16S rRNA gene sequencing and bacteria- and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalteromonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.

Clostridium perfringens (C. perfringens) is an important zoonotic food-borne pathogenic microorganism. Currently, there are many reports on the prevalence of C. perfringens in poultry farms, while few studies on the prevalence and infection source of C. perfringens in egg hatcheries. The present study was undertaken to investigate and track C. perfringens from one breeding duck farm, one duck egg hatchery and one commercial meat duck farm along the production chain. A total of 334 isolates were obtained from 788 samples, including 316 type A strains (94.61 %), 11 type F strains (3.29 %) and seven type G strains (2.10 %). Antimicrobial susceptibility testing revealed that 61.87 % of the tested isolates were multidrug-resistant. Multilocus sequence typing showed that 66 representative isolates encompassed 60 different sequence types (STs), clustered in ten clonal complexes (CCs) and 20 singletons. CC2 was the most popular CC, accounting for 58.82 % (10/17) of the strains from breeding duck farm. Some strains of duck embryos were distributed in the same ST or CC as strains from breeding duck farm and duck egg hatchery, indicating close genetic relationship between them. The study showed that isolates from breeding duck farm had formed a dominant CC through long-term evolution, some duck embryos had been infected with C. perfringens during the incubation period and the infected strains should be from the duck egg hatchery or breeding duck farm with the possibility of vertical transmission. The close relationship between strains from breeding ducks and duck embryos, the high antibiotic resistance of isolates and the presence of cpe-positive or netB-positive isolates indicated that alert should be paid to such risks associated with these.

The nursery stages of mud crab, genus Scylla, proceed from the megalopa stage to crablet instar stages. We review the definition and several of the key stages in mud crab nursery activities. The practice of the direct stocking of megalopa into ponds is not recommended due to their sensitivity. Instead, nursery rearing is needed to grow-out mud crabs of a larger size before pond stocking. Individual nursery rearing results in a higher survival rate at the expense of growth and a more complicated maintenance process compared with communal rearing. The nursery of mud crabs can be done both indoors or outdoors with adequate shelter and feed required to obtain a good survival percentage and growth performance. Artemia nauplii are still irreplaceable as nursery feed, particularly at the megalopa stage, while the survival rate may be improved if live feed is combined with artificial feed such as microbound diet formulations. Water quality parameters, identical to those proposed in tiger shrimp cultures, can be implemented in mud crab rearing. The transportation of crablets between different locations can be done with or without water. The provision of monosex seeds from mud crab hatcheries is expected to become commonplace, increasing seed price and thus improving the income of farmers. Numerous aspects of a mud crab nursery including nutrition; feeding strategies; understanding their behaviour, i.e., cannibalism; control of environmental factors and practical rearing techniques still need further improvement.

Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery-farmed) or naturalized/wild oysters to move onto a farm (naturalized-farmed). It is therefore important to understand genetic variation among populations and farm types. Here, we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double-digest RAD-sequencing in 182 naturalized, 112 hatchery-farmed, and 72 naturalized-farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean F ST = 0.0019) and low differentiation between countries in the Japan-Canada-France historical translocation lineage (France-Canada F ST = 0.0024; Japan-Canada F ST = 0.0060). Chinese populations were more differentiated (China-Japan F ST = 0.0241). Hatchery-propagated populations had higher interindividual relatedness suggesting family structure. Within-population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were lower in one farm population. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting nonlocal origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery-farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.