Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome

Abstract

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4–V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75–96%). At the family level, 80–95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia, both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium, was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production.

Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary

“…The compositions of the microbiomes of our focal hosts, as measured by Bray–Curtis and Jaccard indices, do vary significantly across PtC, which is consistent with results from other marine invertebrates including corals (Lema et al ., ; Pantos et al ., ; Kellogg et al ., ) and some sponges (Burgsdorf et al ., ) analysed across various dispersal barriers or large geographic distances. In our case, such differentiation is largely driven by composition of rare taxa and changes in the relative abundance of dominant taxa at each site, as has been seen previously in oyster hemolymph microbiomes (Lokmer et al ., ).…”

Pathway and kinetics of malachite green biodegradation by Pseudomonas veronii

“…Sequences with ≥97% identity were assigned to the same operational taxonomic unit (OTU), and each OTU was considered to represent a species. R software(V2.15.3, https://www.R-project.org) was used for statistical analysis and histogram construction based on the relative abundance of OTUs in the samples 29 . The raw data of JWY, 1-3 is deposited at NCBI SRA database under the project PRJNA601309.…”

Local Variability in Microbiome Composition and Growth Suggests Habitat Preferences for Two Reef-Building Cold-Water Coral Species

“…Specific bacteria have already been identified such as Spirochetes or Endozoicomonas, which are observed in L. pertusa or M. oculata (Kellogg et al, 2009;Meistertzheim et al, 2016), and which may be crucial to the host physiology (Neave et al, 2016). It has also been demonstrated that L. pertusa and M. oculata have different species-specific microbial communities that can be maintained across different locations (Schöttner et al, 2012;Kellogg et al, 2017;Jensen et al, 2019). In addition, the bacterial community composition of L. pertusa can exhibit a strong temporal variability, but also differences within colonies, and between polyps from the same colony, contrary to the M. oculata microbiome, which appears much more stable (Meistertzheim et al, 2016;Galand et al, 2018).…”