Complete genome sequence of Serinicoccus sp. JLT9, an actinomycete isolated from the shallow-sea hydrothermal system

Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms

BACKGROUND

Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how these opportunists are involved in the transformation of dissolved organic matter (DOM) when blooms occur and the subsequent impacts on biogeochemical cycles.

RESULTS

We used a combination of genomic, proteomic, and metabolomic approaches to study bacterial diversity, genome traits, and metabolic responses to assess the source and lability of DOM in a spring coastal bloom of Akashiwo sanguinea. We identified molecules that significantly increased during bloom development, predominantly belonging to amino acids, dipeptides, lipids, nucleotides, and nucleosides. The opportunistic members of the bacterial genera Polaribacter, Lentibacter, and Litoricola represented a significant proportion of the free-living and particle-associated bacterial assemblages during the stationary phase of the bloom. Polaribacter marinivivus, Lentibacter algarum, and Litoricola marina were isolated and their genomes exhibited streamlining characterized by small genome size and low GC content and non-coding densities, as well as a smaller number of transporters and peptidases compared to closely related species. However, the core proteomes identified house-keeping functions, such as various substrate transporters, peptidases, motility, chemotaxis, and antioxidants, in response to bloom-derived DOM. We observed a unique metabolic signature for the three species in the utilization of multiple dissolved organic nitrogen compounds. The metabolomic data showed that amino acids and dipeptides (such as isoleucine and proline) were preferentially taken up by P. marinivivus and L. algarum, whereas nucleotides and nucleosides (such as adenosine and purine) were preferentially selected by L. marina.

CONCLUSIONS

The results suggest that the enriched DOM in stationary phase of phytoplankton bloom is a result of ammonium depletion. This environment drives genomic streamlining of opportunistic bacteria to exploit their preferred nitrogen-containing compounds and maintain nutrient cycling. Video abstract.

Serinicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island

A Gram-stain-positive, non-flagellated, non-gliding, coccoid bacterial strain, designated JLT9^T, was isolated from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan, ROC. Strain JLT9^T was aerobic, chemoheterotrophic and grew optimally at 35 °C, at pH 6.0 and in the presence of 2.5 % (w/v) NaCl. Strain JLT9^T exhibited highest 16S rRNA gene sequence similarity to Serinicoccus marinus DSM 15273^T (98.83 %). Phylogenetic trees based on 16S rRNA gene sequences revealed that strain JLT9^T belonged to the genus Serinicoccus, clustering with Serinicoccus marinus JC1078^T, Serinicoccus profundi MCCC 1A05965^T, Serinicoccus sediminis GP-T3-3^T and Serinicoccus chungangensis CAU9536^T. The digital DNA-DNA genome hybridization values between strain JLT9^T and the closest related strain S. marinus DSM 15273^T was 34.30 %. The DNA G+C content was 72.43 mol%. The dominant fatty acids were identified as iso-C_15 : 0 (41.4 %) and iso-C_16 : 0 (24.7 %). The polar lipids of strain JLT9^T comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified glycolipid and an unidentified phospholipid. The predominant isoprenoid quinone was MK-8 (H₄). The cell wall contained ornithine and serine, and no diaminopimelic acid. On the basis of phylogenetic data and several distinct phenotypic characteristics, strain JLT9^T represents a novel species of the genus Serinicoccus, for which the name Serinicoccus hydrothermalis sp. nov. is proposed. The type strain is JLT9^T (=CGMCC 1.15779^T=JCM 31502^T).

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity

Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile genetic potential to adapt to the unique environmental conditions.