Current status and future perspectives of Italian finfish aquaculture

Currently available data show that shellfish and finfish production in Italy, derived both from fisheries and aquaculture activities, is on the order of 474,000 tons, each activity representing 50 % of the total amount. In this context, the finfish aquaculture industry contributes on average 31 % to the national aquaculture production and on average 59 % of its value, giving a total amount of 72,000 tons and a value of around 351 million € (2010). According to FEAP statistics, Italy is the fourth largest finfish producer in EU27, after the UK, Greece, and Spain, while it is also one of the six largest finfish producers among the non-EU and EU member countries, together with Norway, UK, Greece, Turkey, and Spain. Presently, fish culture activities are mainly focused on rainbow trout (Oncorhynchus mykiss, 55.5 %), followed by European sea bass (Dicentrarchus labrax, 13.6 %), gilthead sea bream (Sparus aurata, 12.2 %), gray mullet (Mugil cephalus, 5.3 %), sturgeon (Acipenser spp., 2 %), and European eel (Anguilla anguilla, 1.7 %). Over the last 20 years, freshwater fish production and aquaculture (trout, carp, and eel) have decreased in Italy, with the exception of sturgeon. In contrast, marine fish production has significantly increased during the same period, and the two leading species, European sea bass and gilthead sea bream, presently contribute 25.8 % of the finfish production. From 1,900 tons in 1990, production reached 19,000 tons in 2010, with a 900 % increase, at an average percentage of 4.5 %. In addition, new marine fish species were successfully cultured over the same period. This review outlines the past and present situation of finfish culture in Italy and discusses future developments and priorities, with particular emphasis on new, emerging aquaculture species.     

Predation and the Control of the Sea Urchin Echinometra viridisand Fleshy Algae in the Patch Reefs of Glovers Reef, Belize

The massive reduction in sea urchin Diadema antillarum populations since the mid-1980s has been associated with large increases in the abundance of fleshy algae on many Caribbean reefs despite the availability of other sea urchin and finfish grazers. This study examined the ecology of a grazer living sympatrically with D. antillarum, the common and abundant sea urchin Echinometra viridis. I examined the role that finfish and invertebrate predators play in controlling the distribution of E. viridis as well as the ability of this sea urchin to control exposed fleshy algae on the patch reefs of the Glovers Reef Atoll lagoon. I found that the major predators of this sea urchin were Calamus bajonado (jolthead porgy), Balistes vetula and Canthidermis sufflamen (queen and ocean triggerfish), Lachnolaimus maximus (hogfish), and a gastropod, probably Cassis madagascariensis. The abundance of E. viridis is constrained by predation, which restricts E. viridis to cryptic locations, such as crevices. Sea urchins bit a smaller percentage of experimental algal assays than finfish. Finfish herbivory was associated positively with patch reef topographic complexity. Unexpectedly, E. viridis abundance was positively correlated with fleshy algal abundance, but negatively correlated with the frequency of finfish bites. Predators restrict E. viridis to crevices and therefore reduce their influence on exposed fleshy algae, even at moderately high population densities (up to 10 per square meter). Since net benthic primary production of coral reefs is most strongly associated with herbivory on exposed surfaces, it would appear that E. viridis is unable to maintain the same production as reefs dominated by D. antillarum. Received 5 November 1998; accepted 2 June 1999.     

Present status of fisheries in Turkey

Turkey’s natural and ecological situations are very suitable for aquaculture. Turkey also has a wide variety of freshwater and marine species comprising trout, carp, sea bass, sea bream, turbot, mussel, crayfish, etc. The total production of fish and shellfish was 646,310 tons in 2008. The contribution of freshwater catch to total fishery production is relatively small. Capture fisheries production amounted to 494,124 tons whilst aquaculture production was 152,186 tons in the same year. In Turkey, Engraulis encrasicholus (anchovy) is the main caught sea fish species. Fisheries in the Black Sea are the most important fishery by far and show the greatest variations in total catch. Alburnus tarichii (a local species belonging to Cyprinidae) and Cyprinus carpio (the common carp) are the most important species caught from freshwaters. Aquaculture is going to play an increasingly important role in the Turkish economy, as fishery products are the only products of animal origin that can be exported to the EU. There has been a fast increase in the aquaculture production in Turkey with the implementation of scientific and technological modernization. For example, total aquaculture production for 1986 and 2008 was 3,075 and 152,186 tons, respectively. The percentage of aquaculture in total fish production has been rising every year. The ratio of cultured fish production to total fish production was 1.5% in 1990 s, 13.57% in 2000 and more than 20% in 2005. It was 23.55% in 2008. Trouts are the main cultured freshwater fish species. Raceways and floating cages are employed in culture of trout. Carps are also important cultured freshwater fish species. Sea bass and gilthead sea bream are grown marine fish species. Floating cages, off-shore and earthen ponds are used for marine fish species culture. There has been an increase in fishery exports and imports in recent years. It was more than US500 million in 2008, but that of 2004 was just over US 500 million in 2008, but that of 2004 was just over US 233 million. However, aquaculture production is still far away from the production targets and fisheries sector is not an important part of the economy at present.     

The composite trophic status index (TRIX) as a potential tool for the regulation of Turkish marine aquaculture as applied to the eastern Aegean coast (Izmir Bay)

This research examines the current water quality status of Izmir Bay, using the trophic index (TRIX) as a tool for the regulation of Turkish marine finfish aquaculture. In 2007, new legislation was enacted in Turkey related to the protection of coastal waters, especially those of enclosed bays and gulfs, from pollution by fish farming. However, the legislation does not apply to any other coastal zone stakeholders; for this reason the entire Izmir Bay was examined. Use of the composite trophic status index (TRIX) produced mean TRIX values of 3.6 for the aquaculture area (AA) and 2.5 for areas of the outer bay where no aquaculture takes place; this indicates ‘no risk of eutrophication’ as defined by Turkish law. In the inner Izmir Bay, there is a mean TRIX value of 4.3, which is above the threshold of four and typical for ‘high eutrophication risk’ areas, as expected because of heavy urbanization. The study then applied the UNTRIX indices adjusted to local conditions, revealing that both the inner bay and the aquaculture area (AA) can be classified as of ‘poor’ status whereas the outer bay can be defined as ‘good’. The UNTRIX‐based trophic classification is in good agreement with TRIX for both the outer and inner parts of the bay; however, there is no agreement regarding the classification of the aquaculture area.     

Marine finfish hatchery technology in the USA – status and future

In 1993, about 52% of the 433 698 tons of thetotal US aquaculture production came from theproduction of freshwater catfish. Excludingsalmonid culture, the percentage of marine finfishculture in total aquaculture production in the UShas been negligible. Commercial scale production ofmarine finfish in hatcheries is very limited in theUS.Studies on eggs and larvae of marine finfishspecies in the US have stemmed from theconsideration of fisheries management rather thanaquaculture. Most of the marine finfish larvaeproduced in the laboratory has been for the purposeof providing materials for other academic relatedstudies. Results of these studies can be applied inthe development of marine finfish hatcherytechnology. Hatchery technology for several marinefinfish species has been developed for stockenhancement, technology transfer and aquaculture. This paper reviews the current hatchery technologyof striped mullet (Mugil cephalus), dolphinfish (Coryphaena hippurus), red drum (Sciaenops ocellatus), and other potentialaquaculture species.     

The innate immune response of finfish--a review of current knowledge

The decline in the fisheries of traditional marine species has been an incentive for the diversification of today's aquaculture sector into the intensive rearing of many finfish species. The increasing interest in commercial farming of different finfish species is expected to result in similar environmental and husbandry-related problems as have been experienced in the development of the salmonid farming industry. An understanding of the biology of the fish species being cultured, in particular the immune response is important for improved husbandry and health management of the species. The innate immune system of fish has generated increasing interest in recent years and is now thought to be of key importance in primary defence and in driving adaptive immunity. This review focuses on key components (cellular and humoral) of the innate immune responses of different fish species of commercial importance.     

Responses of foraminifera communities to aquaculture‐derived organic enrichment as revealed by environmental DNA metabarcoding

Current monitoring methods to assess benthic impacts of marine finfish aquaculture are based on complex biological indices and/or geochemistry data. The former requires benthic macrofauna morpho‐taxonomic characterization that is time‐ and cost‐intensive, while the latter provides rapid assessment of the organic enrichment status of sediments but does not directly measure biotic impacts. In this study, sediment samples were collected from seven stations at six salmon farms in British Columbia, Canada, and analyzed for geochemical parameters and by eDNA metabarcoding to investigate linkages between geochemistry and foraminifera. Sediment texture across farm sites ranged from sand to silty loam, while the maximum sediment pore‐water sulphide concentration at each site ranged from 1,000 to 13,000 μM. Foraminifera alpha diversity generally increased with distance from cage edge. Adonis analyses revealed that farm site explained the most variation in foraminifera community, followed by sediment type, enrichment status, and distance from cage edge. Farm‐specific responses were observed in diversity analyses, taxonomic difference analyses, and correlation analyses. Results demonstrated that species diversity and composition of foraminifera characterized by eDNA metabarcoding generated signals consistent with benthic biodiversity being impacted by finfish farming activities. This substantiates the validity of eDNA metabarcoding for augmenting current approaches to benthic impact assessments by providing more cost‐effective and practicable biotic measures than traditional morpho‐taxonomy. To capitalize on this potential, further work is needed to design a new nomogram that combines eDNA metabarcoding data and geochemistry data to enable accurate monitoring of benthic impacts of fish farming in a time‐ and cost‐efficient way.     

Jellyfish Stings Trigger Gill Disorders and Increased Mortality in Farmed Sparus aurata (Linnaeus, 1758) in the Mediterranean Sea

Jellyfish are of particular concern for marine finfish aquaculture. In recent years repeated mass mortality episodes of farmed fish were caused by blooms of gelatinous cnidarian stingers, as a consequence of a wide range of hemolytic, cytotoxic, and neurotoxic properties of associated cnidocytes venoms. The mauve stinger jellyfish Pelagia noctiluca (Scyphozoa) has been identified as direct causative agent for several documented fish mortality events both in Northern Europe and the Mediterranean Sea aquaculture farms. We investigated the effects of P. noctiluca envenomations on the gilthead sea bream Sparus aurata by in vivo laboratory assays. Fish were incubated for 8 hours with jellyfish at 3 different densities in 300 l experimental tanks. Gill disorders were assessed by histological analyses and histopathological scoring of samples collected at time intervals from 3 hours to 4 weeks after initial exposure. Fish gills showed different extent and severity of gill lesions according to jellyfish density and incubation time, and long after the removal of jellyfish from tanks. Jellyfish envenomation elicits local and systemic inflammation reactions, histopathology and gill cell toxicity, with severe impacts on fish health. Altogether, these results shows P. noctiluca swarms may represent a high risk for Mediterranean finfish aquaculture farms, generating significant gill damage after only a few hours of contact with farmed S. aurata. Due to the growth of the aquaculture sector and the increased frequency of jellyfish blooms in the coastal waters, negative interactions between stinging jellyfish and farmed fish are likely to increase with the potential for significant economic losses.     

Freshwater salmon aquaculture in Chile and transferable antimicrobial resistance

Large amounts of antimicrobials are used in salmonid aquaculture in Chile. Most are used in marine aquaculture, but appreciable amounts are also employed in freshwater aquaculture. Much research and many publications have examined transferable antimicrobial resistance in bacteria isolated from marine salmon farms, but much less attention has been paid to this area in freshwater salmon farming. A recent paper by Domínguez et al. (2019) has as least in part remedied this situation. We now comment on some of its interpretations and have attempted to point out its areas of strength and weakness in light of the published scientific literature. Seen in this setting, the important results presented by Domínguez et al. (2019) underline the need for increased awareness of the challenge to animal and human health posed by excessive use of antimicrobials in aquaculture.     

The mangrove-based coastal and nearshore fisheries of Bangladesh: ecology,exploitation and management

The mangrove forest of Bangladesh, the largest continuous mangrove forest of the world, is one of the most important coastal features of the country. The existence of the mangrove has increased the values of other coastal and marine resources such as the coastal and marine fisheries by increasing productivity and supporting a wide biological diversity. The artisanal fishery, which is highly influenced by mangroves, has been contributing 85–95% of the total coastal and marine catch of Bangladesh. The mangrove also supports offshore and deep sea fisheries by playing a significant role as nursery ground for many deep sea fishes and shrimps including the giant tiger shrimp (Penaeus monodon) which is the major species of the industrial bottom trawl fishery of Bangladesh. The mangrove also contributes significantly in shrimp farming which has been the most significant export-oriented industry since the 1970s. However, the mangrove fisheries have been under intensive pressure from deleterious fishing activities and deliberate aquaculture development by destructing mangrove habitats. The impacts of mangrove have been reflected in the contribution of artisanal fishery catch that has been in a continuous decline since the 1980s. Shrimp farming has been the most destructive contributor to mangrove destruction with a corresponding loss of biological resources particularly the wild shrimp fishery. This paper reviews different aspects of the mangrove fisheries of Bangladesh and discusses the impacts of different fisheries. The paper identifies the importance of reviewing, amending and/or replacing the traditional management approaches by the new management techniques such as habitat restoration and stock enhancement in the natural environment; the paper also identifies the need for research findings in formulating and implementing new management approaches.     

How sea lice from salmon farms may cause wild salmonid declines in Europe and North America and be a threat to fishes elsewhere

Fishes farmed in sea pens may become infested by parasites from wild fishes and in turn become point sources for parasites. Sea lice, copepods of the family Caligidae, are the best-studied example of this risk. Sea lice are the most significant parasitic pathogen in salmon farming in Europe and the Americas, are estimated to cost the world industry €300 million a year and may also be pathogenic to wild fishes under natural conditions.Epizootics, characteristically dominated by juvenile (copepodite and chalimus) stages, have repeatedly occurred on juvenile wild salmonids in areas where farms have sea lice infestations, but have not been recorded elsewhere. This paper synthesizes the literature, including modelling studies, to provide an understanding of how one species, the salmon louse, Lepeophtheirus salmonis, can infest wild salmonids from farm sources. Three-dimensional hydrographic models predicted the distribution of the planktonic salmon lice larvae best when they accounted for wind-driven surface currents and larval behaviour. Caligus species can also cause problems on farms and transfer from farms to wild fishes, and this genus is cosmopolitan. Sea lice thus threaten finfish farming worldwide, but with the possible exception of L. salmonis, their host relationships and transmission adaptations are unknown. The increasing evidence that lice from farms can be a significant cause of mortality on nearby wild fish populations provides an additional challenge to controlling lice on the farms and also raises conservation, economic and political issues about how to balance aquaculture and fisheries resource management.     

Biofouling in marine aquaculture: a review of recent research and developments

Biofouling in marine aquaculture is one of the main barriers to efficient and sustainable production. Owing to the growth of aquaculture globally, it is pertinent to update previous reviews to inform management and guide future research. Here, the authors highlight recent research and developments on the impacts, prevention and control of biofouling in shellfish, finfish and seaweed aquaculture, and the significant gaps that still exist in aquaculturalists’ capacity to manage it. Antifouling methods are being explored and developed; these are centred on harnessing naturally occurring antifouling properties, culturing fouling-resistant genotypes, and improving farming strategies by adopting more sensitive and informative monitoring and modelling capabilities together with novel cleaning equipment. While no simple, quick-fix solutions to biofouling management in existing aquaculture industry situations have been developed, the expectation is that effective methods are likely to evolve as aquaculture develops into emerging culture scenarios, which will undoubtedly influence the path for future solutions.     

A Scoping Analysis of Peer-Reviewed Literature About Linkages Between Aquaculture and Determinants of Human Health

For many of the world’s poor, aquatic products are critical for food security and health. Because the global population is increasing as wild aquatic stocks are declining, aquaculture is an increasingly important source of aquatic products. We undertook a scoping review of the English-language peer-reviewed literature to evaluate how the research community has examined the impacts of aquaculture on four key determinants of human health: poverty, food security, food production sustainability, and gender equality. The review returned 156 primary research articles. Most research (75%) was focused in Asia, with limited research from Africa (10%) and South America (2%). Most research (80%) focused on freshwater finfish and shrimp production. We used qualitative content analysis of records which revealed 11 themes: famer income; the common environment; shared resources; integrated farming/ polyculture; employment; extensive vs. intensive production; local vs. distant ownership; food security; income equity; gender equality; and input costs. We used quantitative content analysis of records and full-text publications about freshwater finfish and shrimp aquaculture to record the frequency with which themes were represented and the positive or negative impacts of aquaculture associated with each theme. Scatter plots showed that no theme was identified in more than half of all articles and publications for both production types. Farmer income was a theme that was identified commonly and was positively impacted by both shrimp and fresh water finfish aquaculture. Polyculture, employment, and local ownership were identified less often as themes, but were also associated with positive impacts. The common environment and shared resources were more common themes in shrimp aquaculture than freshwater finfish aquaculture research, while polyculture and local ownership were more common themes in freshwater finfish aquaculture than shrimp aquaculture. Gender equality, employment, and food security were themes found in a lower percentage of records than full-text publications for both production types.     

Genetic interactions between marine finfish species in European aquaculture and wild conspecifics

The principal species of marine aquaculture in Europe are Atlantic salmon (Salmo salar), sea bass (Dicentrarchus labrax) and sea bream (Sparus auratus). For Atlantic salmon and sea bass, a substantial part of total genetic variation is partitioned at the geographical population level. In the case of sea bream, gene flow across the Azores/Mediterranean scale appears to be extensive and population structuring is not detected. For Atlantic salmon and sea bass, natural population structure is at risk from genetic interaction with escaped aquaculture conspecifics. The locally adaptive features of populations are at risk from interbreeding with non‐local aquaculture fish. Wild populations, generally, are at risk from interactions with aquaculture fish that have been subject to artificial selection or domestication. Atlantic salmon is the main European aquaculture species and its population genetics and ecology have been well‐studied. A general case regarding genetic interactions can be based on the information available for salmon and extended to cover other species, in the appropriate context. A generalized flow chart for interactions is presented. Salmon escape from aquaculture at all life stages, and some survive to breed among wild salmon. Reproductive fitness in the escaped fish is lower than in native, wild fish because of behavioural deficiencies at spawning. However, as the number of salmon in aquaculture greatly exceeds the number of wild fish, even small fractional rates of escape may result in the local presence of large numbers, and high frequencies, of escaped fish. At present, policy and legislation in relation to minimizing genetic interactions between wild and aquaculture fish is best developed for Atlantic salmon, through the recommendations of the Oslo Agreement developed by the North Atlantic Salmon Conservation Organization and subsequent agreements on their implementation. In future, the potential use of genetically modified fish in aquaculture will make additional policy development necessary. Improved containment is recommended as the key to minimizing the numbers and therefore the effects of escaped fish. Emergency recovery procedures are recommended as a back‐up measure in the case of containment failure. Reproductive sterility is recommended as a future key to eliminating the genetic potential of escaped fish. The maintenance of robust populations of wild fish is recommended as a key to minimizing the effects of escaped fish on wild populations.     

Detection of SJNNV and RGNNV genotypes using a relative quantification RT‐PCR assay

Viral Encephalopathy and Retinopathy (VER), is caused by a nodavirus included within the Betanodavirus genus of the Nodaviridae family. This disease affects more than 30 marine fish species worldwide and has been a major obstacle in the aquaculture industry; control of the disease is based on virus detection, essentially in carrier specimens. This study describes a real time PCR procedure for viral nervous necrosis virus detection from several organs of sea bass, Senegalese sole, and gilt‐head sea bream, from fish displaying either clinical symptoms or asymptomatic cases. The sensitivity of this technique was about 10⁶‐fold higher than that of the conventional RT‐PCR. The newly designed primers detected nodavirus isolates belonging to the RGNNV and SJNNV genotypes.     

Impact of Aquaculture on Commercial Fisheries: Fishermen’s Local Ecological Knowledge

The Bay of Fundy along the southwest coast of New Brunswick, Canada is one of the most densely stocked finfish aquaculture areas in the world. An inshore multi-species fishery that dates back to the earliest European settlement shares these waters, and has been the economic mainstay of coastal communities. These inshore fishermen are increasingly displaced by the expanding aquaculture industry. A recent study conducted among fishermen in Southwest New Brunswick recorded their observations about the environmental impact of finfish aquaculture and the consequences for their commercial fishery. Fishermen all reported significant environmental degradation around aquaculture sites. Within 2 years of an operation being established, fishermen reported that gravid female lobsters as well as herring avoid the area, scallop and sea urchin shells become brittle, scallop meat and sea urchin roe becomes discolored. The use of chemicals to control sea lice on farmed salmon has also caused lobster, crab and shrimp kills. These and other concerns suggest that more comprehensive and detailed studies are required to establish the environmental and economic interactions of aquaculture and the inshore fishery, as well as on the stocks on which that fishery rely. The study also points to the need for more effective use of fishermen’s knowledge in designing such studies.     

Application of genome editing in aquatic farm animals: Atlantic salmon

Gene editing offers opportunities to solve fish farming sustainability issues that presently hampers expansion of the aquaculture industry. In for example Atlantic salmon farming, there are now two major bottlenecks limiting the expansion of the industry. One is the genetic impact of escaped farmed salmon on wild populations, which is considered the most long-term negative effect on the environment. Secondly and the utmost acute problem is the fish parasite salmon lice, which is currently causing high lethality in wild salmonids due to high concentrations of the parasite in the sea owing to sea cage salmon farming. There are also sustainability issues associated with increased use of vegetable-based ingredients as replacements for marine products in fish feed. This transition comes at the expense of the omega-3 content both in fish feed and the fish filet of the farmed fish. Reduced fish welfare represents another obstacle, and robust farmed fish is needed to avoid negative stress associated phenotypes such as cataract, bone and fin deformities, precocious maturity and higher disease susceptibility. Gene editing could solve some of these problems as genetic traits can be altered positively to reach phenotype of interest such as for example disease resistance and increased omega-3 production.

     

Microalgae aquaculture feeds

Microalgae feeds are currently used in relatively small amounts in aquaculture, mainly for the production of larvae and juvenile shell- and finfish, as well as for raising the zooplankton required for feeding of juvenile animals. The blue-green algaSpirulina is used in substantial amounts (over 100 t y^–1) as a fish and shrimp feed, and even larger markets can be projected if production costs could be reduced. Another potential large-scale application of microalgae is the cultivation ofHaematococcus for the production of the carotenoid astaxanthin, which gives salmon flesh its reddish color. In the long-term microalgae biomass high in lipids (omega-3 fatty acids) may be developed as substitutes for fish oil-based aquaculture feeds. In shrimp ponds the indigenous algal blooms supply a part of the dietary requirements of the animals, but it is difficult to maximize algal productivities. A separate algal production system could feed the shrimps and minimize the need for added feed. Bivalves feed essentially exclusively on marine microalgae throughout their life cycle. The development of cultivation technologies for such microalgae would allow the onshore production of these animals, with greatly improved product quality and safety.This paper was presented at the Symposium on Applied Phycology at the Fourth International Phycological Congress, Duke University.     

Factors influencing return rate and marine residence duration in sea trout populations in Central Norway

Brown trout (Salmo trutta) display extensive plasticity in marine migratory behaviours, with marine migrations considered to be an adaptive strategy which enables sea trout to maximize growth and reproductive potential. However, marine migrations are not without associated costs, including threats posed by ever-increasing salmon lice (Lepeophtheirus salmonis) infestations. In the present study, we used passive integrated transponder technology to characterize variability in sea trout migration behaviour amongst three catchments situated in a region of intensive salmon farming in central Norway. Specifically, we investigate how lice infestation, out-migration date and body size alter sea trout return rate and marine residence duration during the first out-migration to sea from each catchment. Distinct catchment-specific differences in sea trout out-migration size and the number of cohorts were observed, but larger body size did not guarantee the successful return of migrating trout. The marine residence duration of individuals that successfully returned to freshwater was positively correlated with lice infestation risk, suggesting for these individuals the lethal infestation threshold had not been reached. Our results also suggest that sea trout populations from lotic-dominated catchments are potentially at greater risk from size-related threats to their survival encountered during their marine migrations than sea trout from lentic-dominated catchments. The variability in sea trout migratory behaviour amongst catchments observed here emphasizes the challenges fisheries managers face when deciding the best actions to take to protect the anadromous portion of brown trout populations.     

Integrative Approach for the Reliable Detection and Specific Identification of the Microsporidium Loma morhua in Atlantic Cod (Gadus morhua)

Microsporidia are fungal parasites that infect diverse invertebrate and vertebrate hosts. Finfish aquaculture supports epizootics due to high host density and the high biotic potential of these parasites. Reliable methods for parasite detection and identification are a necessary precursor to empirical assessment of strategies to mitigate the effects of these pathogens during aquaculture. We developed an integrative approach to detect and identify Loma morhua infecting Atlantic cod. We show that the spleen is more reliable than the commonly presumed gills as best organ for parasite detection in spite of substantial morphological plasticity in xenoma complexes. We developed rDNA primers with 100% sensitivity in detecting L. morhua and with utility in distinguishing some congeneric Loma species. ITS sequencing is necessary to distinguish L. morhua from other congeneric microsporidia due to intraspecific nucleotide variation. 64% of L. morhua ITS variants from Atlantic cod have a 9‐nucleotide motif that distinguishes it from Loma spp. infecting non‐Gadus hosts. The remaining 36% of ITS variants from Atlantic cod are distinguished from currently represented Loma spp., particularly those infecting Gadus hosts, based on a 14‐nucleotide motif. This research approach is amenable to developing templates in support of reliable detection and identification of other microsporidian parasites in fishes.