Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

ABSTRACT Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified into Flavobacterium, Cetobacterium, the family Sphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea and Nitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls. IMPORTANCE Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs

Sepulveda-Villet and Stepien 2012 - yellow perch and percid haplotypes

Nexus formatted input file with mtDNA control region sequences for 26 yellow perch haplotypes, and reference sequences for Eurasian perch (Perca fluviatilis) and walleye (Sander vitreus)

Data from: Waterscape genetics of the yellow perch (Perca flavescens): patterns across large connected ecosystems and isolated relict populations

Comparisons of a species’ genetic diversity and divergence patterns across large connected populations versus isolated relict areas provide important data for understanding potential response to global warming, habitat alterations, and other perturbations. Aquatic taxa offer ideal case studies for interpreting these patterns, because their dispersal and gene flow often are constrained through narrow connectivity channels that have changed over geological time and/or from contemporary anthropogenic perturbations. Our research objective is to better understand the interplay between historic influences and modern-day factors (fishery exploitation, stocking supplementation, and habitat loss) in shaping population genetic patterns of the yellow perch Perca flavescens (Percidae: Teleostei) across its native North American range. We employ a modified landscape genetics approach, analyzing sequences from the entire mitochondrial DNA control region (912 base pairs) and 15 nuclear DNA microsatellite loci of 664 spawning adults from 24 populations. Results support that perch from three primary glacial refugium areas (Missourian, Mississippian, and Atlantic) founded contemporary northern populations. Genetic diversity today is highest in southern (never glaciated) populations, and also is appreciable in northern areas that were founded from multiple refugia. Divergence is greater among isolated populations, both north and south; the southern Gulf Coast relict populations are the most divergent, reflecting their long history of isolation. Understanding the influence of past and current waterway connections on the genetic structure of yellow perch populations may help us to assess the roles of ongoing climate change and habitat disruptions towards conserving aquatic biodiversity

Sepulveda-Villet & Stepien 2012 - yellow perch Haplotypes

Arlequin formatted input file with all mtDNA control region haplotypes recovered, sampling sites and number of occurrences per haplotype

The role of phototaxis in the initial swim bladder inflation of larval yellow perch (Perca flavescens)

Abstract The yellow perch (Perca flavescens) is a high priority species for aquaculture, with strong demand in the USA. Unfortunately, numerous developmental problems during larval rearing prevent its commercial viability. Failed swim bladder inflation (SBI) has been reported in the culture of numerous physoclistous fish species and is a prominent problem in the culture of yellow perch. Initial SBI occurs within a short period of ontogeny, and missing this opportunity results in permanent malformation of the organ. Lighting cues appear to play a role in triggering the response of rising to the surface to swallow the air required for initial SBI in several fishes including yellow perch. Larval yellow perch are photopositive, and this phototactic response seems to co-occur with the window of opportunity for SBI. Thus, we examined the role of phototactic behavior and low-intensity, moonlight-like illumination in initial SBI in yellow perch. Lights were positioned below and above the water surface in larval culture tanks to see if the presence of nighttime illumination impacted SBI success, and if the phototactic behavior of yellow perch helps them find the water surface when inflating at night. The results of this study reveal that even very low-intensity nighttime light reduces the proportion of yellow perch larvae to initially inflate regardless of the direction of the light source. Also, on treatment with no nighttime illumination, higher than expected SBI was observed, and the culture conditions that produced this success should be examined when focusing on improving SBI in the future. This research suggests that the photopositive response of yellow perch is not involved in SBI success, and lighting could play a role in hindering the process

Sepulveda-Villet & Stepien 2012 - yellow perch broadscale populations

Arlequin formatted input file including all sampling sites used in study. File includes 664 individuals with 15 nuclear microsatellite loci

Stripping away the soil : Plant growth promoting microbiology opportunities in aquaponics

As the processes facilitated by plant growth promoting microorganisms (PGPMs) become better characterized, it is evident that PGPMs may be critical for successful sustainable agricultural practices. Microbes enrich plant growth through various mechanisms, such as enhancing resistance to disease and drought, producing beneficial molecules, and supplying nutrients and trace metals to the plant rhizosphere. Previous studies of PGPMs have focused primarily on soil-based crops. In contrast, aquaponics is a water-based agricultural system, in which production relies upon internal nutrient recycling to co-cultivate plants with fish. This arrangement has management benefits compared to soil-based agriculture, as system components may be designed to directly harness microbial processes that make nutrients bioavailable to plants in downstream components. However, aquaponic systems also present unique management challenges. Microbes may compete with plants for certain micronutrients, such as iron, which makes exogenous supplementation necessary, adding production cost and process complexity, and limiting profitability and system sustainability. Research on PGPMs in aquaponic systems currently lags behind traditional agricultural systems, however, it is clear that certain parallels in nutrient use and plant-microbe interactions are retained from soil-based agricultural systems

Effects of Cortisol and Lipopolysaccharide on Expression of Select Growth-, Stress- and Immune-Related Genes in Rainbow Trout Liver

Many studies have shown that stress-induced cortisol levels negatively influence growth and immunity in finfish. Despite this knowledge, few studies have assessed the direct effects of cortisol on liver immune function. Using real-time PCR, the expression of three cortisol-responsive genes (GR: glucocorticoid receptor, IGF-1: insulin-like growth factor-I and SOCS-1: suppressor of cytokine signaling-I), genes involved with innate and adaptive immunity (IL-1β: interleukin-1 beta, IgM: immunoglobin-M and Lyz: lysozyme), and liver-specific antimicrobial peptides (hepcidin and LEAP-2A: liver-expressed antimicrobial peptide-2A) was studied in vitro using rainbow trout liver slices. The abundances of GR, SOCS-1 and IGF-1 mRNAs were suppressed by cortisol treatment. Abundance of IL-1β mRNA was upregulated by LPS and suppressed by cortisol treatment in a time-dependent manner. While abundance of IgM mRNA was suppressed by cortisol treatment and stimulated by LPS, there were no effects of cortisol or LPS on abundance of Lyz mRNA. Abundance of hepcidin and LEAP-2A mRNA levels were suppressed by cortisol treatment and stimulated by LPS. These results demonstrate that cortisol directly suppresses abundance of GR, IGF-1, IL-1β, IgM, hepcidin, LEAP-2A and SOCS-1 mRNA transcripts in the rainbow trout liver. We report for the first time, a suppressive effect of cortisol (within 8 h of treatment) on hepcidin and LEAP-2A mRNAs in rainbow trout liver, which suggests that acute stress may negatively affect liver immune function in rainbow trout