Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

Thalassotalea aquiviva sp. nov., and Thalassotalea maritima sp. nov., Isolated from Seawater of the Coast in South Korea

Two novel bacterial strains, 273M-4T and Sam97T, were isolated from seawater in the Yellow Sea, Muan-gun, South Korea, and identified as members of the genus Thalassotalea. Both strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, non-flagellated, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains 273M-4T and Sam97T were most closely related to Thalassotalea ponticola KCTC 42155T, with sequence similarities of 97.5% and 98.3%, respectively. Optimal growth for strain 273M-4T occurred at 25-30 °C, pH 7.0, and 2% NaCl, while strain Sam97T grew optimally at 30 °C, pH 8.0, and 2% NaCl. Genome sizes of strains 273M-4T and Sam97T were 3.37 and 3.31 Mb, with DNA G + C contents of 41.0 mol% and 42.9 mol%, respectively. The orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 71.6% and 24.4%, respectively, indicating that they are distinct species. Further genomic analyses of these two strains revealed OrthoANI values of < 73.5% and dDDH values of < 26.7% within the genus Thalassotalea, suggesting their distinctiveness from other Thalassotalea species. The predominate fatty acids of strains 273M-4T and Sam97T were summed feature 3 (consisting of C16:1 ω7c/C16:1 ω6c) and C16:0. All strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids and ubiquinone-8 (Q-8) as the primary respiratory quinone. Based on phenotypic, phylogenetic, genotypic, and chemotaxonomic data, strains 273M-4T (= KCTC 8644T = LMG 33695T) and Sam97T (= KCTC 8645T = LMG 33694T) represent novel species of the genus Thalassotalea, named Thalassotalea aquiviva sp. nov. and Thalassotalea maritima sp. nov..

What shapes a microbiome? Differences in bacterial communities associated with helminth-amphipod interactions

The fast technological advances of molecular tools have enabled us to uncover a new dimension hidden within parasites and their hosts: their microbiomes. Increasingly, parasitologists characterise host microbiome changes in the face of parasitic infections, revealing the potential of these microscopic fast-evolving entities to influence host-parasite interactions. However, most of the changes in host microbiomes seem to depend on the host and parasite species in question. Furthermore, we should understand the relative role of parasitic infections as microbiome modulators when compared with other microbiome-impacting factors (e.g., host size, age, sex). Here, we characterised the microbiome of a single intermediate host species infected by two parasites belonging to different phyla: the acanthocephalan Plagiorhynchus allisonae and a dilepidid cestode, both infecting Transorchestia serrulata amphipods collected simultaneously from the same locality. We used the v4 hypervariable region of the 16S rRNA prokaryotic gene to identify the hemolymph bacterial community of uninfected, acanthocephalan-infected, and cestode-infected amphipods, as well as the bacteria in the amphipods' immediate environment and in the parasites infecting them. Our results show that parasitic infections were more strongly associated with differences in host bacterial community richness than amphipod size, presence of amphipod eggs in female amphipods, and even parasite load. Amphipods infected by acanthocephalans had the most divergent bacterial community, with a marked decrease in alpha diversity compared with cestode-infected and uninfected hosts. In accordance with the species-specific nature of microbiome changes in parasitic infections, we found unique microbial taxa associating with hosts infected by each parasite species, as well as taxa only shared between a parasite species and their infected hosts. However, there were some bacterial taxa detected in all parasitised amphipods (regardless of the parasite species), but not in uninfected amphipods or the environment. We propose that shared bacteria associated with all hosts parasitised by distantly related helminths may be important either in helping host defences or parasites' success, and could thus interact with host-parasite evolution.

Characterization of microbiota and histology of cultured sea cucumber Isostichopus badionotus juveniles during an outbreak of skin ulceration syndrome

Due to the dramatic reduction of sea cucumber Isostichopus badionotus populations in the Yucatan Peninsula by overfishing and poaching, aquaculture has been encouraged as an alternative to commercial catching and restoring wild populations. However, the scarcity of broodstock, the emergence of a new disease in the auricularia larvae stage, and the development of skin ulceration syndrome (SUS) in the culture have limited aquaculture development. This study presents the changes in the intestine and skin microbiota observed in early and advanced stages of SUS disease in cultured juvenile I. badionotus obtained during an outbreak in experimental culture through 16S rRNA gene sequencing and histological evidence. Our results showed inflammation in the intestines of juveniles at both stages of SUS. However, more severe tissue damage and the presence of bacterial clusters were detected only in the advanced stages of SUS. Differences in the composition and structure of the intestinal and skin bacterial community from early and advanced stages of SUS were detected, with more evident changes in the intestinal microbial communities. These findings suggest that SUS was not induced by a single pathogenic bacterium. Nevertheless, a decrease in the abundance of Vibrio and an increase in Halarcobacter (syn. Arcobacter) was observed, suggesting that these two bacterial groups could be keystone genera involved in SUS disease.

Thalassotalea psychrophila sp. nov., Thalassotalea nanhaiensis sp. nov. and Thalassotalea fonticola sp. nov., three psychrophilic bacteria isolated from deep-sea sediment

Three psychrophilic bacteria, designated as strains SQ149T, SQ345T, and S1-1T, were isolated from deep-sea sediment from the South China Sea. All three strains were the most closely related to Thalassotalea atypica RZG4-3-1T based on the 16S rRNA gene sequence analysis (similarity ranged from 96.45 to 96.67 %). Phylogenetic analysis based on the 16S rRNA gene and core-genome sequences showed that three strains formed a cluster within the genus Thalassotalea. The average amino acid identity, average nucleotide identity, and digital DNA-DNA hybridization values among the three strains and closest Thalassotalea species were far below the cut-off value recommended for delineating species, indicating they each represented a novel species. All three strains were Gram-stain-negative, rod-shaped, and contained summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) as the predominant fatty acid, Q-8 as the major respiratory quinone, and phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids. Based on the genomic, phylogenetic, and phenotypic characterizations, each strain is considered to represent a novel species within the genus Thalassotalea, for which the names Thalassotalea psychrophila sp. nov. (type strain SQ149T=MCCC 1K04231T=JCM 33807T), Thalassotalea nanhaiensis sp. nov. (type strain SQ345T=MCCC 1K04232T=JCM 33808T), and Thalassotalea fonticola sp. nov. (type strain S1-1T=MCCC 1K06879T=JCM 34824T) are proposed.

Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvae

The genus Thalassotalea is ubiquitous in marine environments, and up to 20 species have been described so far. A Gram-staining-negative, aerobic bacterium, designated strain PTE2T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PTE2T was closely related to Thalassotalea sediminis N211T (= KCTC 42588T = MCCC 1H00116T) with 97.9% sequence similarity. ANI and in silico DDH values against Thalassotalea species were 68.5-77.0% and 19.7-24.6%, respectively, indicating the novelty of PTE2T. Based on genome-based taxonomic approaches, strain PTE2T (= JCM 34608T = KCTC 82592T) is proposed as a new species, Thalassotalea hakodatensis sp. nov.