Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish,Scomber japonicus

Abstract

Changing ocean conditions driven by anthropogenic activity may have a negative impact on fisheries by increasing stress and disease with the mucosal microbiome as a potentially important intermediate role. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, GI, and pyloric caeca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning one year from the Scripps Institution of Oceanography Pier, making this the largest and longest wild marine fish microbiome survey. Mucosal sites had unique communities significantly different from the surrounding sea water and sediment communities with over 10 times more diversity than sea water alone. Although, external surfaces such as skin and gill were more similar to sea water, digesta was similar to sediment. Both alpha and beta diversity of the skin and gill was explained by environmental and biological factors, especially sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by migrations of chub mackerel sub-populations by nanopore sequencing a 14 769 bp region of the 16 568 bp mitochondria. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year, but highest in the skin, GI, and digesta between June and September. Our study evaluates the extent which the environment and host biology drives mucosal microbial ecology, establishing a baseline for long term monitoring surveys for linking environment stressors to mucosal health of wild marine fish.

Visualizing ’omic feature rankings and log-ratios using Qurro

“…1(b)). This observation corroborates the initial study of this dataset on the frequency of Shewanella particular to the fish gill microbiome [14].…”

“…The initial study of this dataset [14] agreed with prior work [26] on the frequency of Shewanella spp. in the fish gill microbiome.…”

“…Using this functionality, we can add additional perspectives to our previously-reached observation. Age has been discussed as a factor impacting the microbiota of fish gills in this and other datasets [26,14].…”

“…To demonstrate the utility of Qurro, we applied it to an extant dataset of V4-region 16S rRNA sequencing data from Pacific chub mackerel (Scomber japonicus) and environmental samples [14]. This dataset includes samples taken from five Scomber japonicus body sites (digesta, GI, gill, pyloric caeca, and skin) from 229 fish captured across 38 time points in 2017, along with many seawater, marine sediment, positive/negative control, and non-Scomber japonicus fish samples.…”

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

“…In this study, we have investigated freshwater fish and identified Alphaproteobacteria as having the highest median relative abundance, highlighting their dominance as a possible feature of some freshwater fish skin microbiomes, compared to marine fish [15,46]. Such a difference is conceivable due to consistent abiotic differences between marine and freshwater habitats, and the resulting differences in fish biology between them.…”