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Sea urchin is an indicator of coastal environmental changes in the global warming era, and is also a model organism in developmental biology and evolution. Due to the depletion of wild resources, new aquaculture techniques for improving stocks have been well studied. The gut microbiome shapes various aspects of a host’s physiology. However, these microbiome structures and functions on sea urchins, particularly  Mesocentrotus nudus  and  Strongylocentrotus intermedius  which are important marine bioresources commonly found in Japan, have not been fully investigated yet. Using metagenomic approaches including meta16S and shotgun metagenome sequencings, the structures, functions, and dynamics of the gut microbiome of  M. nudus  and  S. intermedius , related to both habitat environment and host growth, were studied. Firstly, a broad meta16S analysis revealed that at the family level,  Psychromonadaceae  and  Flavobacteriaceae  reads (38–71%) dominated in these sea urchins, which is a unique feature observed in species in Japan.  Flavobacteriaceae  reads were more abundant in individuals after rearing in an aquarium with circulating compared to one with running water.  Campylobacteraceae  and  Vibrionaceae  abundances increased in both kinds of laboratory-reared sea urchins in both types of experiments. 2-weeks feeding experiments of  M. nudus  and  S. intermedius  transplanted from the farm to laboratory revealed that these gut microbial structures were affected by diet rather than rearing environments and host species. Secondly, further meta16S analysis of microbial reads related to  M. nudus  growth revealed that at least four Amplicon Sequence Variant (ASV) affiliated to  Saccharicrinis fermentans , which is known to be a nitrogen (N 2 ) fixing bacterium, showed a significant positive correlation to the body weight and test diameter. Interestingly, gut microbiome comparisons using shotgun metagenome sequencing of individuals showing higher and lower growth rates revealed a significant abundance of “Nitrate and nitrite ammonification” genes in the higher-grown individuals under the circulating water rearing. These findings provide new insights on the structure-function relationship of sea urchin gut microbiomes beyond previously reported nitrogen fixation function in sea urchin in 1950s; we discovered a nitrate reduction function into ammonium for the growth promotion of sea urchin.

The Structure and Function of Gut Microbiomes of Two Species of Sea Urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, in Japan