title: Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system.
abstract: Biofloc technology (BFT), a rearing method with little or no water exchange, is gaining popularity in aquaculture. In the water column, such systems develop conglomerates of microbes, algae and protozoa, together with detritus and dead organic particles. The intensive microbial community presents in these systems can be used as a pond water quality treatment system, and the microbial protein can serve as a feed additive. The current problem with BFT is the difficulty of controlling its bacterial community composition for both optimal water quality and optimal shrimp health. The main objective of the present study was to investigate microbial diversity of samples obtained from different culture environments (Biofloc technology and clear seawater) as well as from the intestines of shrimp reared in both environments through high-throughput sequencing technology.
  
  
  
  Analyses of the bacterial community identified in water from BFT and "clear seawater" (CW) systems (control) containing the shrimp Litopenaeus stylirostris revealed large differences in the frequency distribution of operational taxonomic units (OTUs). Four out of the five most dominant bacterial communities were different in both culture methods. Bacteria found in great abundance in BFT have two principal characteristics: the need for an organic substrate or nitrogen sources to grow and the capacity to attach to surfaces and co-aggregate. A correlation was found between bacteria groups and physicochemical and biological parameters measured in rearing tanks. Moreover, rearing-water bacterial communities influenced the microbiota of shrimp. Indeed, the biofloc environment modified the shrimp intestine microbiota, as the low level (27 %) of similarity between intestinal bacterial communities from the two treatments.
  
  
  
  This study provides the first information describing the complex biofloc microbial community, which can help to understand the environment-microbiota-host relationship in this rearing system.
authors.affiliation: Ifremer, UMR 241 EIO, UPF-ILM-IRD, Labex Corail, B.P. 7004, 98719, Taravao, Tahiti, French Polynesia.|Ifremer, Unité de recherche Lagons, Ecosystèmes et Aquaculture Durable en Nouvelle Calédonie, Nouméa, New Caledonia.
authors.forename: Emilie
authors.initials: E
authors.lastname: Cardona
authors.affiliation: Ifremer, UMR 241 EIO, UPF-ILM-IRD, Labex Corail, B.P. 7004, 98719, Taravao, Tahiti, French Polynesia.|Ifremer, UMR 5244 IHPE, UPVD, CNRS, Université de Montpellier, F-34095, Montpellier, France.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Gueguen
authors.affiliation: Ifremer, UMR 241 EIO, UPF-ILM-IRD, Labex Corail, B.P. 7004, 98719, Taravao, Tahiti, French Polynesia.
authors.forename: Kevin
authors.initials: K
authors.lastname: Magré
authors.affiliation: Ifremer, UMR 241 EIO, UPF-ILM-IRD, Labex Corail, B.P. 7004, 98719, Taravao, Tahiti, French Polynesia.
authors.forename: Bénédicte
authors.initials: B
authors.lastname: Lorgeoux
authors.affiliation: ACOBIOM, 1682 rue de la Valsière, Cap Delta - CS77394, 34184, Montpellier Cedex 4, France.
authors.forename: David
authors.initials: D
authors.lastname: Piquemal
authors.affiliation: ACOBIOM, 1682 rue de la Valsière, Cap Delta - CS77394, 34184, Montpellier Cedex 4, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Pierrat
authors.affiliation: ACOBIOM, 1682 rue de la Valsière, Cap Delta - CS77394, 34184, Montpellier Cedex 4, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Noguier
authors.affiliation: Ifremer, UMR 241 EIO, UPF-ILM-IRD, Labex Corail, B.P. 7004, 98719, Taravao, Tahiti, French Polynesia. denis.saulnier@ifremer.fr.
authors.forename: Denis
authors.initials: D
authors.lastname: Saulnier
mesh_terms: D064751:Ammonium Compounds / Q000032:analysis; D000818:Animals; D017756:Aquaculture / Q000379:methods; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D044822:Biodiversity; D002734:Chlorophyll / Q000032:analysis; D000077194:Chlorophyll A; D004777:Environment; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006863:Hydrogen-Ion Concentration; D007422:Intestines / Q000382:microbiology*; D064307:Microbiota; D009585:Nitrogen Dioxide / Q000032:analysis; D033561:Penaeidae / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater; D012758:Shellfish / Q000382:microbiology*; D014867:Water / Q000737:chemistry; D014871:Water Microbiology
chemical_list: D064751:Ammonium Compounds; D012336:RNA, Ribosomal, 16S; D014867:Water; D002734:Chlorophyll; D009585:Nitrogen Dioxide; D000077194:Chlorophyll A
keywords: Bacterial communities; Biofloc; Clear sea water; Culture environment; Microbiota; Shrimp