Bibliographie

Holt CC, van der Giezen M, Daniels CL, Stentiford GD, Bass D. 2020. Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus). *ISME Journal* 14:531–543.

DOI: 10.1038/s41396-019-0546-1.

Holt CC, Bass D, Stentiford GD, van der Giezen M. 2021. Understanding the role of the shrimp gut microbiome in health and disease. *Journal of Invertebrate Pathology* 186:107387.

DOI: 10.1016/j.jip.2020.107387.

Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. 2020. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. *Frontiers in Microbiology* 11.

DOI: 10.3389/fmicb.2020.00468.

Huang Z, Li X, Wang L, Shao Z. 2016. Changes in the intestinal bacterial community during the growth of white shrimp, Litopenaeus vannamei. *Aquaculture Research* 47:1737–1746.

DOI: 10.1111/are.12628.

Huang F, Pan L, Song M, Tian C, Gao S. 2018. Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health. *Applied Microbiology and Biotechnology* 102:8585–8598.

DOI: 10.1007/s00253-018-9229-5.

Hutchins DA, Fu F. 2017. Microorganisms and ocean global change. *Nature Microbiology* 2:1–11.

DOI: 10.1038/nmicrobiol.2017.58.

Huttenhower C, Gevers D, Knight R, Abubucker S, ..., White O. 2012. Structure, function and diversity of the healthy human microbiome. *Nature* 486:207–214.

DOI: 10.1038/nature11234.

I

Ikeda-Ohtsubo W, Brugman S, Warden CH, Rebel JMJ, Folkerts G, Pieterse CMJ. 2018. How Can We Define “Optimal Microbiota”?: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture. *Frontiers in Nutrition* 5:1–18.

DOI: 10.3389/fnut.2018.00090.

Infante-Villamil S, Huerlimann R, Jerry DR. 2021. Microbiome diversity and dysbiosis in aquaculture. *Reviews in Aquaculture* 13:1077–1096.

DOI: 10.1111/raq.12513.

J

Jiravanichpaisal P, Lee BL, Söderhäll K. 2006. Cell-mediated immunity in arthropods: Hematopoiesis, coagulation, melanization and opsonization. *Immunobiology* 211:213–236.

DOI: 10.1016/j.imbio.2005.10.015.

Jiravanichpaisal P, Puanglarp N, Petkon S, Donnuea S, Söderhäll I, Söderhäll K. 2007. Expression of immune-related genes in larval stages of the giant tiger shrimp, Penaeus monodon. *Fish and Shellfish Immunology* 23:815–824.

DOI: 10.1016/j.fsi.2007.03.003.

K

Kamada N, Seo S-U, Chen GY, Núñez G. 2013. Role of the gut microbiota in immunity and inflammatory disease. *Nature Reviews Immunology* 13:321–335.

DOI: 10.1038/nri3430.

Karunasagar I, Pai R, Malathi GR, Karunasagar I. 1994. Mass mortality of Penaeus monodon larvae due to antibiotic-resistant Vibrio harveyi infection. *Aquaculture* 128:203–209.

DOI: 10.1016/0044-8486(94)90309-3.

Karunasagar I, Karunasagar I, Umesha RK. 2001. Microbial Diseases in Shrimp Aquaculture. *Fish Pathology*:121–134.

Kembel SW, Wu M, Eisen JA, Green JL. 2012. Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. 8:16–18.

DOI: 10.1371/journal.pcbi.1002743.

Kim BR, Guevarra RB, Lee JH, Kim DW, Seol KH, Lee JH, Kim HB, Isaacson RE. 2017. Deciphering diversity indices for a better understanding of microbial communities. *Journal of Microbiology* and *Biotechnology* 27:2089–2093.

DOI: 10.4014/jmb.1709.09027.

Kitani H. 1986. Larval development of the blue shrimp Penaeus stylirostris STIMPSON reared in the laboratory. *NIPPON SUISAN GAKKAISHI* 52:1121–1130.

DOI: 10.2331/suisan.52.1121.

L

Lahti L, Shetty S. 2020. Tools for microbiome analysis in R. Version 2.1.28.

http://microbiome.github.com/microbiome

Lane-Petter W. 1962. The Provision and Use of Pathogen-Free Laboratory Animals. *Journal of the Royal Society of Medicine* 55:253–263.

DOI: 10.1177/003591576205500402.

Larenas J, Bartholomew J, Troncoso O, Fernández S, Ledezma H, Sandoval N, Vera P, Contreras J, Smith P. 2003. Experimental vertical transmission of Piscirickettsia salmonis and in vitro study of attachment and mode of entrance into the fish ovum. *Diseases of Aquatic Organisms* 56:25–30.

DOI: 10.3354/dao056025.

Lee J, Hyeon DY, Hwang D. 2020. Single-cell multiomics: technologies and data analysis methods. *Experimental and Molecular Medicine* 52:1428–1442.

DOI: 10.1038/s12276-020-0420-2.

Lee JW, Chiu ST, Wang ST, Liao YC, Chang HT, Ballantyne R, Lin JS, Liu CH. 2022. Dietary SYNSEA probiotic improves the growth of white shrimp, Litopenaeus vannamei and reduces the risk of Vibrio infection via improving immunity and intestinal microbiota of shrimp. *Fish and Shellfish Immunology* 127:482–491.

DOI: 10.1016/j.fsi.2022.06.071.

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. *Frontiers in Microbiology* 8:1–17.

DOI: 10.3389/fmicb.2017.02664.

Lein EY, Lal MTM, Maran BAV, Ch'ng CL, Hamasaki K, Sano M, Tuzan AD. 2022. Gastrointestinal Microbiota of Spiny Lobster: A Review. *Fishes* 7:1–17.

DOI: 10.3390/fishes7030108.

Lemonnier H, Herbland A, Salery L, Soulard B. 2006. "Summer syndrome" in Litopenaeus stylirostris grow out ponds in New Caledonia: Zootechnical and environmental factors. *Aquaculture* 261:1039–1047.

DOI: 10.1016/j.aquaculture.2006.08.036.

Lemos LN, Fulthorpe RR, Triplett EW, Roesch LFW. 2011. Rethinking microbial diversity analysis in the high throughput sequencing era. *Journal of Microbiological Methods* 86:42–51.

DOI: 10.1016/j.mimet.2011.03.014.

Leung TLF, Poulin R, Leung TLF, Parasitism RP, Explor- M, Leung TLF, Poulin R. 2021. Mutualism : exploring the many shades of symbioses. *Life & Environment. 2008.* pp107-115
hal-03246057
Li E, Xu C, Wang X, Wang S, Zhao Q, Zhang M, Qin JG, Chen L. 2018. Gut Microbiota and its Modulation for Healthy Farming of Pacific White Shrimp Litopenaeus vannamei. *Reviews in Fisheries Science & Aquaculture* 26:381–399.

DOI: 10.1080/23308249.2018.1440530.

Li Z, Zhao Z, Luo L, Wang S, Zhang R, Guo K, Yang Y. 2023. Immune and intestinal microbiota responses to heat stress in Chinese mitten crab (Eriocheir sinensis). *Aquaculture* 563.

DOI: 10.1016/j.aquaculture.2022.738965.

Lightner DV, Redman RM, Bell TA. 1983. Infectious hypodermal and hematopoietic necrosis, a newly recognized virus disease of penaeid shrimp. *Journal of Invertebrate Pathology* 42:62–70.

DOI: 10.1016/0022-2011(83)90202-1.

Lightner DV, Bell TA, Redman RM. 1989. A Review of the Known Hosts, Geographic Range and Current Diagnostic Procedures for the Virus Diseases of Cultured Penaeid Shrimp. Actes de colloques Ifremer, Tahiti, French Polynesia, 20 Feb – 4 Mar 1989, n°9, chap. 13, pp.113–126.

https://archimer.ifremer.fr/doc/00000/1481/

Lin H, Peddada SD. 2020. Analysis of compositions of microbiomes with bias correction. *Nature Communications* 11:1–11.

DOI: 10.1038/s41467-020-17041-7.

Liu H, Wang L, Liu M, Wang B, Jiang K, Ma S, Li Q. 2011. The intestinal microbial diversity in Chinese shrimp (Fenneropenaeus chinensis) as determined by PCR–DGGE and clone library analyses. *Aquaculture* 317:32–36.

DOI: 10.1016/j.aquaculture.2011.04.008.

Liu C, Cui Y, Li X, Yao M. 2021. microeco: an R package for data mining in microbial community ecology. *FEMS Microbiology Ecology* 97:1–9.

DOI: 10.1093/femsec/fiaa255.

Lo CF, Ho CH, Chen CH, Liu KF, Chiu YL, Yeh PY, Peng SE, Hsu HC, Liu HC, Chang CF, Su M Sen, Wang CH, Kou GH. 1997. Detection and tissue tropism of white spot syndrome baculovirus (WSBV) in captured brooders of Penaeus monodon with a special emphasis on reproductive organs. *Disease of Aquatic Organisms* 30:53–72.

DOI: 10.3354/dao030053.

Lokmer A, Mathias Wegner K. 2015. Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. *ISME Journal* 9:670–682.

DOI: 10.1038/ismej.2014.160.

Lokmer A, Goedknegt MA, Thieltges DW, Fiorentino D, Kuenzel S, Baines JF, Mathias Wegner K. 2016. Spatial and temporal dynamics of pacific oyster hemolymph microbiota across multiple scales. *Frontiers in Microbiology* 7:1–18.

DOI: 10.3389/fmicb.2016.01367.

Longeon A, Peduzzi J, Barthélemy M, Corre S, Nicolas JL, Guyot M. 2004. Purification and partial identification of novel antimicrobial protein from marine bacterium Pseudoalteromonas species strain X153. *Marine Biotechnology* 6:633–641.

DOI: 10.1007/s10126-004-3009-1.

López-Carvallo JA, Cruz-Flores R, Dhar AK. 2022. The emerging pathogen Enterocytozoon hepatopenaei drives a degenerative cyclic pattern in the hepatopancreas microbiome of the shrimp (Penaeus vannamei). *Scientific reports* 12:14766.

DOI: 10.1038/s41598-022-19127-2.

de Lorgeril J, Lucasson A, Petton B, ..., Mitta G. 2018. Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters. *Nature Communications* 9.

DOI: 10.1038/s41467-018-06659-3.

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. :1–21.

DOI: 10.1186/s13059-014-0550-8.

Lu Z, Ren Z, Lin W, Shi C, Mu C, Wang C, Wu Q, Ye Y. 2022. Succession, sources, and assembly of bacterial community in the developing crab larval microbiome. *Aquaculture* 548:737600.

DOI: 10.1016/j.aquaculture.2021.737600.

Lv X, Li S, Yu Y, Zhang X, Li F. 2020. Characterization of a gill-abundant crustin with microbiota modulating function in Litopenaeus vannamei. *Fish and Shellfish Immunology* 105:393–404.

DOI: 10.1016/j.fsi.2020.07.014.

M

Ma KY, Chan TY, Chu KH. 2011. Refuting the six-genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. *Zoologica Scripta* 40:498–508.

DOI: 10.1111/j.1463-6409.2011.00483.x.

Maddox MB, Manzi JJ. 1976. The Effects Of Algal Supplements On Static System Culture Of Macrobrachium rosenbergii (De Man) Larvae1,2. *Proceedings of the annual meeting - World Mariculture Society* 7:677–698.

DOI: 10.1111/j.1749-7345.1976.tb00096.x.

Magoc T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. *Bioinformatics* 27:2957–2963.

DOI: 10.1093/bioinformatics/btr507.

Magurran A. 2004. Measuring Biological Diversity. Blackwell Science Ltd, Oxford, United Kingdom.

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. 2014. Swarm: robust and fast clustering method for amplicon-based studies. *PeerJ* 2:e593.

DOI: 10.7717/peerj.593.

Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. 2015. Analysis of composition of microbiomes: a novel method for studying microbial composition. *Microbial Ecology in Health & Disease* 26.

DOI: 10.3402/mehd.v26.27663.

Maraci Ő, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. 2021. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estridid Finches, the Bengalese Finch and the Zebra Finch. *Frontiers in Microbiology* 12:1–15.

DOI: 10.3389/fmicb.2021.619141

Marchesi JR, Ravel J. 2015. The vocabulary of microbiome research: a proposal. *Microbiome* 3:31.

DOI: 10.1186/s40168-015-0094-5.

Martin D, Rybicki E. 2000. RDP: detection of recombination amongst aligned sequences. *Bioinformatics. Oxford Journals* 16:562–563.

DOI: 10.1093/16.6.562

Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. *EMBnet.journal* 17:10–12.

DOI: 10.14806/ej.17.1.200

Martin BD, Schwab E. 2012. Current Usage of Symbiosis and Associated Terminology. *International Journal of Biology* 5:32–45.

DOI: 10.5539/ijb.v5n1p32.

McMurdie PJ, Holmes S. 2013. Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. *PLoS ONE* 8:1–11.

DOI: 10.1371/journal.pone.0061217.

McMurdie PJ, Holmes S. 2014. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. *PLoS Computational Biology* 10:e1003531.

DOI: 10.1371/journal.pcbi.1003531.

McNeil NI. 1984. The contribution of the large intestine to energy supplies in man. *The American Journal of Clinical Nutrition* 39:338–342.

DOI: 10.1093/ajcn/39.2.338.
Mermoud I, Costa R, Ferré O, Goarant C, Haffner P. 1998. 'Syndrome 93' in New Caledonian outdoor rearing ponds of Penaeus stylirostris: history and description of three major outbreaks. *Aquaculture* 164:323-335.

DOI: 10.1016/S0044-8486(98)00197-5.

Methou P, Hernández-Ávila I, Aube J, Cueff-Gauchard V, Gayet N, Amand L, Shillito B, Pradillon F, Cambon-Bonavita MA. 2019. Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development. *Frontiers in Microbiology* 10:1-19.

DOI: 10.3389/fmicb.2019.00808.

Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. 2011. How many species are there on earth and in the ocean? *PLoS Biology* 9:1-8.

DOI: 10.1371/journal.pbio.1001127.

Motte E, Yugcha E, Luzardo J, Castro F, Leclercq G, Rodríguez J, Miranda P, Borja O, Serrano J, Terreros M, Montalvo K, Narváez A, Tenorio N, Cedeño V, Mialhe E, Boulo V. 2003. Prevention of IHHNV vertical transmission in the white shrimp Litopenaeus vannamei. *Aquaculture* 219:57-70.

DOI: 10.1016/S0044-8486(02)00631-2.

Murphy J, Riley JP. 1962. A modified single solution method for the determination of phosphate in natural waters. *Analytica Chimica Acta* 27:31-36.

DOI: 10.1016/S0003-2670(00)88444-5.

N

Nayak SK. 2010. Role of gastrointestinal microbiota in fish. *Aquaculture Research* 41:1553-1573.

DOI: 10.1111/j.1365-2109.2010.02546.x.

Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. *Journal of Molecular Biology* 48:443-453.

DOI: 10.1016/0022-2836(70)90057-4.

Nyholm SV. 2020. In the beginning: egg-microbe interactions and consequences for animal hosts. *Philosophical Transactions of the Royal Society B: Biological Sciences* 375:20190593.

DOI: 10.1098/rstb.2019.0593.

O

Offret C, Paulino S, Gauthier O, Château K, Bidault A, Corporeau C, Miner P, Petton B, Pernet F, Fabioux C, Paillard C, Le Blay G. 2020. The marine intertidal zone shapes oyster and clam digestive bacterial microbiota. *FEMS Microbiology Ecology* 96:1-12.

DOI: 10.1093/femsec/fiaa078

Offret C, Gauthier O, Despréaux G, Bidault A, Corporeau C, Miner P, Petton B, Pernet F, Fabioux C, Paillard C, Le Blay G. 2022. Microbiota of the digestive glands and extrapallial fluids of clams evolve differently over time depending on the intertidal position. *Microbial Ecology* 85:288-297

DOI: 10.1007/s00248-022-01959-0

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H. 2020. CRAN - Package vegan. https://cran.rproject.org/web/packages/vegan/index.html

Olesen SW, Duvallet C, Alm EJ. 2017. dbOTU3: A new implementation of distribution-based OTU calling. *PLOS ONE* 12:e0176335.

DOI: 10.1371/journal.pone.0176335.

Oliphant K, Allen-Vercoe E. 2019. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. *Microbiome* 7:91.

DOI: 10.1186/s40168-019-0704-8.

Ooi MC, Goulden EF, Smith GG, Nowak BF, Bridle AR. 2017. Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus. *FEMS Microbiology Ecology* 93:1-10.

DOI: 10.1093/femsec/fix159.

Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, Poirier C, Richards TA, Keeling PJ, Worden AZ, Santoro AE. 2016. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. *ISME Journal* 10:2158-2173.

DOI: 10.1038/ismej.2016.20.

Osterholz H, Kirchman DL, Niggemann J, Dittmar T. 2018. Diversity of bacterial communities and dissolved organic matter in a temperate estuary. *FEMS microbiology ecology* 94:1-11.

DOI: 10.1093/femsec/fiy119.

P

Paillard C, Gueguen Y, Wegner M, Bass D, Pallavicini A, Vezzulli L, Arzul I. 2022. Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture. *Current Opinion in Biotechnology* 73:225-232

DOI: 10.1016/j.copbio.2021.07.026

Della Patrona L, Brun P. 2009. Elevage de la Crevette Bleue en Nouvelle-Calédonie. Litopenaeus Stylirostris. Bases biologiques et zootechnie. https://archimer.ifremer.fr/doc/00251/36229/.

Paulson JN, Colin Stine O, Bravo HC, Pop M. 2013. Differential abundance analysis for microbial marker-gene surveys. *Nature Methods* 10:1200-1202.

DOI: 10.1038/nmeth.2658.

Péricard P. 2017. Algorithmes pour la reconstruction de séquences de marqueurs conservés dans des données de métagénomique. Université de Lille.

Petersen C, Round JL. 2014. Defining dysbiosis and its influence on host immunity and disease. *Cellular Microbiology* 16:1024-1033.

DOI: 10.1111/cmi.12308.

Pham D. 2011. Les capacités osmorégulatrices chez la crevette bleue Litopenaeus stylirostris, au cours de l'ontogenèse. Université de la Polynésie Française.

Pham D, Ansquer D, Chevalier A, Dauga C, Peyramale A, Wabete N, Labreuche Y. 2014. Selection and characterization of potential probiotic bacteria for Litopenaeus stylirostris shrimp hatcheries in New Caledonia. *Aquaculture* 432:475-482.

DOI: 10.1016/j.aquaculture.2014.04.031.

Pierce ML, Ward JE. 2018. Microbial Ecology of the Bivalvia, with an Emphasis on the Family Ostreidae. *Journal of Shellfish Research* 37:793-806.

DOI: 10.2983/035.037.0410.

Pierce ML, Evan J. 2019. and the Blue Mussel (Mytilus edulis): Temporal Variation and Communities. 4:1-17.

DOI: 10.1128/mSphere.00730-19.

Porter TM, Hajibabaei M. 2020. Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis. *Frontiers in Ecology and Evolution* 8:1-15.

DOI: 10.3389/fevo.2020.00248.

Prescott SL. 2017. History of medicine: Origin of the term microbiome and why it matters. *Human Microbiome Journal* 4:24-25.

DOI: 10.1016/j.humic.2017.05.004.

Price MN, Dehal PS, Arkin AP. 2009. Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix. *Molecular Biology and Evolution* 26:1641-1650.

DOI: 10.1093/molbev/msp077.
Prodan A, Tremaroli V, Brolin H, Zwinderman AH, Nieuwdorp M, Levin E. 2020. Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing. PLOS ONE 15:e0227434.

DOI: 10.1371/journal.pone.0227434.

Q

Qiao F, Liu YK, Sun YH, Wang XD, Chen K, Li TY, Li EC, Zhang ML. 2017. Influence of different dietary carbohydrate sources on the growth and intestinal microbiota of Litopenaeus vannamei at low salinity. *Aquaculture Nutrition* 23:444-452.

DOI: 10.1111/anu.12412.

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 Research* 41:590-596.

DOI: 10.1093/nar/gks1219.

R

Rahul K, Sasikala C, Tushar L, Debadrita R, Ramana C V. 2014. Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond. *International journal of systematic and evolutionary microbiology* 64:3553-3558.

DOI: 10.1099/ijs.0.061168-0.

Ramette A. 2007. Multivariate analyses in microbial ecology. *FEMS Microbiology Ecology* 62:142-160.

DOI: 10.1111/j.1574-6941.2007.00375.x.

Reichenbach H. 1992. The Order Cytophagales. In: *The Prokaryotes*. New York, NY: Springer New York, 3631-3675.

DOI: 10.1007/978-1-4757-2191-1_37.

Restrepo L, Domínguez-Borbor C, Bajaña L, Betancourt I, Rodríguez J, Bayot B, Reyes A. 2021. Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus). *Microbiome* 9:88. DOI: 10.1186/s40168-021-01043-8.

Robinson MD, McCarthy DJ, Smyth GK. 2009. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. *Bioinformatics* 26:139-140.

DOI: 10.1093/bioinformatics/btp616.

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versatile open source tool for metagenomics. *PeerJ* 4:e2584.

DOI: 10.7717/peerj.2584.

Le Roux F, Labreuche Y, Davis BM, Iqbal N, Mangenot S, Goarant C, Mazel D, Waldor MK. 2011. Virulence of an emerging pathogenic lineage of Vibrio nigripulchritudo is dependent on two plasmids. *Environmental Microbiology* 13:296-306.

DOI: 10.1111/j.1462-2920.2010.02329.x.

RStudio Team. 2020. RStudio: Integrated Development for R. RStudio, PBC, Boston, MA.

S

Sadeghi-Nassaj SM, Catalá TS, Álvarez PA, Reche I. 2018. Sea cucumbers reduce chromophoric dissolved organic matter in aquaculture tanks. *PeerJ* 2018:1-20.

DOI: 10.7717/peerj.4344.

Santiago-Rodriguez TM, Hollister EB. 2021. Multi 'omic data integration: A review of concepts, considerations, and approaches. *Seminars in Perinatology* 45:151456.

DOI: 10.1016/j.semperi.2021.151456.

Sathish Kumar T, Vidya R, Kumar S, Alavandi SV, Vijayan KK. 2017. Zoea-2 syndrome of Penaeus vannamei in shrimp hatcheries. *Aquaculture* 479:759-767.

DOI: 10.1016/j.aquaculture.2017.07.022.

Satpathy KK, Mohanty AK, Natesan U, Prasad MVR, Sarkar SK. 2010. Seasonal variation in physicochemical properties of coastal waters of Kalpakkam, east coast of India with special emphasis on nutrients. *Environmental Monitoring and Assessment* 164:153-171.

DOI: 10.1007/s10661-009-0882-0.

Saulnier D, Avarre J, Le Moullac G, Ansquer D, Levy P, Vonau V. 2000. Rapid and sensitive PCR detection of Vibrio penaeicida, the putative etiological agent of Syndrome 93 in New Caledonia. *Diseases of Aquatic Organisms* 40:109-115.

DOI: 10.3354/dao040109.

Sha H, Lu J, Chen J, Xiong J. 2022. A meta-analysis study of the robustness and universality of gut microbiota-shrimp diseases relationship. *Environmental Microbiology* 24:3924-3938.

DOI: 10.1111/1462-2920.16024.

Shade A, Handelsman J. 2012. Beyond the Venn diagram: The hunt for a core microbiome. *Environmental Microbiology* 14:4-12.

DOI: 10.1111/j.1462-2920.2011.02585.x.

Simpson E. 1949. Measurment of Diversity. *Nature* 163:688.

Smith VH, Schindler DW. 2009. Eutrophication science: where do we go from here? *Trends in Ecology and Evolution* 24:201-207.

DOI: 10.1016/j.tree.2008.11.009.

Soergel DAW, Dey N, Knight R, Brenner SE. 2012. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. *ISME Journal* 6:1440-1444.

DOI: 10.1038/ismej.2011.208.

Sonnenschein EC, Jimenez G, Castex M, Gram L. 2021. The Roseobacter-Group Bacterium Phaeobacter as a Safe Probiotic Solution for Aquaculture. *Applied and Environmental Microbiology* 87:1-15.

DOI: 10.1128/AEM.02581-20.

Sorieul L, Rückert C, Al-Dilaimi A, Winkler A, Kalinowski J, Pham D, Wabete N, Boulo V. 2019. Whole-Genome Sequence of Pseudoalteromonas sp. NC201, a Probiotic Strain for Litopenaeus stylirostris Hatcheries in New Caledonia. *Microbiology Resource Announcements* 8:23-24.

DOI: 10.1128/MRA.00477-19.

Sorieul L, Wabete N, Ansquer D, Mailliez J-R, Pallud M, Zhang C, Lindivat M, Boulo V, Pham D. 2018. Survival improvement conferred by the Pseudoalteromonas sp. NC201 probiotic in Litopenaeus stylirostris exposed to Vibrio nigripulchritudo infection and salinity stress. *Aquaculture* 495:888-898.

DOI: 10.1016/j.aquaculture.2018.06.058.

Stimpson W. 1871. Notes on North American Crustacea, in the Museum of the Smithsonian Institution. No. III. *Annals of The Lyceum of Natural History of New York* 10:92-136.

DOI: 10.1111/j.1749-6632.1874.tb00028.x.

Stoeck T, Zuendorf A, Breiner HW, Behnke A. 2007. A molecular approach to identify active microbes in environmental eukaryote clone libraries. *Microbial Ecology* 53:328-339.

DOI: 10.1007/s00248-006-9166-1.

Stoler N, Nekrutenko A. 2021. Sequencing error profiles of Illumina sequencing instruments. *NAR Genomics and Bioinformatics* 3:1-9.

DOI: 10.1093/nargab/lqab019.

Sugita H, Miyajima C, Deguchi Y. 1990. The Vitamin B₁₂-Producing Ability of Intestinal Bacteria Isolated from Tilapia and Channel Catfish. *Nippon Suisan Gakkaishi* 56:701-701.

DOI: 10.2331/suisan.56.701.

Sun P, Jin M, Ding L, Lu Y, Ma H, Yuan Y, Zhou Q. 2018a. Dietary lipid levels could improve growth and intestinal microbiota of juvenile swimming crab, Portunus trituberculatus. *Aquaculture* 490:208-216.

DOI: 10.1016/j.aquaculture.2018.02.018.
Bibliographie

Sun Z, Hao S, Gong Y, Zhang M, Aweya JJ, Tran NT, Zhang Y, Ma H, Li S. 2018b. Dual oxidases participate in the regulation of hemolymph microbiota homeostasis in mud crab Scylla paramamosain. *Developmental and Comparative Immunology* 89:111–121.
DOI: 10.1016/j.dci.2018.08.009.

Sun Y, Han W, Liu J, Liu F, Cheng Y. 2020. Microbiota comparison in the intestine of juvenile Chinese mitten crab Eriocheir sinensis fed different diets. *Aquaculture* 515:734518.
DOI: 10.1016/j.aquaculture.2019.734518.

Sylvain FÉ, Derome N. 2017. Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny. *Scientific Reports* 7:1–14.
DOI: 10.1038/s41598-017-05662-w.

T

Tassanakajon A, Somboonwiwat K, Supungul P, Tang S. 2013. Discovery of immune molecules and their crucial functions in shrimp immunity. *Fish & Shellfish Immunology*. 34:954-967.
DOI: 10.1016/j.fsi.2012.09.021.

Theopold U, Schmidt O, Söderhäll K, Dushay MS. 2004. Coagulation in arthropods: Defence, wound closure and healing. *Trends in Immunology* 25:289–294.
DOI: 10.1016/j.it.2004.03.004.

Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The Human Microbiome Project. *Nature* 449:804–810.
DOI: 10.1038/nature06244.

V

Van Den Broeck N, Moutin T, Rodier M, Le Bouteiller A. 2004. Seasonal variations of phosphate availability in the SW Pacific Ocean near New Caledonia. *Marine Ecology Progress Series* 268:1–12.
DOI: 10.3354/meps268001.

Vadstein O, Attramadal KJK, Bakke I, Forberg T, Olsen Y, Verdegem M, Giatsis C, Skjermo J, Aasen IM, Gatesoupe F-J, Dierckens K, Sorgeloos P, Bossier P. 2018a. Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture. *Frontiers in Microbiology* 9:1–22.
DOI: 10.3389/fmicb.2018.01820.

Vadstein O, Attramadal KJK, Bakke I, Olsen Y. 2018b. K-selection as microbial community management strategy: A method for improved viability of larvae in aquaculture. *Frontiers in Microbiology* 9:1–17.
DOI: 10.3389/fmicb.2018.02730.

Valle-Gough RE, Samaniego-Gámez BY, Apodaca-Hernández JE, Chiappa-Carrara FX, Rodríguez-Dorantes M, Arena-Ortiz ML. 2022. RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (Litopenaeus vannamei) in Different Stages of Development. *Applied Sciences (Switzerland)* 12.
DOI: 10.3390/app12052483.

Vandenberghe J, Verdonck L, Robles-Arozarena R, Rivera G, Bolland A, Balladares M, Gomez-Gil B, Calderon J, Sorgeloos P, Swings J. 1999. Vibrios Associated with Litopenaeus vannamei Larvae, Postlarvae, Broodstock, and Hatchery Probiotics. *Applied and Environmental Microbiology* 65:2592–2597.
DOI: 10.1128/AEM.65.6.2592-2597.1999.

Vargas-Albores F, Martínez-Córdova LR, Hernández-Mendoza A, Cicala F, Lago-Lestón A, Martínez-Porchas M. 2021. Therapeutic modulation of fish gut microbiota, a feasible strategy for aquaculture? *Aquaculture* 544:737050.
DOI: 10.1016/j.aquaculture.2021.737050.

Verschuere L, Rombaut G, Sorgeloos P, Verstraete W. 2000. Probiotic Bacteria as Biological Control Agents in Aquaculture. *Microbiology and Molecular Biology Reviews* 64:655–671.
DOI: 10.1128/mmbr.64.4.655-671.2000.

W

Wabete N. 2005. Etude écophysiologique du métabolisme respiratoire et nutritionnel chez la crevette pénéide Litopenaeus stylirostris. Application à la crevetticulture en Nouvelle-Calédonie. Université de Bordeaux I.

Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. *Applied and Environmental Microbiology* 73:5261–5267.
DOI: 10.1128/AEM.00062-07.

Wang XW, Xu JD, Zhao XF, Vasta GR, Wang JX. 2014. A Shrimp C-type Lectin Inhibits Proliferation of the Hemolymph Microbiota by Maintaining the Expression of Antimicrobial Peptides. *Journal of Biological Chemistry* 289:11779–11790.
DOI: 10.1074/jbc.M114.552307.

Wang H, Huang J, Wang P, Li T. 2020a. Insights into the microbiota of larval and postlarval Pacific white shrimp (Penaeus vannamei) along early developmental stages: a case in pond level. *Molecular Genetics and Genomics* 295:1517–1528. DOI: 10.1007/s00438-020-01717-2.

Wang Y, Wang K, Huang L, Dong P, Wang S, Chen H, Lu Z, Hou D, Zhang D. 2020b. Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle. *Microbiome* 8:106.
DOI: 10.1186/s40168-020-00879-w.

Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. 2017. Normalization and microbial differential abundance strategies depend upon data characteristics. *Microbiome* 5:27.
DOI: 10.1186/s40168-017-0237-y.

Whipps J, Lewis K, Cooke R. 1988. Mycoparasitism and plant disease control. Manchester University Press.

Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: The unseen majority. *Proceedings of the National Academy of Sciences* 95:6578–6583.
DOI: 10.1073/pnas.95.12.6578.

Wickham H. 2016. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York.
DOI: ISBN 978-3-319-24277-4.

Winogradsky S. 1949. *Microbiologie du sol: problèmes et méthodes.*
Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. *Proceedings of the National Academy of Sciences* 74:5088–5090.
DOI: 10.1073/pnas.74.11.5088.

X

Xiong J, Zhu J, Wang K, Wang X, Ye X, Liu L, Zhao Q, Hou M, Qiuqian L, Zhang D. 2014. The Temporal Scaling of Bacterioplankton Composition: High Turnover and Predictability during Shrimp Cultivation. *Microbial Ecology* 67:256–264.
DOI: 10.1007/s00248-013-0336-7.

Xiong J, Wang K, Wu J, Qiuqian L, Yang K, Qian Y, Zhang D. 2015. Changes in intestinal bacterial communities are closely associated with shrimp disease severity. *Applied Microbiology and Biotechnology* 99:6911–6919.
DOI: 10.1007/s00253-015-6632-z.
Xiong J, Dai W, Zhu J, Liu K, Dong C, Qiu Q. 2017. The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimp. *Microbial Ecology* 73:988-999.

DOI: 10.1007/s00248-016-0910-x.

Xiong J, Yu W, Dai W, Zhang J, Qiu Q, Ou C. 2018. Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota. *Applied Microbiology and Biotechnology* 102:3315-3326.

DOI: 10.1007/s00253-018-8874-z.

Xue M, Wu L, He Y, Liang H, Wen C. 2018. Biases during DNA extraction affect characterization of the microbiota associated with larvae of the Pacific white shrimp, Litopenaeus vannamei. *PeerJ* 6:e5257.

DOI: 10.7717/peerj.5257.

Y

Yang W, Zheng C, Zheng Z, Wei Y, Lu K, Zhu J. 2018. Nutrient enrichment during shrimp cultivation alters bacterioplankton assemblies and destroys community stability. *Ecotoxicology and Environmental Safety* 156:366-374.

DOI: 10.1016/j.ecoenv.2018.03.043.

Yang X, Xu M, Huang G, Zhang C, Pang Y, Cheng Y. 2019. Effect of dietary L-tryptophan on the survival, immune response and gut microbiota of the Chinese mitten crab, Eriocheir sinensis. *Fish and Shellfish Immunology* 84:1007-1017.

DOI: 10.1016/j.fsi.2018.10.076.

Yang CH, MA KY, Chu KH, Chan TY. 2023. Making sense of the taxonomy of the most commercially important shrimps Penaeus Fabricicus, 1789 s. l. (Crustacea : Decapoda: Penaeidae), a way forward. *Aquaculture* 563:738955

DOI: 10.1016/j.aquaculture.2022.738955

Yates MC, Derry AM, Cristescu ME. 2021. Environmental RNA: A Revolution in Ecological Resolution? *Trends in Ecology & Evolution* 36:601-609.

DOI: 10.1016/j.tree.2021.03.001.

Yu W, Wu JH, Zhang J, Yang W, Chen J, Xiong J. 2018. A meta-analysis reveals universal gut bacterial signatures for diagnosing the incidence of shrimp disease. *FEMS Microbiology Ecology* 94:1-10.

DOI: 10.1093/femsec/fiy147.

Yukgehnaish K, Kumar P, Sivachandran P, Marimuthu K, Arshad A, Paray BA, Arockiaraj J. 2020. Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish. *Reviews in Aquaculture* 12:1903-1927.

DOI: 10.1111/raq.12416.

Z

Zeng S, Huang Z, Hou D, Liu J, Weng S, He J. 2017. Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages. *PeerJ* 5:e3986.

DOI: 10.7717/peerj.3986.

Zhang M, Sun Y, Chen K, Yu N, Zhou Z, Chen L, Du Z, Li E. 2014a. Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources. *Aquaculture* 434:449-455.

DOI: 10.1016/j.aquaculture.2014.09.008.

Zhang D, Wang X, Xiong J, Zhu J, Wang Y, Zhao Q, Chen H, Guo A, Wu J, Dai H. 2014b. Bacterioplankton assemblages as biological indicators of shrimp health status. *Ecological Indicators* 38:218-224.

DOI: 10.1016/j.ecolind.2013.11.002.

Zhang M, Sun Y, Chen L, Cai C, Qiao F, Du Z, Li E. 2016a. Symbiotic bacteria in gills and guts of Chinese mitten crab (Eriocheir sinensis) differ from the free-living bacteria in water. *PLoS ONE* 11.

DOI: 10.1371/journal.pone.0148135.

Zhang M, Sun Y, Liu Y, Qiao F, Chen L, Liu WT, Du Z, Li E. 2016b. Response of gut microbiota to salinity change in two euryhaline aquatic animals with «reverse» salinity preference. *Aquaculture* 454:72-80.

DOI: 10.1016/j.aquaculture.2015.12.014.

Zhang X, Zhang M, Zheng H, Ye H, Zhang X, Li S. 2020. Source of hemolymph microbiota and their roles in the immune system of mud crab. *Developmental and Comparative Immunology* 102:103470.

DOI: 10.1016/j.dci.2019.103470.

Zheng Y, Yu M, Liu J, Qiao Y, Wang L, Li Z, Zhang XH, Yu M. 2017. Bacterial Community Associated with Healthy and Diseased Pacific White Shrimp (Litopenaeus vannamei) Larvae and Rearing Water across Different Growth Stages. *Frontiers in Microbiology* 8:1-11.

DOI: 10.3389/fmicb.2017.01362.

Zhou J, Ning D. 2017. Stochastic Community Assembly: Does It Matter in Microbial Ecology? *Microbiology and Molecular Biology Reviews* 81:1-32.

DOI: 10.1128/MMBR.00002-17.

Zhou D, Liu S, Guo G, He X, Xing C, Miao Q, Chen G, Chen X, Yan H, Zeng J, Zheng Z, Deng H, Weng S, He J. 2022. Virome Analysis of Normal and Growth Retardation Disease-Affected Macrobrachiumrosenbergii. *Microbiology Spectrum* 10.

DOI: 10.1128/spectrum.01462-22.
# Annexes

## VIII.1- Annexe 1 – Le séquençage de Sanger

La mise au point du séquençage de Sanger a été initiée par l'élaboration de di-désoxyribonucléotides (ddNTP) consistant en des dNTP sans groupement hydroxyle en position 3' du pentose (Fig. S1). Au cours de l'elongation de l'ADN, l'incorporation d'un ddNTP empêche la formation d'une liaison phosphodiester avec un autre nucléotide entraînant l'arrêt de la polymérisation. Au cours du séquençage de Sanger, un mélange réactionnel contenant la séquence d'intérêt, une ADN polymérase, des ddNTP radiomarqués et des dNTP en concentration plus importante est utilisé. Au cours de la réplication de la séquence nucléotidique d'intérêt, l'incorporation aléatoire de ddNTP entraîne l'arrêt de l'elongation. Des séquences complémentaires de longueurs variables et dont le dernier nucléotide est radiomarqué sont alors produites. Chaque ddNTP étant radiomarqué de la même manière, il est impossible de les distinguer. Le séquençage de Sanger nécessite donc 4 réactions distinctes, une pour chaque ddNTP (ddATP, ddCTP, ddGTP ou ddTTP). Lorsque les réactions sont terminées, une migration sur gel de polyacrylamide par électrophorèse suivie d'une autoradiographie permet de distinguer les poids moléculaires, et donc la longueur, des séquences synthétisées. En effet, la séquence ayant migré le plus loin correspond à la première base séquencée alors que la séquence ayant migré le moins loin correspond à la dernière base séquencée. Il est ainsi possible de déduire la séquence complémentaire de la séquence d'intérêt (Fig. S2).

<figure><img src="image_136.png" /><figcaption>FIGURE SUPPLÉMENTAIRE 1 – Di-désoxyribonucléotide.</figcaption></figure>
<figure><img src="image_137.png" /><figcaption>FIGURE SUPPLÉMENTAIRE 2 – Séquençage de Sanger.</figcaption></figure>
## VIII.2- Annexe 2- Le pyroséquençage

Le pyroséquençage se base sur la production de pyrophosphate au cours de la synthèse de l'ADN (Fig. S3). En présence de pyrophosphate, une enzyme appelée ATP sulfurase transforme l'adénosine phosphosulfate (APS) en adénosine triphosphate (ATP) lui-même transformé en signal lumineux sous l'action de la luciférase en présence de luciférine (Fig. S4). Le pyroséquençage consiste à observer ce signal lumineux après ajout de dNTP afin de déduire la séquence nucléotidique d'intérêt. Pour cela, la séquence d'intérêt est liguée en 5' à un adaptateur complémentaire d'un oligonucléotide fixé à une bille (Fig. S5). Une amplification par PCR permet alors l'hybridation de la séquence d'intérêt sur cette bille. Toutes les billes ainsi recouvertes de la même séquence nucléotidique d'intérêt, sont ensuite chargées sur une plaque contenant des puits dont le diamètre ne permet la fixation que d'une seule bille. Un mélange réactionnel contenant les éléments nécessaires à l'élongation de la séquence nucléotidique ainsi qu'à la transformation du pyrophosphate en lumière est utilisé. Un seul type de dNTP est ajouté à chaque réaction. Lorsqu'un dNTP est incorporé dans un puit, un signal lumineux est produit. Ce dernier est capté par une caméra munie d'un capteur CCD (Charge Coupled Device) relié à un dispositif informatique. Une fois le signal enregistré, les dNTP présents sur la plaque sont éliminés par une enzyme appelée apyrase et un autre dNTP est ajouté. Le processus continue jusqu'au séquençage complet de la séquence d'intérêt. Il est important de noter que le dATP peut être utilisé par la luciférase. Pour éviter les biais expérimentaux, le dATPαS (2'-déoxyadénosine 5'-(α-thio)triphosphate) est utilisé. Il s'agit d'un dATP dont le phosphate en position α est marqué au ³⁵S et qui est exclusivement utilisable par l'ADN polymérase.
<figure><img src="image_138.png" /><figcaption>FIGURE SUPPLÉMENTAIRE 3 – Principe de synthèse des acides nucléiques.</figcaption></figure>

<figure><img src="image_139.png" /><figcaption>FIGURE SUPPLÉMENTAIRE 4 – Processus de transformation du pyrophosphate en lumière.</figcaption></figure>
<figure><img src="image_140.png" /><figcaption>FIGURE SUPPLÉMENTAIRE 5 – Pyroséquençage 454.</figcaption></figure>
## VIII.3- Annexe 3 - Le séquençage IonTorrent

Le séquençage IonTorrent mesure les variations de pH induites par la libération de protons d'hydrogènes qui accompagne la formation de pyrophosphate. Les premières étapes du séquençage IonTorrent sont similaires à celles du pyroséquençage. En effet, elles consistent à hybrider la séquence nucléotidique d'intérêt sur des billes qui sont ensuite placées dans des puits sur une puce. Cette dernière est composée d'une couche sensible aux ions reliée à un CPU (unité processeur) qui mesure les variations de pH. Comme pour le pyroséquençage, les dNTP sont ajoutés les uns après les autres (Fig. S6).

<figure><img src="image_141.png" /><figcaption>FIGURE SUPPLÉMENTAIRE 6 – Séquençage IonTorrent.</figcaption></figure>
# Appendices

## Appendice 1 : Obtention du Prix Jeunes Talents France Fondation L'Oréal-UNESCO Pour les Femmes et la Science (2022)

**POSTER 1** – Poster présenté lors des échanges scientifiques organisés dans le cadre de la remise des prix.

<figure><img src="image_142.png" /></figure>

### META-ANALYSIS OF MICROBIAL COMMUNITIES FROM LAGOON SEAWATERS TO SHRIMP HATCHERIES IN RELATION TO ENVIRONMENTAL FACTORS

by

Carolane Giraud

• LEAD-NC, Ifremer & ISEA, UNC

• New-Caledonia

<figure><img src="image_143.png" /></figure>

<figure><img src="image_144.png" /></figure>

<figure><img src="image_145.png" /></figure>

<figure><img src="image_146.png" /></figure>

<figure><img src="image_147.png" /></figure>

<figure><img src="image_148.png" /></figure>

<figure><img src="image_149.png" /></figure>

<figure><img src="image_150.png" /></figure>

<figure><img src="image_151.png" /></figure>

Ifremer

### INTRODUCTION

<figure><img src="image_152.png" /></figure>

In New-Caledonia, farming of the Pacific blue shrimp, Penaeus stylirostris, is a very important socio-economic industry. However, massive unexplained larval mortalities, occurring in all the hatcheries, are threatening the entire production¹. Many studies have proved that the microbiota plays a key role in the health and the development of the host².

Therefore, these observed mortalities could be explained by a disruption of the microbiota associated with shrimp larvae and their environment.

In this context, my thesis project is dedicated to the study of the microbial communities associated with healthy and moribund shrimp larval rearings.

<figure><img src="image_153.png" /></figure>

#### Hatcheries

Eggs

Nauplii

Zoea

Mysis

Post-larvae

#### Processing plants

Adults

Farms

Adults

Juveniles

Post-larvae

Post-larvae

### MATERIALS AND METHODS

#### Daily sample collection during healthy and moribund larval rearings

Pumped natural seawater, rearing water, breeders, eggs, larvac, food

#### Active microbial diversity analysis

* RNA extractions

QiaGen RNeasy Power Water kit and minikit

* cDNA retrotranscriptions

Promega M-MLV, ThermoFisher Second Strand kit

* HiSeq Illumina Sequencing
515F/806R primers, V4 region 16S rRNA gene

#### Water quality analysis

* Phosphate & ammonium concentrations

Quantitative analysis by colorimetric reaction¹,⁴

* Colored Dissolved Organic Matter profile

Spectrophotometer absorption spectra⁵

* Temperature, salinity & pH measurements

Mettler Toledo multiparameter probe pH/Cond 3320

#### Larval health and quality assessment

* Survival rates

* Growth index

Counts & observations under binocular magnifying glass

#### Bioinformatics, biostatistics, meta-analysis⁶

* To analyze evolution of all the considered parameters throughout rearing

* To highlight potential correlations and interactions between parameters

* To identify differential microbial lineages and communities between rearings

* To establish a predictive model to further build a decision support system

### EXPECTED RESULTS

**Published results** – The establishment of the larval microbiota is influenced by the rearing water and the breeders⁷,⁸.

**In prep.** – The larval and the water microbiotas are influenced by the rearing day and the larval stage.

**To do** – Meta-analysis of all larval rearings to identify key microbial communities for larval health.

<figure><img src="image_154.png" /></figure>

<figure><img src="image_155.png" /></figure>

#### EXAMPLE OF CONSIDERED ANALYSIS

Venn diagram to
(compare conditions)

Morbund
larvae

Healthy
larvae

Healthy
water

<figure><img src="image_156.png" /></figure>

And also: Canonical Correspondence Analysis (cca), network analysis, predictive modeling

### CONCLUSION

Using an integrated multidisciplinary approach, my project aims to identify the causes of the larval mortalities occurring in shrimp hatcheries.

My goal is to identify key microbial communities which could be monitored during larval rearing, therefore offering a potential solution.

This project should help to contribute to a more sustainable shrimp farming industry in New-Caledonia and could be applied to other agronomic sectors.

### REFERENCES

(1) Pham et al. (2014) DOI:10.1016/j.aquaculture.2014.04.031 (7) Giraud et al. (2021) DOI:10.7717/peerj.12241

(2) Cho & Blaser (2012) DOI:10.1038/nrg3182

(3) Amino & Kérouel (2004) ISBN:978284331335

(4) Holmes et al. (1999) DOI:10.1139/f99-128

(5) Sadeghi-Nassaj et al. (2018) DOI:10.7717/peerj.4344

(6) Cornejo-Granados et al. (2018) DOI:10.7717/peerj.5382
Dossier de presse réalisé dans le cadre de la diffusion prix.

SCIENCES DE L'ENVIRONNEMENT

Carolane Giraud

<figure><img src="image_157.png" /><figcaption>Réduire la mortalité des crevettes en Nouvelle-Calédonie</figcaption></figure>

<figure><img src="image_158.png" /></figure>

Doctorante

UNITE LACON, ÉCOSSÉISTES ET ADJACULTURES DURABLES EN NOUVELLE-CALÉDONIE (LEAD-NQ), PRÉRIEUR LINGOZ EN EUROPE.

INSTITUT DES SCIENCES ECOLOGIQUES (ISEA) UNIVERSITÉ DE L'ANVELLE-CALÉDONIE
ECOLE DOCTORALE DU PARIGQUE (EP)

Doctorante, Carolane Giraud méhe ses recherches, au sein de l'Unité Lagons, Écosystèmes et Aquaculture Durtable de Nouvelle-Calédonie. Dédiée à l'environnement itoral et la biodiversité cascatelle, elle a développé des compétences en aquaculture de crustacés, de poissons et de micro-algues. Tantôt d'un Master spécialisation Biologie et Bioressources Marines à l'Université de la Sorbonne, elle cherchise passionnément miens ses recherches à Nouméa, ou les combattances menacées presant sur la creveticulture constituent un sujet d'étude aussi concerne qu'urgent.

Quel que les enjeux à court et à long terme de ces recherches et leurs applications ?

L'activité crevettcole est un enjeu socio-économique important en Nouvelle-Calédonie. Malheureusement, les mortalités larvaires en édosserie frérent la production. Mon projet vise à identifier leurs couples, car nous manquons de connaissances sur l'évolution des paramètres physico-chimiques de l'eau réellement ancians que sur la dynamique des communautés microbienies impliquées.

Au cours de notre parcours, quel a de l'écumut dérancheur de notre carrière en science ?

Par mes origines médiaterranéennes, je suis passiveurinée depuis toujours par la mer et sa biodiversité. Au cours de mes scolarités, la préparation du vivant (la su que je souhaitais faire un métier qui puisse concilier les deux, et me suis donc orientée vers un Master de biologie intégrative avec une spécialisation en biologie et bioressources marines.

Parquai les feuilles sont-dés si tu n'outraies dans la recherche ?

L'un des plus gros freins est la difficulté d'aller vies professionnelle et personnelle. Lorsque je cherchais des financements de these, un ancien chercheur du CNRS m'a demandé pourquoi je n'avais pas fait un enfant, illico après mon Master pour être « débordant »... Je ne suis malheureusement pas la seule à avoir reçu des renoncues déplacées fées ou gagnées, et je trouve injuste que parfois chose d'assai naturel et biologiquement inchangéable, donner la vie, puisse pénailler nos carrières.

<figure><img src="image_159.png" /></figure>

> Le savoir et l'accès à la connaissance sont nos meilleurs alliés pour l'avenir.

<figure><img src="image_160.png" /></figure>
## Appendice 2 : Diffusions scientifiques

### Présentations orales

<table><thead><tr><td>ÉVÈNEMENT</td><td>DATE</td><td>LOCALISATION</td></tr></thead><tbody><tr><td>Rencontres bioinformatiques de l'Ifremer</td><td>Août 2022</td><td>Tahiti, Polynésie Française</td></tr><tr><td>Séminaire laboratoire IHPE</td><td>Juillet 2022</td><td>Montpellier, France</td></tr><tr><td>Doctoriales de l'École Doctorale du Pacifique</td><td>Août 2021</td><td>Université de la Nouvelle-Calédonie</td></tr><tr><td>Doctoriales de l'UMR 5244</td><td>Juin 2021</td><td>Visioconférence</td></tr></tbody></table>

### Posters

<table><thead><tr><td>ÉVÈNEMENT</td><td>DATE</td><td>LOCALISATION</td></tr></thead><tbody><tr><td>Congrès ISS 10 (International Symbiosis Society) & Holobiont 3</td><td>Juillet 2022</td><td>Lyon, France</td></tr><tr><td>Journée des doctorants de l'Ifremer</td><td>Janvier 2021</td><td>Visioconférence</td></tr><tr><td>Doctoriales de l'École Doctorale du Pacifique</td><td>Septembre 2020</td><td>Université de la Nouvelle-Calédonie</td></tr></tbody></table>
<figure><img src="image_161.png" /><figcaption>POSTER 2 - Poster présenté lors du congrès ISS 10 (International Symbiosis Society) & Holobiont 3 à Lyon (France) en juillet 2022.</figcaption></figure>
<figure><img src="image_162.png" /><figcaption>POSTER 3 – Poster présenté lors de la journée des doctorants de l'Ifremer en janvier 2021 ainsi qu'à l'Université de la Nouvelle-Calédonie lors des Doctoriales de l'École Doctorale du Pacifique en septembre 2020.</figcaption></figure>
## Appendice 3 – Formations

### Formations dispensées par l'École Doctorale du Pacifique

<table><thead><tr><td>INTITULÉ DE LA FORMATION</td><td>DATE</td><td>VOLUME HORAIRE</td></tr></thead><tbody><tr><td>Valorisation de données avec R</td><td>26/10/2021</td><td>3 heures</td></tr><tr><td>Formation Inkscape</td><td>14/04/2021 et 14/04/2021</td><td>8 heures</td></tr><tr><td>Comment rédiger un article scientifique</td><td>23/11/2020, 11/12/2020 et 14/12/2020</td><td>8 heures</td></tr><tr><td>Préparation à la recherche interdisciplinaire</td><td>27/08/2020, 08/10/2020 et 26/11/2020</td><td>6 heures</td></tr><tr><td>Éthique et déontologie de la recherche</td><td>18/08/2020 et 25/08/2020</td><td>10 heures</td></tr><tr><td>Communication et préparation à l'après-thèse</td><td>23/06/2020</td><td>4 heures</td></tr><tr><td>Enseigner dans le supérieur</td><td>Du 25/05/2020 au 27/05/2020</td><td>20 heures</td></tr><tr><td>Formation e-portfolio Mahara</td><td>19/05/2020</td><td>3 heures</td></tr><tr><td>Initiation à l'analyse de données avec le logiciel R</td><td>Du 12/02/2020 au 11/03/2020</td><td>16 heures</td></tr></tbody></table>

### Autres formations

<table><thead><tr><td>INTITULÉ DE LA FORMATION</td><td>ORGANISME</td><td>DATE</td><td>VOLUME HORAIRE</td></tr></thead><tbody><tr><td>Métabarcoding</td><td>SEBIMER, Ifremer</td><td>Septembre et Novembre 2022</td><td>30 heures</td></tr><tr><td>Génomique comparative</td><td>SEBIMER, Ifremer</td><td>Septembre 2022</td><td>8 heures</td></tr><tr><td>Assemblage et annotation de génomes</td><td>SEBIMER, Ifremer</td><td>Septembre 2022</td><td>23 heures</td></tr><tr><td>Apprendre à coder avec Python</td><td>MOOC Université de Bruxelles</td><td>Décembre 2021</td><td>12 heures</td></tr><tr><td>Initiation aux statistiques avec R</td><td>MOOC Université Paris-Sud</td><td>Mai 2020</td><td>25 heures</td></tr><tr><td>Formation à l'utilisation de Datarmor cluster de calcul de l'Ifremer</td><td>SEBIMER, Ifremer</td><td>Novembre 2020</td><td>4 heures</td></tr></tbody></table>
## Appendice 4 – Encadrements et enseignements

### Encadrements

<table><thead><tr><th>ÉTUDIANTS</th><th>FORMATION</th><th>TYPE</th><th>DATE</th><th>INTITULÉ</th></tr></thead><tbody><tr><td>Mathilde NYIKEINE<br>Duc Huy Dimitri TRAN<br>Cassandra LAMATAKI</td><td>Master1 Méthodes<br>Informatiques<br>Appliquées à la Gestion<br>des Entreprises<br>(Université de la<br>Nouvelle-Calédonie)</td><td>Projet tutoré</td><td>Mars à mai 2022<br>(3 mois)</td><td>Analyses<br>multivariées sur<br>des données<br>crevetticoles</td></tr><tr><td>Claudia WABETE</td><td>DEUST1 Géosciences<br>appliquées, mines, eau<br>et environnement<br>(Université de la<br>Nouvelle-Calédonie)</td><td>Stage de fin<br>d'année</td><td>Décembre 2021<br>(1 mois)</td><td>Étude de la qualité<br>de l'eau au cours<br>des élevages<br>larvaires de<br>crevettes</td></tr></tbody></table>

### Enseignements

56 heures de TP de biologie animale dispensées à des étudiants de 1ère année de licence SVT de septembre à octobre 2022 à l'Université de la Nouvelle-Calédonie.

EPS 2022 - Carolane GIRAUD

[EPS] - Etat PRÉVISIONNEL de Service d'Enseignement

Année : 2022 Enseignant(e) : Carolane GIRAUD (154122) Obligation statutaire : 56 (H eqTD)
Enseignant Contractuel Département : DPT - S.T.
Statut : CONTRACTUEL DOCTORANT ENSEIGNANT (Doctorant Contractuel) Obligation de service : 56 (H eqTD)

<table><thead><tr><th>COURS</th><th>TYPE_AP</th><th>H_MAQ<sup>(1)</sup></th><th>H_CHRG_ENS<sup>(2)</sup></th><th>H EDT_ENS<sup>(3)</sup></th><th>H SERV_PREV</th></tr></thead><tbody><tr><td>68_0009 TP : Biologie Animale 1</td><td>TP</td><td>180</td><td>56</td><td>56</td><td>56</td></tr></tbody></table>

<footnote>(1) Nombre d'heures total prévues dans la maquette</footnote>

<footnote>(2) Nombre d'heures qui vous ont été attribuées sur le(s) EC</footnote>

<footnote>(3) Nombre d'heures planifiées dans l'Emploi du temps (SuperPlan)</footnote>
## Appendice 5 – Communication auprès du grand public

### Presse

Revue de presse Prix Jeunes Talents France Fondation L'Oréal-UNESCO Pour les Femmes et la Science :

https://docs.google.com/presentation/d/1es2wL6L1PR6uHYnWzUtPfdMoIVAZhVFpbnDBN8Hso4/edit#slide=id.g170a74fa78d_1_3

### Activités et évènements

#### VIII.3.1.a- Nuit de la Science 2022

Fabrication d'une escape-box sur le thème de l'aquaculture de la crevette bleue du Pacifique Penaeus stylirostris. Activité proposée à la Nuit de la Science de l'Université de la Nouvelle-Calédonie le 16 novembre 2022.

<figure><img src="image_163.png" /></figure>

Sources : F. Bavarin, C. Wabete, C. Giraud
VIII.3.1.b- Journée Mondiale des Océans 2021

Animation du stand de la délégation calédonienne de l'Ifremer à la Journée Mondiale des Océans (Ile aux canards, Nouvelle-Calédonie) le 6 juin 2021.

<figure><img src="image_164.png" /></figure>

Sources : N. Callac, C. Giraud
## Appendice 6 – Articles scientifiques publiés au cours de la thèse mais ne portant pas sur le sujet de thèse

### Article 1 – Microbial diversity and activity during the biodegradation in seawater of various substitutes of conventional plastic cotton swab sticks (Jacquin et al. 2021)

DOI: 10.3389/fmicb.2021.604395

<figure><img src="image_165.png" /></figure>

frontiers
in Microbiology

ORIGINAL RESEARCH
published: 15 July 2021
doi: 10.3389/fmicb.2021.604395

<figure><img src="image_166.png" /></figure>

# Microbial Diversity and Activity During the Biodegradation in Seawater of Various Substitutes to Conventional Plastic Cotton Swab Sticks

Justine Jacquin¹,², Nolwenn Callac¹,³, Jingguang Cheng¹, Carolane Giraud¹,³, Yonko Gorand⁴, Clement Denoual⁵, Mireille Pujo-Pay¹, Pascal Conan¹, Anne-Leila Meistertzheim⁶, Valerie Barbe⁷, Stéphane Bruzaud⁵ and Jean-François Ghiglione¹*

### OPEN ACCESS

Edited by:
Mechthild Schmitt-Jansen,
Helmholtz Centre for Environmental
Research (UFZ), Germany

Reviewed by:
Gabriela Vázquez-Rodríguez,
Autonomous University of the State
of Hidalgo, Mexico
Christian Lott,
HYDRA Marine Sciences GmbH,
Germany

*Correspondence:
Jean-François Ghiglione
ghiglione@obs-banyuls.fr

Specialty section:
This article was submitted to
Microbiotechnology,
a section of the journal
Frontiers in Microbiology

Received: 09 September 2020

Accepted: 12 May 2021

Published: 15 July 2021

Citation:
Jacquin J, Callac N, Cheng J,
Giraud C, Gorand Y, Denoual C,
Pujo-Pay M, Conan P,
Meistertzheim A-L, Barbe V,
Bruzaud S and Ghiglione J-F (2021)
Microbial Diversity and Activity During
the Biodegradation in Seawater
of Various Substitutes to Conventional
Plastic Cotton Swab Sticks.
Front. Microbiol. 12:604395.
doi: 10.3389/fmicb.2021.604395

¹CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France, ²Innovation Plasturgie et Composites, Biopole Clermont Limagne, Saint-Beauzire, France, ³CNRS, UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Ird, Univ Nouvelle-Calédonie, Univ La Réunion, Nouméa, New Caledonia, ⁴Plateforme EnRMAT, Laboratoire PROMES, Rembla de la Thermodynamique, Perpignan, France, ⁵UMR CNRS 6027, Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, Lorient, France, ⁶SAS Plastic@Sea, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France, ⁷Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France

The European Parliament recently approved a new law banning single-use plastic items for 2021 such as plastic plates, cutlery, straws, cotton swabs, and balloon sticks. Transition to a bioeconomy involves the substitution of these banned products with biodegradable materials. Several materials such as polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), poly(butylene succinate) (PBS), polyhydroxybutyrate-valerate (PHBV), Bioplast, and Mater-Bi could be good candidates to substitute cotton swabs, but their biodegradability needs to be tested under marine conditions. In this study, we described the microbial life growing on these materials, and we evaluated their biodegradability in seawater, compared with controls made of non-biodegradable polypropylene (PP) or biodegradable cellulose. During the first 40 days in seawater, we detected clear changes in bacterial diversity (Illumina sequencing of 16S rRNA gene) and heterotrophic activity (incorporation of ³H-leucine) that coincided with the classic succession of initial colonization, growth, and maturation phases of a biofilm. Biodegradability of the cotton swab sticks was then tested during another 94 days under strict diet conditions with the different plastics as sole carbon source. The drastic decrease of the bacterial activity on PP, PLA, and PBS suggested no bacterial attack of these materials, whereas the bacterial activity in PBAT, Bioplast, Mater-Bi, and PHBV presented similar responses to the cellulose positive control. Interestingly, the different bacterial diversity trends observed for biodegradable vs. non-biodegradable plastics allowed to describe potential new candidates involved in the degradation of these materials under marine conditions. This better understanding of the bacterial diversity and activity dynamics during the colonization and biodegradation processes contributes to an expanding baseline to understand plastic biodegradation in marine conditions and provide a foundation for further decisions on the replacement of the banned single-used plastics.

Keywords: plastispHERE, biofouling, plastic biodegradation, single-used plastics, microbial colonization
## Article 2 – Evidence of coupled autotrophy and heterotrophy on plastic biofilms and its influence on surrounding seawater (Conan et al. 2022)

DOI: 10.1016/j.envpol.2022.120463

Environmental Pollution 315 (2022) 120463

<figure><img src="image_167.png" /></figure>

ELSEVIER

Contents lists available at ScienceDirect

### Environmental Pollution

journal homepage: www.elsevier.com/locate/envpol

<figure><img src="image_168.png" /></figure>

# Evidence of coupled autotrophy and heterotrophy on plastic biofilms and its influence on surrounding seawater☆

<figure><img src="image_169.png" /></figure>

Pascal Conan<sup>a, b, *</sup>, Léna Philip<sup>a, c</sup>, Eva Ortega-Retuerta<sup>a</sup>, Charlène Odobel<sup>a</sup>, Clélia Duran<sup>a</sup>, Caroline Pandin<sup>a</sup>, Carolane Giraud<sup>a, d</sup>, Anne-Leila Meistertzheim<sup>c</sup>, Valérie Barbe<sup>e</sup>, Alexandra Ter Hall<sup>f</sup>, Mireille Pujo-Pay<sup>a</sup>, Jean-François Ghiglione<sup>a</sup>

## ARTICLE INFO

**Keywords:**

Microplastic

Plastisphere

Biogeochemical cycles

Primary production

Bacterial production

## ABSTRACT

We measured phytoplankton primary production and heterotrophic bacterial activities on microplastics and seawater in the Northwestern Mediterranean Sea during two 3-month spring periods over 2 consecutive years. Microorganisms growing on a 5 mm diameter low density polyethylene films (LDPE; 200 µm thick) faced two contrasting conditions depending on the year. Spring 2018 was characterized by consistent nutrient inputs and bloom development. In spring 2019, nutrient inputs and bloom were low. For the first time, we observed a clear coupling between primary production and heterotrophic prokaryote production on microplastics during both years, but with different intensity between years that reflected the crucial role of the trophic environmental conditions (nutrient supply) in shaping microbial activities on plastics. We found that high primary production on plastics could support the whole (net autotrophy) or the majority of the bacterial carbon demand needed for heterotrophic activities, supplemented by other carbon sources if surrounding waters are highly productive. We propose that microbial activity on plastics influences the microbial community in the surrounding seawater, especially when the environmental conditions are less favorable. An illustrative image of the role of plastics in the environment could be that of an inverter in an electrical circuit that mitigates both positive and negative variations. Our results highlight the potential role of the plastisphere in shaping biogeochemical cycles in the context of increasing amounts of plastic particles in the marine environment.

<footnote><sup>a</sup> Sorbonne Université, CNRS LOMIC - UMR 7621, Laboratoire d'Océanographie Microbienne, 1 Avenue Pierre Fabre, 66650, Banyuls sur Mer, France</footnote>

<footnote><sup>b</sup> Sorbonne Université, CNRS OSU STAMAR - UAR2017, 4 Place Jussieu, 75252, Paris cedex 05, France</footnote>

<footnote><sup>c</sup> SAS Plastic@Sea, Sorbonne Université (UPMC), CNRS LOMIC - UMR 7621, Laboratoire d'Océanographie Microbienne, 1 Avenue Pierre Fabre, 66650, Banyuls sur Mer, France</footnote>

<footnote><sup>d</sup> CNRS, UMR 9220 ENTROPIE, Ifremer (LEAD-NC), IRD, Univ Nouvelle-Calédonie, Univ La Réunion, Nouméa, New Caledonia</footnote>

<footnote><sup>e</sup> Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France</footnote>

<footnote><sup>f</sup> CNRS, Université de Toulouse, Laboratoire des Interactions Moléculaires et Réactivité Chimique et Photochimique (IMRCP), UMR 5623, Toulouse, France</footnote>
<figure><img src="image_170.png" /></figure>
<figure><img src="image_171.png" /></figure>
Résumé

En Nouvelle-Calédonie, l'élevage de la crevette bleue du Pacifique, *Penaeus stylirostris*, a été initiée dans les années 1970 et représente, à l'heure actuelle, une activité socio-économique majeure à l'échelle du territoire. Cependant, depuis 2005, des mortalités larvaires massives non expliquées impactent l'ensemble des écloseries de l'île et menacent la pérennité des productions. L'eau de mer lagonaire, utilisée pour les élevages, possède des caractéristiques physico-chimiques et des assemblages microbiens susceptibles de varier en fonction de différents facteurs naturels et / ou anthropiques. Or les paramètres environnementaux de l'eau et les communautés microbiennes associées aux élevages influencent la qualité des larves et donc leur survie. Dans ce contexte, cette thèse a eu pour objectif de déterminer si les variations des communautés procaryotiques actives associées aux élevages pouvaient expliquer les mortalités larvaires observées. Les travaux menés ont d'abord mis en évidence l'implication de transmissions verticales et horizontales au cours de la mise en place du microbiote larvaire de *P. stylirostris*. Puis, l'identification d'un core microbien (affiliés aux familles bactériennes *Rhodobacteraceae*, *Vibrionaceae*, *Stappiaceae*, *Alcanivoraceae*, *Litoricolaceae*, *Pseudoalteromonadaceae* et *Alteromonadaceae*), associé à l'ensemble des échantillons d'élevage considérés et initialement présent dans les œufs et les eaux de remplissage des bacs, a suggéré un impact durable de ces transmissions au cours du développement larvaire, et ce indépendamment de l'état de santé des élevages. Une eutrophisation de l'environnement des larves a également été montrée dans tous les élevages soumis ou non à des épisodes de fortes mortalités. Nous avons constaté que cette eutrophisation ainsi que l'ajout d'antibiotique, le développement larvaire et l'état de santé des élevages entraînaient des variations des communautés procaryotiques associées aux élevages larvaires de *P. stylirostris*. Enfin, des biomarqueurs bactériens de la santé (affiliés aux familles *Rhodobacteraceae*, *Bdellovibrionaceae* et *Saprospiraceae* pour les élevages en bonne santé et aux genres *Portibacter*, *Ponticaulis*, *Oceanococcus*, *Turicella*, *P3OB-42* et *Celeribacter* pour les élevages en mauvaise santé) des élevages ont été mis en évidence. À court terme, ces biomarqueurs devraient permettre la mise au point d'outils de détection de type PCR ou qPCR. Cette thèse offre également de nouvelles perspectives de travail quant à une meilleure gestion des communautés microbiennes associées aux élevages notamment par le développement de nouvelles souches probiotiques.

**Mots clés** : communautés procaryotiques actives, biomarqueurs bactériens, élevages larvaires, crevette bleue du Pacifique *Penaeus stylirostris*, méta-analyse

Abstract

In New-Caledonia, rearing of the Pacific blue shrimp, *Penaeus stylirostris*, was initiated in the 70s and currently represents a major socio-economic activity for the territory. However, since 2005, massive unexplained larval mortalities are affecting all of the island's hatcheries and are threatening the entire production. The lagoon seawater, used during larval rearings, possesses physico-chemical characteristics and microbial patterns which are likely to vary according to various natural and / or anthropic factors. Yet, water environmental parameters and microbial communities associated with the rearings influence larval quality et thus larval survival. In this context, this project aimed to define if variations of the prokaryotic communities associated with the larval rearings could explain the observed larval mortalities. This work first evidenced vertical and horizontal transmissions involved during the establishment of the larval microbiota of *P. stylirostris*. The identification of a core microbiota (affiliated to bacterial families *Rhodobacteraceae*, *Vibrionaceae*, *Stappiaceae*, *Alcanivoraceae*, *Litoricolaceae*, *Pseudoalteromonadaceae* et *Alteromonadaceae*), associated with all the considered samples and initially present in the eggs and in the reservoir waters, suggests a lasting impact of these transmissions during the larval development regardless of the larval health status. Eutrophication of the rearing water was also highlighted in all the rearings which were exposed or not to mass larval mortalities. We showed that this eutrophication as well as antibiotic addition, larval development and larval health status induced variations of the prokaryotic communities associated with the larval rearings of *P. stylirostris*. Finally, bacterial biomarkers of larval health status were highlighted (affiliated to bacterial families *Rhodobacteraceae*, *Bdellovibrionaceae* et *Saprospiraceae* in healthy rearings and bacterial genera *Portibacter*, *Ponticaulis*, *Oceanococcus*, *Turicella*, *P3OB-42* et *Celeribacter* in unhealthy rearings). These biomarkers should allow short term development of PCR or qPCR type detection tools. This thesis also offers new work perspectives on better management of the microbial communities associated with the larval rearings through new probiotic strain development.

**Keywords** : active prokaryotic communities, bacterial biomarkers, shrimp larval rearing, Pacific blue shrimp *Penaeus stylirostris*, meta-analysis