Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats

As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.

Motilimonas eburnea gen. nov., sp. nov., isolated from coastal sediment

A novel Gram-stain-negative, non-spore-forming, facultatively anaerobic bacterium, designated YH6T, was isolated from marine sediment in Weihai, China. Cells of starin YH6T were motile, straight rods that formed ivory-white colonies on 2216E agar. Optimal growth occurred at 28-33 °C (range 15-37 °C), in the presence of 2-4 % (w/v) NaCl (range 1-8 %) and at pH 7.5-8.5 (range pH 6.5-9.0). The sole respiratory lipoquinone was Q-8, and the major fatty acids (>10 %) were C16 : 0 and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The polar lipids profile of the novel strain consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and several other unknown lipids (phospholipids, lipid and phosphoaminolipid). The G+C content of the genomic DNA was 46.5 mol%. The closest type strain phylogenetically to strain YH6T was Vibrio variabilis (92.99 % 16S rRNA gene sequence similarity) followed by Paramoritella alkaliphila (92.55 %), Pseudoalteromonas aurantia (92.20 %) and Pseudoalteromonas citrea (92.20 %). Phylogenetic analysis of the 16S rRNA gene sequence placed the novel strain in the order Alteromonadales, class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence data as well as physiological and biochemical characteristics, we concluded that strain YH6T represents a novel species of a new genus. We propose the name of Motilimonas eburnea gen. nov., sp. nov. for this novel species. The type strain of the novel species is YH6T (=KCTC 42594T=MCCC 1H00122T).

Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field

A novel psychrophilic, marine, bacterial strain designated BJ-1(T) was isolated from the Iheya North hydrothermal field in the Okinawa Trough off Japan. Cells were Gram-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 16 °C, with the optimum between 9 and 12 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the closest relatives of strain BJ-1(T) were Shewanella denitrificans OS-217(T) (93.5% similarity), Shewanella profunda DSM 15900(T) (92.9%), Shewanella gaetbuli TF-27(T) (92.9%), Paraferrimonas sedimenticola Mok-106(T) (92.1%) and Ferrimonas kyonanensis Asr22-7(T) (91.7%). The major respiratory quinone was Q-8. The predominant fatty acids were C(16:1)ω7c and C(16:0). The G+C content of the novel strain was 40.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain BJ-1(T) represents a novel species in a new genus, for which the name Psychrobium conchae gen. nov., sp. nov. is proposed. The type strain of Psychrobium conchae is BJ-1(T) ( =JCM 30103(T) =DSM 28701(T)).

Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides

The functional role of the bacterial organisms in the reef ecosystem and their contribution to the coral well-being remain largely unclear. The first step in addressing this gap of knowledge relies on in-depth characterization of the coral microbial community and its changes in diversity across coral species, space and time. In this study, we focused on the exploration of microbial community assemblages associated with an ecologically important Caribbean scleractinian coral, Porites astreoides, using Illumina high-throughput sequencing of the V5 fragment of 16S rRNA gene. We collected data from a large set of biological replicates, allowing us to detect patterns of geographical structure and resolve co-occurrence patterns using network analyses. The taxonomic analysis of the resolved diversity showed consistent and dominant presence of two OTUs affiliated with the order Oceanospirillales, which corroborates a specific pattern of bacterial association emerging for this coral species and for many other corals within the genus Porites. We argue that this specific association might indicate a symbiotic association with the adult coral partner. Furthermore, we identified a highly diverse rare bacterial 'biosphere' (725 OTUs) also living along with the dominant bacterial symbionts, but the assemblage of this biosphere is significantly structured along the geographical scale. We further discuss that some of these rare bacterial members show significant association with other members of the community reflecting the complexity of the networked consortia within the coral holobiont.

Paramoritella sediminis sp. nov., isolated from marine sediment, and emended descriptions of the genus Paramoritella Hosoya et al. 2009 and Paramoritella alkaliphila

A Gram-negative, facultatively anaerobic, rod-shaped (2.04-1.27 × 0.95-1.25 µm) and motile marine bacterium, designated MEBiC06500(T) was isolated from sediment collected at Daebu Island in the Yellow Sea (37° 20' N 126° 41' E), Korea. 16S rRNA gene sequence analysis revealed that strain MEBiC06500(T) showed high similarity with Paramoritella alkaliphila A3F-7(T) (96.5%). Growth was observed at 10.5-30.2 °C (optimum 23.5 °C), at pH 6.0-9.5 (optimum 8.0) and with 0-5% (optimum 1.5%) NaCl. The predominant cellular fatty acids were C14:0, C16:0, C18:1ω7c and summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c). The DNA G+C content was 56.0 mol%. The respiratory quinone is Q-8. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, one unidentified phospholipid and three unidentified aminolipids were detected as major polar lipids. On the basis of this polyphasic taxonomic data, strain MEBiC06500(T) should be classified as a representative of a novel species in the genus Paramoritella, and the proposed name is Paramoritella sediminis sp. nov. The type strain is MEBiC06500(T) (=KCCM 42977(T)=JCM 18292(T)). Emended descriptions of the genus Paramoritella Hosoya et al. 2009 and Paramoritella alkaliphila are also given.