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

Abstract

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.

Differences in diversity and community composition of the shell microbiome of apparently healthy lobsters Homarus americanus across Atlantic Canada

“…A total of 189 lobster samples were used for the analysis and detailed descriptive statistics such as number, size, sex, molt stage of sampled lobsters, sampling months, location, sampling site and water depths are shown in Koepper et al (2023a) which used the same dataset ( Supplementary Table S1 , for rarefied data only). Briefly, a total of 1,277,587 reads (avg.…”

“…A rarefaction curve is provided in Supplementary Figure S1 . Overall, the shell microbiome of apparently healthy lobsters consisted for the most part of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia ( Koepper et al, 2023a ).…”

“…A map of the sampling locations is provided in Figure 1 . A detailed description of sample collection and processing has been given in Koepper et al (2023a) which used the same microbiome data as in the present study. In short, carapace swabs of the lobster shell microbiome were collected in four LFAs within Atlantic Canada.…”

“… Map of sampling locations from commercial vessels or the wharf. Landing wharves are indicated by an “x.” Map after Koepper et al (2023a) . …”

“…The methods and protocols used for bacterial 16S rRNA gene extraction, sequencing and bioinformatics correspond to the ones described in Koepper et al (2023a) . Briefly, DNA was extracted using the Qiagen Blood and Tissue kit according to the manufacturer’s instructions with a prior lysis step.…”