National Cold Water Marine Aquaculture Center

In fishes, performance failure at high temperature is thought to be due to a limitation on oxygen delivery (the theory of oxygen and capacity limited thermal tolerance, OCLTT), which suggests that thermal tolerance and hypoxia tolerance might be functionally associated. Here we examined variation in temperature and hypoxia tolerance among 41 families of Atlantic salmon (Salmo salar), which allowed us to evaluate the association between these two traits. Both temperature and hypoxia tolerance varied significantly among families and there was a significant positive correlation between critical maximum temperature (CTmax) and hypoxia tolerance, supporting the OCLTT concept. At the organ and cellular levels, we also discovered support for the OCLTT concept as relative ventricle mass (RVM) and cardiac myoglobin (Mb) levels both correlated positively with CTmax (R(2)=0.21, P<0.001 and R(2)=0.17, P=0.003, respectively). A large RVM has previously been shown to be associated with high cardiac output, which might facilitate tissue oxygen supply during elevated oxygen demand at high temperatures, while Mb facilitates the oxygen transfer from the blood to tissues, especially during hypoxia. The data presented here demonstrate for the first time that RVM and Mb are correlated with increased upper temperature tolerance in fish. High phenotypic variation between families and greater similarity among full- and half-siblings suggests that there is substantial standing genetic variation in thermal and hypoxia tolerance, which could respond to selection either in aquaculture or in response to anthropogenic stressors such as global climate change.

Abstract Technological advances have contributed to impressive yield gains and have greatly altered US agriculture. Selective breeding and directed molecular techniques address biological shortcomings of plants and animals and overcome environmental limitations. Improvements in mechanization, particularly of power sources and harvest equipment, reduce labor requirements and increase productivity and worker safety. Conservation systems, often designed to overcome problems introduced from other technologies, reduce negative impacts on soil and water and improve the environmental sustainability of production systems. Advances in information systems, largely developed in other disciplines and adapted to agriculture, are only beginning to impact US production practices. This paper is the fourth in the series of manuscripts exploring drivers of US agricultural systems. While development of technology is still largely driven by a need to address a problem, adoption is closely linked with other drivers of agricultural systems, most notably social, political and economic. Here, we explore the processes of innovation and adoption of technologies and how they have shaped agriculture. Technologies have increased yield and net output, and have also resulted in decreased control by producers, increased intensification, specialization and complexity of production, greater dependence on non-renewable resources, increased production inputs and hence decreased return, and an enhanced reliance on future technology. Future technologies will need to address emerging issues in land use, decline in work force and societal support of farming, global competition, changing social values in both taste and convenience of food, and increasing concerns for food safety and the environment. The challenge for farmers and researchers is to address these issues and develop technologies that balance the needs of producers with the expectations of society and create economically and environmentally sustainable production systems.

Over the past decade in the United States, there has been increased interest in the establishment and use of land-based, closed-containment systems [e.g., recirculating aquaculture system (RAS)] for salmonid culture. These culture systems have unique challenges compared to net pen culture of salmonids, including maintenance of pumps and filters as well as the potential growth of certain bacteria within the systems that can render fish off-flavored. The purpose of this study was to determine the impact of implementing a depuration process to purge the “earthy” and “musty” off-flavor compounds geosmin and 2-methylisoborneol (MIB) from Atlantic salmon fillets on fillet quality characteristics (e.g., lipid content, color). During two depuration trials, salmon were depurated without feed in a flow-through tank, a recently “cleaned” RAS system or the originally stocked grow-out tank for up to 20 days. Results from both trials determined that the salmon required depuration in odor-free water for 10–15 days in either a flow-through system or a recently cleaned RAS to obtain the lowest residual levels of geosmin and MIB in the fish flesh. In trial 1, after 20 days, fish had lost significantly more weight (5.8%) compared to day 5 (3.8%). In the second trial, lipid content of the fillet also significantly dropped from 8.2% to 5.1% and moisture content increased from 69.3% to 71.1%. Fillet color quality was not compromised during the 20-day depuration periods. In trial 1, MIB was the main off-flavor compound present in salmon fillets while geosmin was at higher levels than MIB in fish flesh in trial 2. During the second depuration study, three geosmin-producing species of actinomycetes were isolated from the recirculating system and were attributed as the likely sources of geosmin in the salmon fillets. Because fillet color quality was not compromised during the depuration periods used in these studies, the main fillet quality concerns for producers of RAS-cultured salmon are flavor, texture and lipid levels during the pre-harvest purging process.

The normal shape of the salmonid ventricle is a triangular pyramid with the apex pointing caudoventrally. A strong positive correlation has been established between this shape and optimum cardiac output and function. Domesticated salmonids appear to have developed a more rounded ventricle with misaligned bulbus arteriosus. Several reports from fish health veterinarians indicate that fish with abnormal heart morphology have a high mortality rate during stress-inducing situations like grading, transportation and bath treatments. The present paper compares and describes the ventricle morphology of wild vs. farmed Atlantic salmon, and wild steelhead (anadromous rainbow trout) vs. farmed rainbow trout. Several parameters were measured to provide numerical measurement of the differences in shape, i.e. height:width ratio and the angle between the longitudinal ventricular axis and the axis of the bulbus arteriosus. We conclude that the hearts of farmed fish are rounder than those in corresponding wild fish, and that the angle between the ventricular axis and the axis of the bulbus arteriosus is more acute in wild fish than in their farmed counterparts. Further studies are necessary to reveal the prevalence, functional significance and possible causes of these abnormal hearts.

A new Edwardsiella taxon was recently described from fishes of Europe and Asia. Phenotypically similar to E. tarda, extensive genetic and phenotypic characterization determined this new strain does not belong to any established Edwardsiella taxa, leading to the adoption of a new taxon, E. piscicida. Concurrent research in the USA also identified 2 genetically distinct taxa within the group of organisms traditionally classified as E. tarda. Comparisons of gyrB sequences between US isolates and E. piscicida from Europe and Asia identified several US isolates with >99.6% similarity to the gyrB sequence of the E. piscicida type strain (ET883) but <87% similarity to the E. tarda type strain (ATCC #15947). A discriminatory PCR was developed for the identification of E. tarda and 2 genetic variants of E. piscicida (E. piscicida and E. piscicida-like species). Using these PCR assays, a survey was conducted of 44 archived bacterial specimens from disease case submissions to the Aquatic Research and Diagnostic Laboratory (Stoneville, MS, USA) between 2007 and 2012. All 44 isolates, originally identified phenotypically and biochemically as E. tarda, were identified as E. piscicida by PCR. Repetitive sequence-mediated PCR (rep-PCR) analysis of these archived specimens suggests they are largely homogenous, similar to what has been observed for E. ictaluri. The gyrB sequence data, coupled with the E. piscicida specific-PCR and rep-PCR data, confirms that E. piscicida has been isolated from fish disease cases in the southeastern USA. Moreover, our survey data suggests E. piscicida may be more prevalent in catfish aquaculture than E. tarda.

Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, whereby six established genomovars have been described to date. However, little has been done to quantify or characterize this diversity further in a systematic fashion. The objective of this research was to perform phylogenetic analyses of 16S rRNA and housekeeping gene sequences to decipher the genetic diversity of F. columnare. Fifty isolates and/or genomes of F. columnare, originating from diverse years, geographic locations, fish hosts, and representative of the six genomovars were analyzed in this study. A multilocus phylogenetic analysis (MLPA) of the 16S rRNA and six housekeeping genes supported four distinct F. columnare genetic groups. There were associations between genomovar and genetic group, but these relationships were imperfect indicating that genomovar assignment does not accurately reflect F. columnare genetic diversity. To expand the dataset, an additional ninety 16S rRNA gene sequences were retrieved from GenBank and a phylogenetic analysis of this larger dataset also supported the establishment of four genetic groups. Examination of isolate historical data indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from specific fish species or families. It is proposed that F. columnare isolates be assigned to the four genetic groups defined in this study rather than genomovar in order to facilitate a standard nomenclature across the scientific community. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries may allow for the development of improved targeted control and treatment measures for columnaris disease.

Fish cultured within water recirculating aquaculture systems (RAS) can acquire “earthy” or “musty” off-flavors due to bioaccumulation of the compounds geosmin and 2-methylisoborneol (MIB), respectively, which are produced by certain bacterial species present in RAS biosolids and microbial biofilms. Fish cultured in RAS are generally transferred to separate depuration systems that are flushed with water in a single pass or operated with limited water recirculation (with no biofilter), in order to purge these unpalatable flavors. Technologies and standard operating practices that optimize purging kinetics for Atlantic salmon Salmo salar and other species cultured in RAS are needed to improve the consistency and efficacy of depuration. A 2 × 2 factorial trial was conducted to evaluate techniques to mitigate off-flavor from Atlantic salmon cultured to 3–5 kg in a semi-commercial scale freshwater RAS. Twelve replicated depuration systems (0.5 m3) were used to evaluate four combinations (n = 3) of the following standard operating procedure and system design parameters: (1) disinfection of depuration systems as a 1 h static treatment using 250 mg/L hydrogen peroxide (H2O2) prior to stocking fish, (2) no disinfection prior to stocking fish, (3) presence of water aeration media within gas transfer columns of depuration systems, and (4) absence of water aeration media within gas transfer columns of depuration systems. Food-size Atlantic salmon were stocked within the depuration systems and kept off feed for 10 days. Six salmon were harvested from the original RAS on Day 0 and fileted for baseline assessment of off-flavor concentrations. Thereafter, filet samples (n = 3–4) were taken on Days 3, 6, and 10 to evaluate off-flavor kinetics. Hydrogen peroxide disinfection of depuration systems resulted in significantly reduced off-flavor in salmon filets during the depuration period. Results also indicated that the presence of high-surface-area water aeration media shielded biofilms from complete disinfection, resulting in less and slower off-flavor removal from Atlantic salmon filets; while depuration systems void of media resulted in greater and more rapid off-flavor reduction. Thus, water aeration media should not be used in depuration systems because of the challenges posed for effective cleaning, disinfection, and inactivation of off-flavor producing bacteria that may be present, and unit processes and locations that are difficult-to-clean should be excluded. In addition, a wide range of off-flavor concentrations were measured within individual salmon, indicating that one salmon is not a representative sample size to determine market suitability.

The human population is growing and, globally, we must meet the challenge of increased protein needs required to feed this population. Single cell proteins (SCP), when coupled to aquaculture production, offer a means to ensure future protein needs can be met without direct competition with food for people. To demonstrate a given type of SCP has potential as a protein source for use in aquaculture feed, a number of steps need to be validated including demonstrating that the SCP is accepted by the species in question, leads to equivalent survival and growth, does not result in illness or other maladies, is palatable to the consumer, is cost effective to produce and can easily be incorporated into diets using existing technology. Here we examine white shrimp ( Litopenaeus vannamei ) growth and consumer taste preference, smallmouth grunt ( Haemulon chrysargyreum ) growth, survival, health and gut microbiota, and Atlantic salmon ( Salmo salar ) digestibility when fed diets that substitute the bacterium Methylobacterium extorquens at a level of 30% (grunts), 100% (shrimp), or 55% (salmon) of the fishmeal in a compound feed . In each of these tests, animals performed equivalently when fed diets containing M. extorquens as when fed a standard aquaculture diet. This transdisciplinary approach is a first validation of this bacterium as a potential SCP protein substitute in aquafeeds. Given the ease to produce this SCP through an aerobic fermentation process, the broad applicability for use in aquaculture indicates the promise of M. extorquens in leading toward greater food security in the future.

Alternative protein sources for aquafeeds need to be indentified in order to increase the efficiency of production. Many studies have examined terrestrial plant meals/protein concentrates as alternatives. Recently the focus has turned to aquatic protists and plants as well as by-products from other industries, such as breweries. Atlantic salmon, Salmo salar, and Arctic charr, Salvelinus alpinus, were fed diets containing canola meal, soybean meal, corn gluten meal, soy protein concentrate, barley protein concentrate, and solar dried algae included at 30% of the test diet. Barley protein concentrate had the highest apparent protein digestibility values for both species (96.3% for Atlantic salmon and 85.1% for Arctic charr), followed by corn gluten meal. Algae had the highest organic matter digestibility value for arctic charr (80.1%) while corn gluten meal had the highest organic matter digestibility value for Atlantic salmon (88.4%). Algae had a high energy apparent digestibility coefficient (82.4 salmon, 82.7 charr) along with corn gluten meal (78.5 salmon, 82.7 charr) for both species. In general, Atlantic salmon had higher apparent digestibility coefficients compared to Arctic charr for most of the tested ingredients. Both corn gluten and barley protein concentrate appear good candidates as alternative protein sources with both species.

The role of parasitic sea lice (Siphonostomatoida; Caligidae), especially Lepeophtheirus salmonis, in the epidemiology of Infectious Salmon Anemia Virus (ISAv) has long been suspected. The epidemiological studies conducted during the 1998 major Infectious Salmon Anaemia (ISA) outbreak in Scotland demonstrated a strong correlation between sea lice presence and ISAv positive sites or subsequent clinical outbreaks of ISA. The question posed from this observation was "do sea lice infestations on Atlantic salmon make them more susceptible to viral infections?" This study investigated the role that sea lice infestations have on the severity of ISAv infections and disease mortality in experimental populations of farmed Atlantic salmon (Salmo salar). A series of experiments was carried out that investigated the potential of sea lice to modify the outcome of an ISAv infection. Experimental populations of Atlantic salmon were established that had: no lice and no ISAv, a single infection with either ISAv or lice and a co-infection with lice then ISAV. The results were quite clear, the process of infestation by the parasite prior to ISAv exposure significantly increased the mortality and death rates of Atlantic salmon, when compared to uninfected controls and ISAv infected groups only. This was consistent over two source strains of Atlantic salmon (Pennobscot and Saint John River), but the severity and timing was altered. Immunological responses were also consistent in that pro-inflammatory genes were induced in lice only and co-infected fish, whereas the anti-viral response, Mx, MH class I β, Galectin 9 and TRIM 16, 25 genes were down-regulated by lice infection prior to and shortly after co-infection with ISAv. It is concluded that the sea lice settlement on Atlantic salmon and the parasite's subsequent manipulation of the host's immune system, which increases parasite settlement success, also increased susceptibility to ISAv.

Channel catfish Ictalurus punctatus from a commercial farming operation in the Mississippi Delta were submitted for examination for the presence of infection by the trematode Bolbophorus damnificus. The fish were instead found to possess skin nodules suggestive of Henneguya pellis, a species previously described in the blue catfish I. furcatus. Despite the dermal location and distribution of lesions, morphological characteristics of the myxospores were inconsistent with H. pellis. Spores possessed a lanceolate spore body 15.4 +/- 1.5 microm (mean +/- SD; range = 12.2-19.3 microm) in length and 5.5 +/- 0.6 microm (range = 4.5-6.8 microm) in width in valvular view, and 4.7 +/- 0.2 microm (range = 4.2-5.0 microm) in width in sutural view. Polar capsules were pyriform and unequal in both length and width and contained polar filaments with six coils. Polar capsules measured 6.1 +/- 0.8 microm (range = 4.0-7.9 microm) long and 1.7 +/- 0.3 microm (range = 1.0-2.2 microm) wide. The caudal appendages were 50.5 +/- 8.3 microm (range = 34.8-71.4 micorm) long and the total length of the spore was 65.9 +/- 8.6 microm (range = 48.2-90.0 microm). The "blister like" plasmodia were round or ovoid, up to 2 mm in diameter, and randomly distributed throughout the epidermis of the fish. Histologically, plasmodia were confined to the dermis and elicited no inflammatory reaction from the fish. A blast search of the 18S small subunit rDNA sequence obtained by polymerase chain reaction amplification resulted in no identical sequence matches but indicated a close relationship to H. gurlei, H. ictaluri, and H. exilis. The unique host record, spore morphology, and novel genetic sequence derived from this isolate lead us to propose this isolate as a novel species, H. sutherlandi.

The microbiota of teleost fish has gained a great deal of research attention within the past decade, with experiments suggesting that both host-genetics and environment are strong ecological forces shaping the bacterial assemblages of fish microbiomes. Despite representing great commercial and scientific importance, the catfish within the family Ictaluridae, specifically the blue and channel catfish, have received very little research attention directed toward their gut-associated microbiota using 16S rRNA gene sequencing. Within this study we utilize multiple genetically distinct strains of blue and channel catfish, verified via microsatellite genotyping, to further quantify the role of host-genetics in shaping the bacterial communities in the fish gut, while maintaining environmental and husbandry parameters constant. Comparisons of the gut microbiota among the two catfish species showed no differences in bacterial species richness (Observed and Chao1) or overall composition (weighted and unweighted UniFrac) and UniFrac distances showed no correlation with host genetic distances (Rst) according to Mantel tests. The microbiota of environmental samples (diet and water) were found to be significantly more diverse than that of the catfish gut associated samples, suggesting that factors within the host were further regulating the bacterial communities, despite the lack of a clear connection between microbiota composition and host genotype. The catfish gut communities were dominated by the phyla Fusobacteria, Proteobacteria, and Firmicutes; however, differential abundance analysis between the two catfish species using ANCOM detected two differential genera, Cetobacterium and Clostridium XI. The metagenomic pathway features inferred from our dataset suggests the catfish gut bacterial communities possess pathways beneficial to their host such as those involved in nutrient metabolism and antimicrobial biosynthesis, while also containing pathways involved in virulence factors of pathogens. Testing of the inferred KEGG pathways by DESeq2 revealed minor differences in microbiota function, with two metagenomic pathways detected as differentially abundant between the two catfish species. As the first study to characterize the gut microbiota of blue catfish, our study results have direct implications on future ictalurid catfish research. Additionally, our insight into the intrinsic factors driving microbiota structure has basic implications for the future study of fish gut microbiota.

Abstract Ictalurid catfish grown in ponds often acquire undesirable off‐flavors prior to harvest. Off‐flavors develop when odorous, lipophilic substances in food or water are absorbed across gut or gill epithelium and concentrated in edible tissues. The most common causes of catfish off‐flavors are two nontoxic secondary metabolites of planktonic cyanobacteria: geosmin (causing an earthy off‐flavor) and 2‐methylisoborneol (causing a musty off‐flavor). Off‐flavored fish are unacceptable for processing, and harvest must be postponed until the source of the odorous compound disappears and the compound purges from edible fish tissue. Harvest delays caused by episodes of off‐flavor increase production time, interrupt cash flow, and increase the risk of fish loss. Catfish farmers consider off‐flavor to be one of their most important production‐related problems. This paper reviews the causes of off‐flavor in catfish, pharmacokinetics of uptake and loss of odorous compounds in catfish, seasonality and prevalence of off‐flavors, farm‐ and industry‐level impacts, the ecology of cyanobacteria in catfish ponds, and various strategies for preventing or treating cyanobacterial (and other) off‐flavors. A decision‐making system based on knowledge gained from research is presented as a guide to effective use of the limited tools available to manage off‐flavors.

The Aromascan A32S conducting polymer electronic nose was evaluated for the capability of detecting the presence of off-flavor malodorous compounds in catfish meat fillets to assess meat quality for potential merchantability. Sensor array outputs indicated that the aroma profiles of good-flavor (on-flavor) and off-flavor fillets were strongly different as confirmed by a Principal Component Analysis (PCA) and a Quality Factor value (QF > 7.9) indicating a significant difference at (P < 0.05). The A32S e-nose effectively discriminated between good-flavor and off-flavor catfish at high levels of accuracy (>90%) and with relatively low rates (≤5%) of unknown or indecisive determinations in three trials. This A32S e-nose instrument also was capable of detecting the incidence of mild off-flavor in fillets at levels lower than the threshold of human olfactory detection. Potential applications of e-nose technologies for pre- and post-harvest management of production and meat-quality downgrade problems associated with catfish off-flavor are discussed.

Abstract The magnitude of negative environmental impacts generated by food production means it is now imperative we develop food systems in a way that can actively support the recovery of degraded ecosystems, while also meeting increasing demands for food and livelihoods. Aquaculture, when it utilizes the right practices and species and occurs in the right places, can strike this balance, enabling food production that supports the health of aquatic ecosystems. To ensure the efficacy of this approach, however, a clear, common understanding of the ways in which this industry can achieve this outcome is needed. This paper highlights a definition of “restorative aquaculture”, identifies global principles for the use and development of restorative practices, and identifies needs for information, data, and tools that, if addressed, would greatly expand our understanding of the ways in which aquaculture and restorative activities can have positive environmental outcomes. This guidance was developed by a working group of representatives from global aquaculture, environment, economic and academic organizations. It can assist industry and government in making decisions about sustainability as well as restoration and rehabilitation strategies that intersect with aquaculture.

Abstract Hybrid catfish (♀ Channel Catfish Ictalurus punctatus × ♂ Blue Catfish I. furcatus) production ponds often produce a wide size range of fish, and payments to farmers may be reduced due to discounts for larger fish. In general, fish under 1 lb or over 4 lb may decrease the price paid to farmers, but this is highly dependent on individual processors. The present study was conducted to determine the effect of grading hybrid catfish fingerlings on the size distribution of harvested food fish. Three 0.25-acre ponds were stocked with ungraded fingerlings (average weight = 0.05 lb; coefficient of variation [CV] = 78.0%) at 8,000 fish/acre. An additional three 0.25-acre ponds were stocked with double-graded fingerlings of the same average weight (0.05 lb) as the ungraded fingerlings but with a significantly reduced size variation (CV = 26.9%). Grading of the fingerlings had no significant effect on any production variable other than final size variation (ungraded fingerlings: CV = 48.2%; graded fingerlings: CV = 26.1%). Final mean weights were identical (1.1 lb) and feed conversion ratios were nearly identical (1.58 and 1.57) between the treatments. Survival and net production were similar between treatments. Overall, 13.5% of ungraded fish and 1.2% of graded fish were less than 0.5 lb at harvest; 5.6% of the ungraded fish and 0.1% of the graded fish were larger than 2.0 lb. Grading of hybrid catfish fingerlings is an effective means of decreasing food fish size variability without impacting production efficiency.

The non-biofouling properties of a zwitterionic sulfobetaine polymer surface were easily made attractive to bioentities (e.g., proteins and cells) by metal-polyphenol coating, and spatio-selective functionalization of the zwitterionic polymer surface was achieved by using a soft lithographic technique.

Supramolecular Nanosheet evolution into BC₃N matrix improves the hydrogen evolution reaction activity in the pH universality of highly dispersed Pt nanoparticles.

The consumption of seafood enriched in n-3 polyunsaturated fatty acids (PUFA) is associated with a decreased risk of cardiovascular disease. Several n-3 oxidation products from eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (22:6n-3) have known protective effects in the vasculature. It is not known whether the consumption of cooked seafood enriched in n-3 PUFA causes appreciable consumption of lipid oxidation products. We tested the hypothesis that baking Atlantic salmon (Salmo salar) increases the level of n-3 and n-6 PUFA oxidation products over raw salmon. We measured the contents of several monohydroxy-fatty acids (MHFA), prostanoids, and resolvins. Our data demonstrate that baking did not change the overall total levels of MHFA. However, baking resulted in selective regioisomeric loss of hydroxy fatty acids from arachidonic acid (20:4n-6) and EPA, while significantly increasing hydroxyl-linoleic acid levels. The contents of prostanoids and resolvins were reduced several-fold with baking. The inclusion of a coating on the salmon prior to baking reduced the loss of some MHFA but had no effect on prostanoid losses incurred by baking. Baking did not decrease n-3 PUFA contents, indicating that baking of salmon is an acceptable means of preparation that does not alter the potential health benefits of high n-3 seafood consumption. The extent to which the levels of MHFA, prostanoids, and resolvins in the raw or baked fish have physiologic consequence for humans needs to be determined.

BACKGROUND: Apoptosis plays important roles in a variety of functions, including immunity and response to environmental stress. The Inhibitor of Apoptosis (IAP) gene family of apoptosis regulators is expanded in molluscs, including eastern, Crassostrea virginica, and Pacific, Crassostrea gigas, oysters. The functional importance of IAP expansion in apoptosis and immunity in oysters remains unknown. RESULTS: Phylogenetic analysis of IAP genes in 10 molluscs identified lineage specific gene expansion in bivalve species. Greater IAP gene family expansion was observed in C. virginica than C. gigas (69 vs. 40), resulting mainly from tandem duplications. Functional domain analysis of oyster IAP proteins revealed 3 novel Baculoviral IAP Repeat (BIR) domain types and 14 domain architecture types across gene clusters, 4 of which are not present in model organisms. Phylogenetic analysis of bivalve IAPs suggests a complex history of domain loss and gain. Most IAP genes in oysters (76% of C. virginica and 82% of C. gigas), representing all domain architecture types, were expressed in response to immune challenge (Ostreid Herpesvirus OsHV-1, bacterial probionts Phaeobacter inhibens and Bacillus pumilus, several Vibrio spp., pathogenic Aliiroseovarius crassostreae, and protozoan parasite Perkinsus marinus). Patterns of IAP and apoptosis-related differential gene expression differed between the two oyster species, where C. virginica, in general, differentially expressed a unique set of IAP genes in each challenge, while C. gigas differentially expressed an overlapping set of IAP genes across challenges. Apoptosis gene expression patterns clustered mainly by resistance/susceptibility of the oyster host to immune challenge. Weighted Gene Correlation Network Analysis (WGCNA) revealed unique combinations of transcripts for 1 to 12 IAP domain architecture types, including novel types, were significantly co-expressed in response to immune challenge with transcripts in apoptosis-related pathways. CONCLUSIONS: Unprecedented diversity characterized by novel BIR domains and protein domain architectures was observed in oyster IAPs. Complex patterns of gene expression of novel and conserved IAPs in response to a variety of ecologically-relevant immune challenges, combined with evidence of direct co-expression of IAP genes with apoptosis-related transcripts, suggests IAP expansion facilitates complex and nuanced regulation of apoptosis and other immune responses in oysters.