Thurston H, Warnemuende E, Smith DR (2005) Impacts of impervious surface on watershed hydrology: a review. Urban Water J 2:263–275. https://doi.org/10.1080/15730620500386529
Wade R (2018) Urban pollution and ecosystem services. In: Urban pollution: science and management. John Wiley & Sons, Ltd, pp 199-209
Rice J, Westerhoff P (2017) High levels of endocrine pollutants in US streams during low flow due to insufficient wastewater dilution. Nat Geosci 10:587–591. https://doi.org/10.1038/ngeo2984
Barnes KB, Morgan JM, Roberge MC (2001) Impervious surfaces and the quality of natural and built environments. Department of Geography and Environmental Planning, Towson University, Baltimore
Hatt BE, Fletcher TD, Walsh CJ, Taylor SL (2004) The influence of urban density and drainage infrastructure on the concentrations and loads of pollutants in small streams. Environ Manag 34:112–124. https://doi.org/10.1007/s00267-004-0221-8
Xian G, Crane M, Su J (2007) An analysis of urban development and its environmental impact on the Tampa Bay watershed. J Environ Manag 85:965–976. https://doi.org/10.1016/j.jenvman.2006.11.012
Dudgeon D, Arthington AH, Gessner MO, Kawabata ZI, Knowler DJ, Lévêque C, Naiman RJ, Prieur-Richard AH, Soto D, Stiassny MLJ, Sullivan CA (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biol Rev 81:163–182. https://doi.org/10.1017/S1464793105006950
Cowx IG, Portocarrero Aya M (2011) Paradigm shifts in fish conservation: moving to the ecosystem services concept. J Fish Biol 79:1663–1680. https://doi.org/10.1111/j.1095-8649.2011.03144.x
Sullam KE, Essinger SD, Lozupone CA et al (2012) Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol 21:3363–3378. https://doi.org/10.1111/j.1365-294X.2012.05552.x
Stephens WZ, Burns AR, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJM (2016) The composition of the zebrafish intestinal microbial community varies across development. ISME J 10:644–654. https://doi.org/10.1038/ismej.2015.140
Ray AK, Ghosh K, Ringø E (2012)Enzyme-producing bacteria isolated from fish gut: a review. Aquac Nutr 18:465–492. https://doi.org/10.1111/j.1365-2095.2012.00943.x
Gómez GD, Balcázar JL (2008) A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunol Med Microbiol 52:145–154. https://doi.org/10.1111/j.1574-695X.2007.00343.x
Balcázar JL, de Blas I, Ruiz-Zarzuela I et al (2006) The role of probiotics in aquaculture. Vet Microbiol 114:173–186. https://doi.org/10.1016/j.vetmic.2006.01.009
Lazado CC, Caipang CMA (2014) Mucosal immunity and probiotics in fish. Fish Shellfish Immunol 39:78–89. https://doi.org/10.1016/j.fsi.2014.04.015
Cipriano RC, Dove A (2011) Far from superficial: microbial diversity associated with the skin and mucus of fish
Boutin S, Bernatchez L, Audet C, Derôme N (2013) Network analysis highlights complex interactions between pathogen, host and commensal microbiota. PLoS One 8:e84772. https://doi.org/10.1371/journal.pone.0084772
McFall-Ngai M, Hadfield MG, Bosch TCG, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci 110:3229–3236. https://doi.org/10.1073/pnas.1218525110
Singh Y, Ahmad J, Musarrat J, Ehtesham NZ, Hasnain SE (2013) Emerging importance of holobionts in evolution and in probiotics. Gut Pathog 5:12. https://doi.org/10.1186/1757-4749-5-12
Navarrete P, Mardones P, Opazo R, Espejo R, Romero J (2008) Oxytetracycline treatment reduces bacterial diversity of intestinal microbiota of Atlantic Salmon. J Aquat Anim Health 20:177–183. https://doi.org/10.1577/H07-043.1
Larsen A, Tao Z, Bullard SA, Arias CR (2013) Diversity of the skin microbiota of fishes: evidence for host species specificity. FEMS Microbiol Ecol 85:483–494. https://doi.org/10.1111/1574-6941.12136
Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014) Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 5. https://doi.org/10.3389/fmicb.2014.00207
Schmidt V, Gomez-Chiarri M, Roy C, Smith K, Amaral-Zettler L (2017) Subtle microbiome manipulation using probiotics reduces antibiotic-associated mortality in fish. mSystems 2:2. https://doi.org/10.1128/mSystems.00133-17
Pindling S, Azulai D, Zheng B, Dahan D, Perron GG (2018) Dysbiosis and early mortality in zebrafish larvae exposed to subclinical concentrations of streptomycin. FEMS Microbiol Lett 365:365. https://doi.org/10.1093/femsle/fny188
Pratte ZA, Besson M, Hollman RD, Stewart FJ (2018) The gills of reef fish support a distinct microbiome influenced by host-specific factors. Appl Environ Microbiol 84:84. https://doi.org/10.1128/AEM.00063-18
Krotman Y, Yergaliyev TM, Alexander Shani R, Avrahami Y, Szitenberg A (2020) Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system. Microbiome 8:9. https://doi.org/10.1186/s40168-020-0784-5
Merrifield DL, Rodiles A (2015) 10 - The fish microbiome and its interactions with mucosal tissues. In: Beck BH, Peatman E (eds) Mucosal health in aquaculture. Academic Press, San Diego, pp 273–295
Lowrey L, Woodhams DC, Tacchi L, Salinas I (2015) Topographical mapping of the rainbow trout (Oncorhynchus mykiss) microbiome reveals a diverse bacterial community with antifungal properties in the skin. Appl Environ Microbiol 81:6915–6925. https://doi.org/10.1128/AEM.01826-15
Le Pape P, Ayrault S, Quantin C (2012) Trace element behavior and partition versus urbanization gradient in an urban river (Orge River, France). J Hydrol 472–473:99–110. https://doi.org/10.1016/j.jhydrol.2012.09.042
Le Pape P, Quantin C, Morin G et al (2014) Zinc speciation in the suspended particulate matter of an urban river (Orge, France): influence of seasonality and urbanization gradient. Environ Sci Technol 48:11901–11909. https://doi.org/10.1021/es500680x
(2000) EU Water Framework Directive 2000/60/CE. 23 October 2000. Official Journal (OJ L 327) of the European Parliament and Council. 22 December 2000.73p. http://ec.europa.eu/environment/water/water-framework/index_en.html. Accessed 1 Sept 2020
Arrêté du 27 juillet 2018 modifiant l’arrêté du 25 janvier 2010 relatif aux méthodes et critères d’évaluation de l’état écologique, de l’état chimique et du potentiel écologique des eaux de surface pris en application des articles R. 212-10, R. 212-11 et R. 212-18 du code de l’environnement - Légifrance. https://www.legifrance.gouv.fr/jorf/id/JORFTEXT000037347756?r=91VXYdtAGK. Accessed 1 Oct 2020
Klindworth A, Pruesse E, Schweer T et al (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic acids research 41(1):e1–e1
Lane DJ (1991)16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley, New York City, New York
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinforma Oxf Engl 25:1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinforma Oxf Engl 22:2688–2690. https://doi.org/10.1093/bioinformatics/btl446
Miller MA, Pfeiffer W, Schwartz T (2011) The CIPRES science gateway: a community resource for phylogenetic analyses. Proceedings of the 2011 TeraGrid conference: extreme digital discovery. Association for Computing Machinery, Salt Lake City, pp 1–8
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. https://doi.org/10.1093/nar/gks1219
Oksanen J (2011) Vegan: community ecology package. R package ver. 2.0–2. https://www.CRANR-Proj. Accessed 22 April 2020
Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464. https://doi.org/10.1093/bioinformatics/btq166
Webb CO (2000) Exploring the phylogenetic structure of ecological communities: an example for rain Forest trees. Am Nat 156:145–155. https://doi.org/10.1086/303378
Oksanen JAI (2015) Vegan: an introduction to ordination
Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46. https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x
Friedman J, Alm EJ (2012) Inferring correlation networks from genomic survey data. PLoS Comput Biol 8:e1002687. https://doi.org/10.1371/journal.pcbi.1002687
Weiss S, Treuren WV, Lozupone C et al (2016) Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J 10:1669–1681. https://doi.org/10.1038/ismej.2015.235
Kelly C, Salinas I (2017) Under pressure: interactions between commensal microbiota and the teleost immune system. Front Immunol 8. https://doi.org/10.3389/fimmu.2017.00559
Chiarello M, Auguet J-C, Bettarel Y, Bouvier C, Claverie T, Graham NAJ, Rieuvilleneuve F, Sucré E, Bouvier T, Villéger S (2018) Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet. Microbiome 6:147. https://doi.org/10.1186/s40168-018-0530-4
Legrand TPRA, Catalano SR, Wos-Oxley ML, Stephens F, Landos M, Bansemer MS, Stone DAJ, Qin JG, Oxley APA (2018) The inner workings of the outer surface: skin and gill microbiota as indicators of changing gut health in yellowtail kingfish. Front Microbiol 8. https://doi.org/10.3389/fmicb.2017.02664
Derome N, Gauthier J, Boutin S, Llewellyn M (2016) Bacterial opportunistic pathogens of fish. In: Hurst CJ (ed) The Rasputin effect: when commensals and symbionts become parasitic. Springer International Publishing, Cham, pp 81–108
Montenegro D, Astudillo-García C, Hickey T, Lear G (2020) A non-invasive method to monitor marine pollution from bacterial DNA present in fish skin mucus. Environ Pollut 263:114438. https://doi.org/10.1016/j.envpol.2020.114438
Teil M-J, Tlili K, Blanchard M, Chevreuil M, Alliot F, Labadie P (2012) Occurrence of polybrominated diphenyl ethers, polychlorinated biphenyls, and phthalates in freshwater fish from the Orge river (Ile-de France). Arch Environ Contam Toxicol 63:101–113. https://doi.org/10.1007/s00244-011-9746-z
Larsen AM, Bullard SA, Womble M, Arias CR (2015) Community structure of skin microbiome of gulf killifish, Fundulus grandis, is driven by seasonality and not exposure to oiled sediments in a Louisiana salt marsh. Microb Ecol 70:534–544. https://doi.org/10.1007/s00248-015-0578-7
Tacchi L, Lowrey L, Musharrafieh R, Crossey K, Larragoite ET, Salinas I (2015) Effects of transportation stress and addition of salt to transport water on the skin mucosal homeostasis of rainbow trout (Oncorhynchus mykiss). Aquaculture 435:120–127. https://doi.org/10.1016/j.aquaculture.2014.09.027
Rakers S, Gebert M, Uppalapati S, Meyer W, Maderson P, Sell AF, Kruse C, Paus R (2010) ‘Fish matters’: the relevance of fish skin biology to investigative dermatology. Exp Dermatol 19:313–324. https://doi.org/10.1111/j.1600-0625.2009.01059.x
Goberna M, Navarro-Cano JA, Valiente-Banuet A, García C, Verdú M (2014) Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities. Ecol Lett 17:1191–1201. https://doi.org/10.1111/ele.12341
Goberna M, Verdú M (2016) Predicting microbial traits with phylogenies. ISME J 10:959–967. https://doi.org/10.1038/ismej.2015.171
Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33:475–505. https://doi.org/10.1146/annurev.ecolsys.33.010802.150448
Rodriguez-Mozaz S, Chamorro S, Marti E, Huerta B, Gros M, Sànchez-Melsió A, Borrego CM, Barceló D, Balcázar JL (2015) Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river. Water Res 69:234–242. https://doi.org/10.1016/j.watres.2014.11.021
Ory J, Bricheux G, Togola A, Bonnet JL, Donnadieu-Bernard F, Nakusi L, Forestier C, Traore O (2016) Ciprofloxacin residue and antibiotic-resistant biofilm bacteria in hospital effluent. Environ Pollut 214:635–645. https://doi.org/10.1016/j.envpol.2016.04.033
Talwar C, Nagar S, Lal R, Negi RK (2018) Fish gut microbiome: current approaches and future perspectives. Indian J Microbiol 58:397–414. https://doi.org/10.1007/s12088-018-0760-y
Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5:1595–1608. https://doi.org/10.1038/ismej.2011.38
Ghanbari M, Kneifel W, Domig KJ (2015) A new view of the fish gut microbiome: advances from next-generation sequencing. Aquaculture 448:464–475. https://doi.org/10.1016/j.aquaculture.2015.06.033
Li X, Zhou L, Yu Y, Ni J, Xu W, Yan Q (2017) Composition of gut microbiota in the gibel carp (Carassius auratus gibelio) varies with host development. Microb Ecol 74:239–249. https://doi.org/10.1007/s00248-016-0924-4
Carlson JM, Leonard AB, Hyde ER, Petrosino J, Primm T (2017) Microbiome disruption and recovery in the fish Gambusia affinis following exposure to broad-spectrum antibiotic. Infect Drug Resist 10:143–154. https://doi.org/10.2147/IDR.S129055
Dinh QT, Moreau-Guigon E, Labadie P, Alliot F, Teil MJ, Blanchard M, Chevreuil M (2017) Occurrence of antibiotics in rural catchments. Chemosphere 168:483–490. https://doi.org/10.1016/j.chemosphere.2016.10.106
Janda JM, Abbott SL (2010) The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin Microbiol Rev 23:35–73. https://doi.org/10.1128/CMR.00039-09
Beaz-Hidalgo R, Figueras MJ (2013) Aeromonas spp. whole genomes and virulence factors implicated in fish disease. J Fish Dis 36:371–388. https://doi.org/10.1111/jfd.12025
Skwor T, Shinko J, Augustyniak A, Gee C, Andraso G (2014) Aeromonas hydrophila and Aeromonas veronii predominate among potentially pathogenic ciprofloxacin- and tetracycline-resistant Aeromonas isolates from Lake Erie. Appl Environ Microbiol 80:841–848. https://doi.org/10.1128/AEM.03645-13
Austin B, Austin DA (2016) Aeromonadaceae representatives (motile aeromonads). In: Austin B, Austin DA (eds) Bacterial fish pathogens: disease of farmed and wild fish. Springer International Publishing, Cham, pp 161–214
Topic Popovic N, Kazazic SP, Strunjak-Perovic I, Barisic J, Sauerborn Klobucar R, Kepec S, Coz-Rakovac R (2015) Detection and diversity of aeromonads from treated wastewater and fish inhabiting effluent and downstream waters. Ecotoxicol Environ Saf 120:235–242. https://doi.org/10.1016/j.ecoenv.2015.06.011
Lewbart GA (2001) Bacteria and ornamental fish. Semin Avian Exot Pet Med 10:48–56. https://doi.org/10.1053/saep.2001.19543
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The authors are grateful to B. Janvier for technical and laboratory assistance with the experiments.
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This study was supported by funds from the PIREN-Seine research program and an internal call for proposals (UMR METIS).
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The work presented here was carried out in collaboration with all authors. FP and AG defined the research theme. AG, FP, TB, EG, and FA defined sampling strategy and designed methods and experiments. FP, TB, NM, EG, and FA carried out the sampling processing and DNA extraction. Bioinformatic analyses and phylogenetic reconstruction were carried out by YC. Data have been analyzed and interpreted by all authors. YC wrote the article. All authors have contributed to, read, and approved the final manuscript.
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Colin, Y., Berthe, T., Molbert, N. et al. Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads. Microb Ecol 82, 523–536 (2021). https://doi.org/10.1007/s00248-020-01650-2
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DOI: https://doi.org/10.1007/s00248-020-01650-2