ABSTRACT Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus , collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a , and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. 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, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish. IMPORTANCE Pacific chub mackerel, Scomber japonicus , are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.
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Human-provisioned foods reduce gut microbiome diversity in American black bears ( Ursus americanus )
The distal gut is home to the dynamic and influential gut microbiome, which is intimately linked to mammalian health by promoting and facilitating countless physiological functions. In a time of increased anthropogenic pressures on wildlife due to widespread habitat destruction, loss of natural prey/foods, and rapid urbanization, the study of wildlife gut microbiomes could prove to be a valuable tool in wildlife management and conservation. Diet is one of the most influential determinants of a host’s gut microbiome; yet many wildlife agencies allow baiting to facilitate wildlife harvest, although the impact of human-provisioned foods on wildlife gut health is largely unknown. We used stable isotope analysis derived from carbon (δ 13C) to index the use of human-provisioned foods by 35 legally harvested American black bears (Ursus americanus), and16S rRNA gene amplicon sequencing to examine the impact of human-provisioned foods on the gut microbial diversity of black bears. We found that greater long-term consumption of human-provisioned foods was associated with significantly reduced microbial species richness and phylogenetic diversity. Our results indicate that consumption of anthropogenic foods through baiting significantly alters the mammalian gut microbiome.
more » « less- NSF-PAR ID:
- 10387835
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Journal of Mammalogy
- Volume:
- 103
- Issue:
- 2
- ISSN:
- 0022-2372
- Page Range / eLocation ID:
- p. 339-346
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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