More Like this

1. Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

   https://doi.org/10.3389/fmars.2021.676731  

   Minich, Jeremiah J. ; Nowak, Barbara ; Elizur, Abigail ; Knight, Rob ; Fielder, Stewart ; Allen, Eric E. ( May 2021 , Frontiers in Marine Science)

   The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment “BE” and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi , over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased withmore »age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut “allochthonous” microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.« less
2. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

   https://doi.org/10.1128/mSphere.00401-20  

   Minich, Jeremiah J. ; Petrus, Semar ; Michael, Julius D. ; Michael, Todd P. ; Knight, Rob ; Allen, Eric E. ; McMahon, Katherine ( June 2020 , mSphere)

   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,more »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.« less
3. Aquaculture Reuse Water, Genetic Line, and Vaccination Affect Rainbow Trout (Oncorhynchus mykiss) Disease Susceptibility and Infection Dynamics

   https://doi.org/10.3389/fimmu.2021.721048  

   Everson, Jeremy L. ; Jones, Darbi R. ; Taylor, Amy K. ; Rutan, Barb J. ; Leeds, Timothy D. ; Langwig, Kate E. ; Wargo, Andrew R. ; Wiens, Gregory D. ( September 2021 , Frontiers in Immunology)

   Infectious hematopoietic necrosis virus (IHNV) and Flavobacterium psychrophilum are major pathogens of farmed rainbow trout. Improved control strategies are desired but the influence of on-farm environmental factors that lead to disease outbreaks remain poorly understood. Water reuse is an important environmental factor affecting disease. Prior studies have established a replicated outdoor-tank system capable of varying the exposure to reuse water by controlling water flow from commercial trout production raceways. The goal of this research was to evaluate the effect of constant or pulsed reuse water exposure on survival, pathogen prevalence, and pathogen load. Herein, we compared two commercial lines of rainbow trout, Clear Springs Food (CSF) and Troutex (Tx) that were either vaccinated against IHNV with a DNA vaccine or sham vaccinated. Over a 27-day experimental period in constant reuse water, all fish from both lines and treatments, died while mortality in control fish in spring water was <1%. Water reuse exposure, genetic line, vaccination, and the interaction between genetic line and water exposure affected survival ( P <0.05). Compared to all other water sources, fish exposed to constant reuse water had 46- to 710-fold greater risk of death ( P <0.0001). Tx fish had a 2.7-fold greater risk ofmore »death compared to CSF fish in constant reuse water ( P ≤ 0.001), while risk of death did not differ in spring water ( P =0.98). Sham-vaccinated fish had 2.1-fold greater risk of death compared to vaccinated fish ( P =0.02). Both IHNV prevalence and load were lower in vaccinated fish compared to sham-vaccinated fish, and unexpectedly, F. psychrophilum load associated with fin/gill tissues from live-sampled fish was lower in vaccinated fish compared to sham-vaccinated fish. As a result, up to forty-five percent of unvaccinated fish were naturally co-infected with F. psychrophilum and IHNV and the coinfected fish exhibited the highest IHNV loads. Under laboratory challenge conditions, co-infection with F. psychrophilum and IHNV overwhelmed IHNV vaccine-induced protection. In summary, we demonstrate that exposure to reuse water or multi-pathogen challenge can initiate complex disease dynamics that can overwhelm both vaccination and host genetic resistance.« less
4. Life cycle assessment of aquaculture systems: Does burden shifting occur with an increase in production intensity?

   https://doi.org/10.1016/j.aquaeng.2020.102130  

   Ghamkhar, Ramin ; Boxman, Suzanne ; Main, Kevan ; Zhang, Qiong ; Trotz, Maya ; Hicks, Andrea ( January 2021 , Aquacultural engineering)

   Life cycle assessment (LCA), a tool used to assess the environmental impacts of products and processes, has been used to evaluate a range of aquaculture systems. Eighteen LCA studies were reviewed which included assess- ments of recirculating aquaculture systems (RAS), flow-through systems, net cages, and pond systems. This re- view considered the potential to mitigate environmental burdens with a movement from extensive to intensive aquaculture systems. Due to the diversity in study results, specific processes (feed, energy, and infrastructure) and specific impact categories (land use, water use, and eutrophication potential) were analyzed in-depth. The comparative analysis indicated there was a possible shift from local to global impacts with a progression from extensive to intensive systems, if mitigation strategies were not performed. The shift was partially due to increased electricity requirements but also varied with electricity source. The impacts from infrastructure were less than 13 % of the environmental impact and considered negligible. For feed, the environmental impacts were typically more dependent on feed conversion ratio (FCR) than the type of system. Feed also contributed to over 50 % of the impacts on land use, second only to energy carriers. The analysis of water use indicated intensive recirculating systems efficiently reducemore »water use as compared to extensive systems; however, at present, studies have only considered direct water use and future work is required that incorporates indirect and consumptive water use. Alternative aquaculture systems that can improve the total nutrient uptake and production yield per material and energy based input, thereby reducing the overall emissions per unit of feed, should be further investigated to optimize the overall of aquaculture systems, considering both global and local environmental impacts. While LCA can be a valuable tool to evaluate trade-offs in system designs, the results are often location and species specific. Therefore, it is critical to consider both of these criteria in conjunction with LCA results when developing aquaculture systems.« less
5. Differential Patterns of Microbiota Recovery in Symbiotic and Aposymbiotic Corals following Antibiotic Disturbance

   https://doi.org/10.1128/mSystems.01086-20  

   Bent, Shavonna M. ; Miller, Carolyn A. ; Sharp, Koty H. ; Hansel, Colleen M. ; Apprill, Amy ( April 2021 , mSystems)

   Raina, Jean-Baptiste (Ed.)

   ABSTRACT Microbial relationships are critical to coral health, and changes in microbiomes are often exhibited following environmental disturbance. However, the dynamics of coral-microbial composition and external factors that govern coral microbiome assembly and response to disturbance remain largely uncharacterized. Here, we investigated how antibiotic-induced disturbance affects the coral mucus microbiota in the facultatively symbiotic temperate coral Astrangia poculata , which occurs naturally with high (symbiotic) or low (aposymbiotic) densities of the endosymbiotic dinoflagellate Breviolum psygmophilum . We also explored how differences in the mucus microbiome of natural and disturbed A. poculata colonies affected levels of extracellular superoxide, a reactive oxygen species thought to have both beneficial and detrimental effects on coral health. Using a bacterial and archaeal small-subunit (SSU) rRNA gene sequencing approach, we found that antibiotic exposure significantly altered the composition of the mucus microbiota but that it did not influence superoxide levels, suggesting that superoxide production in A. poculata is not influenced by the mucus microbiota. In antibiotic-treated A. poculata exposed to ambient seawater, mucus microbiota recovered to its initial state within 2 weeks following exposure, and six bacterial taxa played a prominent role in this reassembly. Microbial composition among symbiotic colonies was more similar throughout the 2-weekmore »recovery period than that among aposymbiotic colonies, whose microbiota exhibited significantly more interindividual variability after antibiotic treatment and during recovery. This work suggests that the A. poculata mucus microbiome can rapidly reestablish itself and that the presence of B. psygmophilum , perhaps by supplying nutrients, photosynthate, or other signaling molecules, exerts influence on this process. IMPORTANCE Corals are animals whose health is often maintained by symbiotic microalgae and other microorganisms, yet they are highly susceptible to environmental-related disturbances. Here, we used a known disruptor, antibiotics, to understand how the coral mucus microbial community reassembles itself following disturbance. We show that the Astrangia poculata microbiome can recover from this disturbance and that individuals with algal symbionts reestablish their microbiomes in a more consistent manner compared to corals lacking symbionts. This work is important because it suggests that this coral may be able to recover its mucus microbiome following disturbance, it identifies specific microbes that may be important to reassembly, and it demonstrates that algal symbionts may play a previously undocumented role in microbial recovery and resilience to environmental change.« less