PMID- 37391154
OWN - NLM
STAT- MEDLINE
DCOM- 20230920
LR  - 20230920
IS  - 1879-1026 (Electronic)
IS  - 0048-9697 (Linking)
VI  - 896
DP  - 2023 Oct 20
TI  - Comparison of the gill and gut microbiomes of common carp (Cyprinus carpio) and 
      zebrafish (Danio rerio) and their RAS environment.
PG  - 165212
LID - S0048-9697(23)03835-4 [pii]
LID - 10.1016/j.scitotenv.2023.165212 [doi]
AB  - Recirculating aquaculture systems (RAS) are increasingly being used to grow fish, 
      as intensive water reuse reduces water consumption and environmental impact. RAS 
      use biofilters containing nitrogen-cycling microorganisms that remove ammonia 
      from the aquaculture water. Knowledge of how RAS microbial communities relate to 
      the fish-associated microbiome is limited, as is knowledge of fish-associated 
      microbiota in general. Recently, nitrogen-cycling bacteria have been discovered 
      in zebrafish and carp gills and shown to detoxify ammonia in a manner similar to 
      the RAS biofilter. Here, we compared RAS water and biofilter microbiomes with 
      fish-associated gut and gill microbial communities in laboratory RAS housing 
      either zebrafish (Danio rerio) or common carp (Cyprinus carpio) using 16S rRNA 
      gene amplicon sequencing. The phylogeny of ammonia-oxidizing bacteria in the 
      gills and the RAS environment was investigated in more detail by phylogenetic 
      analysis of the ammonia monooxygenase subunit A (amoA). The location from which 
      the microbiome was sampled (RAS compartments and gills or gut) had a stronger 
      effect on community composition than the fish species, but species-specific 
      differences were also observed. We found that carp- and zebrafish-associated 
      microbiomes were highly distinct from their respective RAS microbiomes, 
      characterized by lower overall diversity and a small core microbiome consisting 
      of taxa specifically adapted to the respective organ. The gill microbiome was 
      also defined by a high proportion of unique taxa. Finally, we found that amoA 
      sequences from the gills were distinct from those from the RAS biofilter and 
      water. Our results showed that the gut and gill microbiomes of carp and zebrafish 
      share a common and species-specific core microbiome that is distinct from the 
      microbially-rich RAS environment.
CI  - Copyright (c) 2023 The Authors. Published by Elsevier B.V. All rights reserved.
FAU - Mes, Wouter
AU  - Mes W
AD  - Cluster Microbiology, Radboud Institute for Biological and Environmental 
      Sciences, Radboud University, Nijmegen, the Netherlands; Cluster Ecology & 
      Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud 
      University, Nijmegen, the Netherlands.
FAU - Lucker, Sebastian
AU  - Lucker S
AD  - Cluster Microbiology, Radboud Institute for Biological and Environmental 
      Sciences, Radboud University, Nijmegen, the Netherlands.
FAU - Jetten, Mike S M
AU  - Jetten MSM
AD  - Cluster Microbiology, Radboud Institute for Biological and Environmental 
      Sciences, Radboud University, Nijmegen, the Netherlands.
FAU - Siepel, Henk
AU  - Siepel H
AD  - Cluster Ecology & Physiology, Radboud Institute for Biological and Environmental 
      Sciences, Radboud University, Nijmegen, the Netherlands.
FAU - Gorissen, Marnix
AU  - Gorissen M
AD  - Cluster Ecology & Physiology, Radboud Institute for Biological and Environmental 
      Sciences, Radboud University, Nijmegen, the Netherlands.
FAU - van Kessel, Maartje A H J
AU  - van Kessel MAHJ
AD  - Cluster Microbiology, Radboud Institute for Biological and Environmental 
      Sciences, Radboud University, Nijmegen, the Netherlands. Electronic address: 
      maartje.vankessel@science.ru.nl.
LA  - eng
PT  - Journal Article
DEP - 20230628
PL  - Netherlands
TA  - Sci Total Environ
JT  - The Science of the total environment
JID - 0330500
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 7664-41-7 (Ammonia)
RN  - 059QF0KO0R (Water)
RN  - N762921K75 (Nitrogen)
SB  - IM
MH  - Animals
MH  - *Gastrointestinal Microbiome/genetics
MH  - Zebrafish/genetics
MH  - Gills
MH  - *Carps
MH  - Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
MH  - Ammonia
MH  - Aquaculture
MH  - *Microbiota
MH  - Water
MH  - Nitrogen
OTO - NOTNLM
OT  - Ammonia-oxidizing bacteria
OT  - Biofilter
OT  - Microbiome
OT  - Recirculating aquaculture system
OT  - Symbionts
COIS- Declaration of competing interest The authors declare that they have no known 
      competing financial interests or personal relationships that could have appeared 
      to influence the work reported in this paper.
EDAT- 2023/07/01 11:41
MHDA- 2023/09/20 06:42
CRDT- 2023/06/30 19:18
PHST- 2023/03/23 00:00 [received]
PHST- 2023/06/12 00:00 [revised]
PHST- 2023/06/27 00:00 [accepted]
PHST- 2023/09/20 06:42 [medline]
PHST- 2023/07/01 11:41 [pubmed]
PHST- 2023/06/30 19:18 [entrez]
AID - S0048-9697(23)03835-4 [pii]
AID - 10.1016/j.scitotenv.2023.165212 [doi]
PST - ppublish
SO  - Sci Total Environ. 2023 Oct 20;896:165212. doi: 10.1016/j.scitotenv.2023.165212. 
      Epub 2023 Jun 28.