Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach

Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov

A strictly aerobic Gram-negative bacterium, designated 2012CJ34-2T, was isolated from marine sponge to Chuja-do in Jeju-island, Republic of Korea and taxonomically characterized. Cells were catalase- and oxidase-positive, and non-motile rods (without flagella). Growth was observed at 15-42 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7), and in the presence of 0.5-10% (w/v) NaCl (optimum, 2-3%). The major cellular fatty acid and respiratory quinones were identified summed feature 3 (C16:1 ω7c/C16:1 ω6c), and Q-8 and Q-9, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified phospholipids, and three unidentified lipids. The DNA G+C content was 48.0 mol%. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences showed that strain 2012CJ34-2T formed a clade with Parendozoicomonas haliclonae S-B4-1UT and Sansalvadorimonas verongulae LMG 29871T within the family Endozoicomodaceae. Genome relatedness values, including dDDH, ANI and AF, and AAI and POCP, among strain 2012CJ34-2T, P. haliclonae S-B4-1UT, and S. verongulae LMG 29871T were within the range of the bacterial genus cut-off values. Based on the phylogenetic, chemotaxonomic, and genomic analyses, strain 2012CJ34-2T represents a novel bacterial species of the family Endozoicomodaceae, for which the name Parendozoicomonas callyspongiae sp. nov. is proposed. The type strain is 2012CJ34-2T (= KACC 22641T = LMG 32581T). Additionally, we proposed the reclassification of Sansalvadorimonas verongulae of the family Hahellaceae as Parendozoicomonas verongulae of the family Endozoicomonadaceae.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

High-Quality Genome Sequences of Two Octocoral-Associated Bacteria, Endozoicomonas euniceicola EF212T and Endozoicomonas gorgoniicola PS125T

Endozoicomonas euniceicola EF212^T and Endozoicomonas gorgoniicola PS125^T were isolated from soft corals (Eunicea fusca and Plexaura sp., respectively) and sequenced using a PacBio Sequel IIe sequencer. This is the first report of the genome sequences of culturable octocoral-isolated Endozoicomonas strains.

Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral

BACKGROUND

Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of Endozoicomonas species, genome analysis has been limited due to contamination of host-derived sequences and difficulties in culture and metagenomic analysis. Therefore, the evolutionary and functional potential of individual Endozoicomonas species symbiotic with the same coral species remains unresolved.

RESULTS

In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genomes (SAGs) for uncultured coral-associated Endozoicomonas spp. We obtained seven novel Endozoicomonas genomes and quantitative bacterial composition from Acropora tenuis corals at four sites in Japan. Our quantitative 16S rRNA gene and comparative genomic analysis revealed that these Endozoicomonas spp. belong to different lineages (Clade A and Clade B), with widely varying abundance among individual corals. Furthermore, each Endozoicomonas species possessed various eukaryotic-like genes in clade-specific genes. It was suggested that these eukaryotic-like genes might have a potential ability of different functions in each clade, such as infection of the host coral or suppression of host immune pathways. These Endozoicomonas species may have adopted different host adaptation strategies despite living symbiotically on the same coral.

CONCLUSIONS

This study suggests that coral-associated Endozoicomonas spp. on the same species of coral have different evolutional strategies and functional potentials in each species and emphasizes the need to analyze the genome of each uncultured strain in future coral-Endozoicomonas relationships studies. Video Abstract.

Diversity assessment of photosynthesizers: comparative analysis of pre-cultivated and natural microbiome of sediments from Cerrado biome in Maranhão, Brazil

Photosynthetic microorganisms are important components of most ecosystems and have important roles regarding biogeochemical cycles and the basis of the trophic chain. However, they sometimes are present in low abundance compared to other heterotrophic organisms. The Chapada das Mesas National Park (PNCM) is a Conservation Unit in Brazilian Cerrado biome, which is considered a hotspot for biodiversity conservation and possesses important rivers, waterfalls, and springs with economical and touristic importance. The aim of this study was to perform a comparative analysis of enriched and total microbiome of sediments to understand the impact of pre-cultivation in discovery of underrepresented groups like photosynthesizers. All sediment samples were cultivated in BG-11 medium under illumination to enrich for photosynthetic microorganisms and both the raw samples and the enriched ones were submitted to DNA extraction and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene on the Ion Torrent platform. The reads were analyzed using QIIME2 software and the Phyloseq package. The enrichment allowed detection and identification of many genera of cyanobacteria in the Chapada das Mesas National Park (PNCM), which would probably not be possible without the combination of approaches. A total of 58 groups of photosynthetic microorganisms were classified in the samples from the enrichments and their relative abundance based on amplified 16S rRNA sequences were estimated, highlighting the genus Synechocystis which represented 10.10% of the abundance of the phylum Cyanobacteria and the genus Dunaliella, which represented 45.66% of the abundance of algae as the most abundant groups at the PNCM. In the enrichments, microorganisms from the phyla Proteobacteria (45.2%), Bacteroidetes (18%), and Planctomycetes (3.3%) were also identified, since there are ecological associations between the photosynthetic community and other groups of heterotrophic microorganisms. As for the functional analysis, metabolic functions associated with methanotrophy and methylotrophy, hydrocarbon degradation, phototrophy, and nitrogen fixation were predicted. The results highlight a great diversity of photosynthetic microorganisms in Cerrado and the importance of using a combination of approaches when analyzing target groups which are usually underrepresented such as cyanobacteria and microalgae.

Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle

Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.

Proposal of Zooshikellaceae fam. nov. to accommodate the genera Zooshikella and Spartinivicinus and reclassification of Zooshikella marina as a later heterotypic synonym of Zooshikella ganghwensis based on whole genome sequence analysis

The genus Spartinivicinus, affiliated to the class Gammaproteobacteria, is an important marine member that produces prodiginines. Currently, its taxonomic assignment to family level is not well presented. Phylogeny of 16S rRNA gene sequences indicated that Spartinivicinus forms a monophyletic clade with Zooshikella, which is neighboured by Aestuariirhabdus of the family Aestuariirhabdaceae and another monophyletic clade of the family Endozoicomonadaceae. The 16S rRNA gene of Spartinivicinus ruber S2-4-1H^T had sequence similarities to those of Aestuariirhabdus litorea GTF13^T, Zooshikella members and Endozoicomonas members of 93.4%, 93.2-93.4  and <92.5 %, respectively. Phylogenomic analysis based on 120 bacterial conserved single-copy genes highly supported placing Spartinivicinus as a sister member of Zooshikella, neighboured by Aestuariirhabdaceae and Endozoicomonadaceae members, indicating that Spartinivicinus and Zooshikella could be considered to belong to the same family. Thus, Zooshikellaceae fam. nov. is proposed to accommodate the two genera. Colonies of Spartinivicinus and Zooshikella are red-pigmented, which is different from Aestuariirhabdus (pale-yellow pigmented). The major respiratory quinone of S. ruber was ubiquinone (Q-9), similar to Zooshikella, but distinct from Aestuariirhabdus (Q-9 and Q-8). The predominant fatty acids and polar lipids of Spartinivicinus also showed a similar patterns to Zooshikella, but they were different from Aestuariirhabdus. Lastly, Spartinivicinus possessed a genome size of 6.68 Mbp and DNA G+C content of 40.1mol%, similar to Zooshikella, but much larger than Aestuariirhabdus. In addition, the 16S rRNA genes of Z. ganghwensis JC2044^T and Z. marina JC333^T possess sequence similarity of 99.79 %. Whole genome comparisons indicated that they shared 79.8 % digital DNA-DNA hybridization, 97.78 % average nucleotide identity and 97.31 % average amino acid identity values. Activities of catalase and oxidase for the two strains were positive. Hydrolysis of skimmed milk and Tweens (40, 60 and 80) was positive. Interestingly, the two strains produced different kinds of prodiginines. We propose that Z. marina is a later heterotypic synonym of Zooshikella ganghwensis.

Aestuariirhabdus litorea gen. nov., sp. nov., isolated from a sea tidal flat and proposal of Aestuariirhabdaceae fam. nov

A Gram-negative, moderately halophilic and facultatively aerobic bacterium, designated strain GTF13^T, was isolated from a sea tidal flat. Cells were curved rods and motile by a single polar flagellum showing catalase and oxidase activities. Growth was observed at 20-37 °C, pH 5.0-8.5 and 1.0-6.0 % (w/v) NaCl. Strain GTF13^T contained C_16:0, summed feature 3 (comprising C_16 : 1  ω6c/C_16 : 1  ω7c), summed feature 8 (comprising C_18 : 1  ω6c/C_18 : 1  ω7c) and C_12 : 0 3-OH as major fatty acids and ubiquinone-9 and ubiquinone-8 as major quinones. Phosphatidylethanolamine and two unidentified phospholipids were detected as major polar lipids. The G+C content of the genomic DNA was 59.8 mol%. Strain GTF13^T was most closely related to Simiduia agarivorans SA1^T, Endozoicomonas montiporae CL-33^T and Pseudomonas segetis FR1439^T, belonging to different families or orders of the class Gammaproteobacteria, with less than 92.0 % 16S rRNA gene sequence similarities. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GTF13^T formed a phylogenetic lineage with the family Litoricolaceae, but the genome-based phylogenomic tree showed that strain GTF13^T formed a distinct phylogenetic lineage within the order Oceanospirillales. The very low 16S rRNA gene sequence similarities and distinct phylogenetic relationships, together with distinct phenotypic and chemotaxonomic properties, served to differentiate strain GTF13^T from phylogenetically closely related families. Here, strain GTF13^T is proposed as a novel genus and species, for which the name Aestuariirhabdus litorea gen. nov., sp. nov. is proposed, within a new family Aestuariirhabdaceae fam. nov. of the order Oceanospirillales. The type strain is GTF13^T (=KACC 19788^T=JCM 32043^T).

Endozoicomonas coralli sp. nov., isolated from the coral Acropora sp

A novel bacterium, designated strain Acr-12^T, was isolated from the coral Acropora sp. off coast of Southern Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Acr-12^T belonged to the genus Endozoicomonas and had closest phylogenetic identity to Endozoicomonas acroporae Acr-14^T (98.7%) and Endozoicomonas atrinae WP70^T (97.8%). Cells of strain Acr-12^T were Gram-negative, aerobic, non-motile, poly-β-hydroxybutyrate-accumulating, rod-shaped and formed creamy white colonies. Optimal growth occurred at 30 °C, pH 7, and in the presence of 3% NaCl. Strain Acr-12^T contained summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and C_16:0 as the predominant fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant isoprenoid quinone was Q-9. The genomic DNA G + C content was 49.6 mol%. The DNA-DNA relatedness of strain Acr-12^T with respect to the closest species of the genus Endozoicomonas was less than 30%. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Endozoicomonas. On the basis of the genotypic, chemotaxonomic, and phenotypic data, strain Acr-12^T represents a novel species in the genus Endozoicomonas, for which the name Endozoicomonas coralli sp. nov. is proposed. The type strain is Acr-12^T (= BCRC 80921^T = KCTC 42900^T).

Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity

Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity.

Description of Sansalvadorimonas verongulae gen. nov., sp. nov., a gammaproteobacterium isolated from the marine sponge Verongula gigantea

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain RKSG058^T, was isolated from the marine sponge Verongula gigantea, collected off the west coast of San Salvador, The Bahamas. Phylogenetic analyses based on 16S rRNA gene sequences revealed that RKSG058^T formed a distinct lineage within the family Hahellaceae (order Oceanospirillales, class Gammaproteobacteria), and was most closely related to the genus Endozoicomonas, with sequence similarities to members of this genus ranging from 92.0 to 93.7 %. Optimal growth occurred at 30 °C, at pH 7 and in the presence of 2-3 % (w/v) NaCl. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The major and minor respiratory quinones were Q-9 and Q-8, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid and five unidentified lipids. The DNA G+C content was 42.3 mol%. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strain RKSG058^T represents the first cultured isolate of a novel bacterial genus and species within the family Hahellaceae, for which the name Sansalvadorimonas verongulae gen. nov., sp. nov. is proposed. The type strain of Sansalvadorimonas verongulae is RKSG058^T (=TSD-72^T=LMG 29871^T). An emended description of the genus Kistimonas is provided.

Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil

Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67E^T and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47^T and Alteromonas macleodii ATCC 27126^T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67E^T and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A. macleodii ATCC 27126^T and A. marina SW-47^T. The DNA G + C contents of PEL67E^T and PEL68C were 44.5%. The phenotypic features that differentiate PEL67E^T and PEL68C strains from their close neighbors were assimilation of galactose and activity of phosphatase, and lack of mannitol, maltose, acetate, xylose and glycerol assimilation and lack of lipase, α and β-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67E^T (= CBAS 610^T = CAIM 1925^T).

Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas

Two Gram-stain-negative, facultative anaerobic, motile, rod-shaped strains, S-B4-1U^T and JOB-63a, forming small whitish transparent colonies on marine agar, were isolated from a sponge of the genus Haliclona. The strains shared 99.7% 16S rRNA gene sequence identity and a DNA-DNA hybridization value of 100%, but were differentiated by genomic fingerprinting using rep-PCRs. 16S rRNA gene sequence phylogeny placed the strains as a sister branch to the monophyletic genus Endozoicomonas (Oceanospirillales; Gammaproteobacteria) with 92.3-94.3% 16S rRNA gene sequence similarity to Endozoicomonas spp., 91.9 and 92.1% to Candidatus Endonucleobacter bathymodiolin, and 91.9 to 92.1% to the type strains of Kistimonas spp. Core genome based phylogeny of strain S-B4-1U^T confirmed the phylogenetic placement. Major fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and 8 (C_18:1 ω7c/C_18:1 ω6c) followed by C_10:0 3-OH, C_16:0, and C_18:0. The G+C content was 50.1-51.4mol%. The peptidoglycan diamino acid of strain S-B4-1U^T was meso-diaminopimelic acid, the predominant polyamine spermidine, the major respiratory quinone ubiquinone Q-9; phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were major polar lipids. Based on the clear phylogenetic distinction, the genus Parendozoicomonas gen. nov. is proposed, with Parendozoicomonas haliclonae sp. nov. as type species and strain S-B4-1U^T (=CCM 8713^T=DSM 103671^T=LMG 29769^T) as type strain and JOB-63a as a second strain of the species. Based on the 16S rRNA gene sequence phylogeny of the Oceanospirillales within the Gammaproteobacteria, the Endozoicomonaceae fam. nov. is proposed including the genera Endozoicomonas, Parendozoicomonas, and Kistimonas as well as the Candidatus genus Endonucleobacter.

Ecogenomics and Taxonomy of Cyanobacteria Phylum

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

Endozoicomonas acroporae sp. nov., isolated from Acropora coral

Strain Acr-14^T, isolated from Acropora coral, was characterized by using a polyphasic taxonomy approach. Cells of strain Acr-14^T were Gram-stain-negative, aerobic, non-motile, poly-β-hydroxybutyrate-accumulating, rod-shaped and formed creamy white colonies. Optimal growth occurred at 30 °C, pH 7 and in the presence of 2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Acr-14^T belonged to the genus Endozoicomonas and was most closely related to Endozoicomonas atrinae WP70^T with sequence similarity of 96.7 %. Strain Acr-14^T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the predominant fatty acids. The predominant isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain Acr-14^T was 49.1 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrated that strain Acr-14^T should be classified as a novel species of the genus Endozoicomonas, for which the name Endozoicomonas acroporae sp. nov. is presented. The type strain is Acr-14^T (=BCRC 80922^T=LMG 29482^T=KCTC 42901^T).

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts

Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25-100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.

Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.