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Aims  The Hawaiian Bobtail Squid ( Euprymna scolopes ) is a model organism for investigating host–symbiont relationships. The current scientific focus is on the microbiome within  E .  scolopes , while very little is known about the microbiome of the tanks housing  E .  scolopes . We examined the hypothesis that bacterial communities and geochemistry within the squid tank environment correlate with the production of viable paralarval squid.    Methods and Results  Total DNA was extracted from sediment and filtered water samples from ‘productive’ squid cohorts with high embryonic survival and paralarval hatching, ‘unproductive’ cohorts with low embryonic survival and paralarval hatching. As a control total DNA was extracted from environmental marine locations where  E .  scolopes  is indigenous. Comparative analysis of the bacterial communities by the 16S rRNA gene was performed using next generation sequencing. Thirty‐eight differentially abundant genera were identified in the adult tank waters. The majority of the sequences represented unclassified, candidate or novel genera. The characterized genera included  Aquicella ,  Woeseia  and  Ferruginibacter , with  Hyphomicrobium  and  Rhizohapis  were found to be more abundant in productive adult tank water. In addition, nitrate and pH covaried with productive cohorts, explaining 67% of the bacterial populations. The lower abundance of nitrate‐reducing bacteria in unproductive adult tank water could explain detected elevated nitrate levels.    Conclusions  We conclude that microbiome composition and water geochemistry can negatively affect  E .  scolopes  reproductive physiology in closed tank systems, ultimately impacting host‐microbe research using these animals.    Significance and Impact of study  These results identify the tight relationship between the microbiome and geochemistry to  E .  scolopes . From this study, it may be possible to design probiotic counter‐measures to improve aquaculture conditions for  E .  scolopes .

journal of applied microbiology

Aquaculture production of hatchling Hawaiian Bobtail Squid ( Euprymna scolopes ) is negatively impacted by decreasing environmental microbiome diversity