Microbial diversity of mid-stage Palinurid phyllosoma from Great Barrier Reef waters

Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada

The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.

Gastrointestinal Microbiota of Spiny Lobster: A Review

The gastrointestinal (GI) microbiota is a group of complex and dynamic microorganisms present in the GI tract of an organism that live in symbiosis with the host and benefit the host with various biological functions. The communities of GI microbiota are formed by various aerobic, anaerobic, and facultatively anaerobic bacteria in aquatic species. In spiny lobsters, common GI microorganisms found in the GI tract are Vibrio, Pseudomonas, Bacillus, Micrococcus, and Flavobacterium, where the structure and abundance of these microbes are varied depending on the environment. GI microbiotas hold an important role and significantly affect the overall condition of spiny lobsters, such as secreting digestive enzymes (lipase, protease, and cellulase), helping in digesting food intake, providing nutrition and synthesising vitamins needed by the host system, and protecting the host against infection from pathogens and diseases by activating an immune mechanism in the GI tract. The microorganisms in the water column, sediment, and diet are primarily responsible for altering, manipulating, and shaping GI microbial structures and communities. This review also highlights the possibilities of isolating the indigenous GI microbiota as a potential probiotic strain and introducing it to spiny lobster juveniles and larvae for better health management.

Pathology and genetic connectedness of the mangrove crab (Aratus pisonii) – a foundation for understanding mangrove disease ecology

Mangrove forests are productive ecosystems, acting as a sink for CO2, a habitat for a diverse array of terrestrial and marine species, and as a natural barrier to coastline erosion. The species that reside within mangrove ecosystems have important roles to play, including litter decomposition and the recycling of nutrients. Crustacea are important detritivores in such ecosystems and understanding their limitations (i.e. disease) is an important endeavour when considering the larger ecological services provided.

Histology and metagenomics were used to identify viral (Nudiviridae, Alphaflexiviridae), bacterial (Paracoccus sp., 'Candidatus Gracilibacteria sp.’, and Pseudoalteromonas sp.), protozoan, fungal, and metazoan diversity that compose the symbiome of the mangrove crab, Aratus pisonii. The symbiotic groups were observed at varying prevalence under histology: nudivirus (6.5%), putative gut epithelial virus (3.2%), ciliated protozoa (35.5%), gonad fungus (3.2%), gill ectoparasitic metazoan (6.5%). Metagenomic analysis of one specimen exhibiting a nudivirus infection provided the complete host mitochondrial genome (15,642 bp), nudivirus genome (108,981 bp), and the genome of a Cassava common mosaic virus isolate (6387 bp). Our phylogenetic analyses group the novel nudivirus with the Gammanudivirus and protein similarity searches indicate that Carcinus maenas nudivrius is the most similar to the new isolate. The mitochondrial genome were used to mine short fragments used in population genetic studies to gauge an idea of diversity in this host species across the USA, Caribbean, and central and southern America.

This study report several new symbionts based on their pathology, taxonomy, and genomics (where available) and discuss what effect they may have on the crab population. The role of mangrove crabs from a OneHealth perspective were explored, since their pathobiome includes cassava-infecting viruses. Finally, given that this species is abundant in mangrove forests and now boasts a well-described pathogen profile, we posit that A. pisonii is a valuable model system for understanding mangrove disease ecology.

Aquimarina sp. Associated With a Cuticular Disease of Cultured Larval Palinurid and Scyllarid Lobsters

Shell (cuticular) disease manifests in various forms and affects many crustaceans, including lobsters. Outbreaks of white leg disease (WLD) with distinct signs of pereiopod tissue whitening and death have been observed in cultured larvae (phyllosomas) of ornate spiny lobster Panulirus ornatus, eastern rock lobster Sagmariasus verreauxi, and slipper lobster Thenus australiensis. This study aimed to characterise and identify the causative agent of WLD through morphological and molecular (16S rRNA gene and whole genome sequencing) analysis, experimental infection of damaged/undamaged P. ornatus and T. australiensis phyllosomas, and bacterial community analysis (16S rRNA gene amplicon sequencing) of P. ornatus phyllosomas presenting with WLD during an outbreak. Bacterial communities of WLD-affected pereiopods showed low bacterial diversity and dominant abundance of Aquimarina spp. compared to healthy pereiopods, which were more diverse and enriched with Sulfitobacter spp. 16S rRNA gene Sanger sequencing of cultures from disease outbreaks identified the dominant bacterial isolate (TRL1) as a Gram-negative, long non-flagellated rod with 100% sequence identity to Aquimarina hainanensis. Aquimarina sp. TRL1 was demonstrated through comparative genome analysis (99.99% OrthoANIu) as the bacterium reisolated from experimentally infected phyllosomas presenting with typical signs of WLD. Pereiopod damage was a major predisposing factor to WLD. Histopathological examination of WLD-affected pereiopods showed masses of internalised bacteria and loss of structural integrity, suggesting that Aquimarina sp. TRL1 could enter the circulatory system and cause death by septicaemia. Aquimarina sp. TRL1 appears to have important genomic traits (e.g., tissue-degrading enzymes, gliding motility, and aggregate-promoting factors) implicated in the pathogenicity of this bacterium. We have shown that Aquimarina sp. TRL1 is the aetiological agent of WLD in cultured Palinurid and Scyllarid phyllosomas and that damaged pereiopods are a predisposing factor to WLD.

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)

Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.

Probiont niche specialization contributes to additive protection against Vibrio owensii in spiny lobster larvae

The development of efficient probiotic application protocols for use in marine larviculture relies on comprehensive understanding of pathogen-probiont-host interactions. The probiont combination of Pseudoalteromonas sp. PP107 and Vibrio sp. PP05 provides additive protection against vectored Vibrio owensii DY05 infection in larvae (phyllosomas) of ornate spiny lobster, Panulirus ornatus. Here, fluorescently tagged strains were used to demonstrate niche specialization of these probionts in both the live feed vector organism Artemia and in phyllosomas. The pathogen was vulnerable to direct interaction with PP05 in the bacterioplankton as well as in the Artemia gut and the phyllosoma foregut and midgut gland. In contrast, PP107 was localized on external surfaces of Artemia and phyllosomas, and direct interaction with the pathogen was limited to the bacterioplankton. While PP107 was the overall dominant ectobiont on the phyllosoma cephalothorax and inner leg segments, PP05 was the primary colonizer of outer leg segments, nutrient-rich locales that may promote ingestion during feeding. This study shows that niche specialization can contribute to the additive probiotic effect of a probiotic mixture and highlights that probiotic enrichment of Artemia cultures can intercept the infection cycle of V. owensii DY05 in early-stage P. ornatus phyllosomas.

The role of coral-associated bacterial communities in Australian Subtropical White Syndrome of Turbinaria mesenterina

Australian Subtropical White Syndrome (ASWS) is an infectious, temperature dependent disease of the subtropical coral Turbinaria mesenterina involving a hitherto unknown transmissible causative agent. This report describes significant changes in the coral associated bacterial community as the disease progresses from the apparently healthy tissue of ASWS affected coral colonies, to areas of the colony affected by ASWS lesions, to the dead coral skeleton exposed by ASWS. In an effort to better understand the potential roles of bacteria in the formation of disease lesions, the effect of antibacterials on the rate of lesion progression was tested, and both culture based and culture independent techniques were used to investigate the bacterial communities associated with colonies of T. mesenterina. Culture-independent analysis was performed using the Oligonucleotide Fingerprinting of Ribosomal Genes (OFRG) technique, which allowed a library of 8094 cloned bacterial 16S ribosomal genes to be analysed. Interestingly, the bacterial communities associated with both healthy and disease affected corals were very diverse and ASWS associated communities were not characterized by a single dominant organism. Treatment with antibacterials had a significant effect on the rate of progress of disease lesions (p = 0.006), suggesting that bacteria may play direct roles as the causative agents of ASWS. A number of potential aetiological agents of ASWS were identified in both the culture-based and culture-independent studies. In the culture-independent study an Alphaproteobacterium closely related to Roseovarius crassostreae, the apparent aetiological agent of juvenile oyster disease, was found to be significantly associated with disease lesions. In the culture-based study Vibrio harveyi was consistently associated with ASWS affected coral colonies and was not isolated from any healthy colonies. The differing results of the culture based and culture-independent studies highlight the importance of using both approaches in the investigation of microbial communities.