Microbiome profile of the Antarctic clam Laternula elliptica

Abstract

The filter feeder clam Laternula elliptica is a key species in the Antarctic ecosystem. As a stenothermal benthic species, it has a poor capacity for adaptation to small temperature variations. Despite their ecological importance and sensitivity to climate change, studies on their microbiomes are lacking. The goal of this study was to characterize the bacterial communities of L. elliptica and the tissues variability of this microbiome to provide an initial insight of host-microbiota interactions. We investigated the diversity and taxonomic composition of bacterial communities of L. elliptica from five regions of the body using high-throughput 16S rRNA gene sequencing. The results showed that the microbiome of L. elliptica tended to differ from that of the surrounding seawater samples. However, there were no significant differences in the microbial composition between the body sites, and only two OTUs were present in all samples, being considered core microbiome (genus Moritella and Polaribacter). No significant differences were detected in diversity indexes among tissues (mean 626.85 for observed OTUs, 628.89 Chao1, 5.42 Shannon, and 0.87 Simpson). Rarefaction analysis revealed that most tissues reached a plateau of OTU number according to sample increase, with the exception of Siphon samples. Psychromonas and Psychrilyobacter were particularly abundant in L. elliptica whereas Fluviicola dominated seawater and siphons. Typical polar bacteria were Polaribacter, Shewanella, Colwellia, and Moritella. We detected the prevalence of pathogenic bacterial sequences, particularly in the family Arcobacteraceae, Pseudomonadaceae, and Mycoplasmataceae. The prokaryotic diversity was similar among tissues, as well as their taxonomic composition, suggesting a homogeneity of the microbiome along L. elliptica body. The Antarctic clam population can be used to monitor the impact of human activity in areas near Antarctic stations that discharge wastewater.

Keywords: 16S rRNA; Antarctica; Bacteria; Cold-water invertebrates; Filter-feeding.

Fig. 1

Relative abundances of the most frequent Prokaryotic Phylum (a) and Class (b) levels associate to L. elliptica tissues and surrounding seawater. The number of samples were n = 4 for sea water, n = 3 for siphon, n = 5 for mantle, n = 3 for gill and n = 2 for digestive gland

Fig. 2

Shared OTUs among the different tissues of L. elliptica and seawater samples, with at least one sequence in at least one sample of tissue or seawater. Barplots show the abundance of present OTUs for each sample type

Fig. 3

Bray-Curtis PCA of prokaryotic assembly at OTUs level associated with L. elliptica tissues and surrounding seawater

Fig. 4

Alpha-Diversity indexes in different tissues of Laternula elliptica for observed OTUs (a), Chao1 (b), Shannon (c), and Simpson (d)

Fig. 5

Relative abundances of microbial groups associated with the Antarctic soft clam Laternula elliptica. The circos plot displays the relative abundance of most abundant prokaryotic bacteria at Phylum level (a), Class level (b), and OTU level (c) from samples of different tissues and natural sea water. Each plot was generated from the OTU table grouped by phylum, class level, and OTU level with at least 1% of relative abundance in at least one tissue or natural sea water sample. Values were multiplied by 1000 and rounded without decimals in order to perform the circos plot analysis. The relative abundance of each categories is directly proportional to the width of each ribbon connecting prokaryotic taxa to its respective sample. Each phylum is assigned a specific color. The inner ring represents the total relative abundances (multiplied by 100) for a specific taxon and the proportion assigned to each locality. The outer ring represents the percentage of each taxon assigned to each tissue or natural sea water