Seabed morphology is known to influence the dynamics of the physical and chemical properties (e.g. dissolved and particulate organic matter, oxygen saturation and current regimes) of the deep-sea 40 including the upper PBC 41. These properties can potentially influence the composition of microbial communities on CWCs, sediment and the ambient water 26, 6. Coral microbiologists have recognised that there is divergence among microbial communities inhabiting corals, sediments and the ambient water 24. In the present study, divergence in the microbial composition associated with the scleractinian corals, water and sediment samples were observed in the upper PBC (Fig. 1C). However, there was no divergence in the microbial communities in relation to site locations and coral species (Figs. 1A and B), even though geographical distribution can cause differences in host-bacterial composition 36. In this context, observations in relation to CWCs in the present study should be interpreted with caution as only two samples of Madrepora oculata were used.
Shannon’s diversity observed for CWCs in the present study seems to be higher than what has been reported in some microbial studies 3, 16 yet similar to other research 17, 36. Röthig et al. 18 and Hansson et al. 24 observed species-specific differences in coral-associated bacterial composition as well as divergence in bacterial composition across corals and water samples. Meistertzheim et al. 16 reason that differences in the feeding strategies and thermal tolerance between the framework-forming corals L. pertusa and M. oculata are responsible for the structure observed in the host-bacterial community composition. In line with Neulinger et al. 21, this study suggests that variations in water mass does not play a major role in structuring the bacterial communities across the different samples as these were collected between 600–800 m, where the only prevailing water mass is the Eastern North Atlantic Water 19. Nevertheless, inherent local physical conditions (e.g., salinity, pH, temperature and oxygen saturation 14, 10) might have contributed to the observed divergence in microbial composition across the different samples in the present study.
In the present study, Alteromonadales were abundant in non-coral (water and sediment) samples while unclassified Gammaproteobacteria were abundant in corals. Also, between the two coral species, we observed that unclassified Gammaproteobacteria were more abundant in M. oculata than in L. pertusa. In general, we observed that CWCs showed high microbial diversity compared to the surrounding environments. Similarly, Schöttner et al. 26 noticed that bacterial communities associated with coral habitats were significantly more biodiverse than those associated with non-coral habitats due to mucus release of corals which dissolves in the water and can fuel the growth of microbes. Scleractinian corals can produce and release dissolved and particulate organic matter in the form of mucus 42, 43, which microbes use as a source of carbon for growth 44.
Coral associated microbial communities perform different functions that are important to the coral host and ensure the general health and existence of the corals 45. The order-level bacterial communities including Clostridiales, Flavobacteriales, Rhodobacterales and Rickettsiales were consistently represented in relatively high abundance. However, Clostridiales, although detected in great quantity in this study, are generally highly abundant in diseased corals 46. Bacteroidales are often associated with diseased corals 9, 46 while some members are recognised for their antimicrobial protein production 47. Some members of Flavobacteriales contain genes that can perform nitrogen cycling while others have been used for contaminant removal 48, 49. That said, pathogenic forms have also been identified 50 as being overrepresented in stressed corals 18. They have been observed in both azooxanthallate cold-water and zooxanthallate tropical corals 51.
Neulinger et al. 21, associated the distribution of Lophelia pertusa phenotypes in the northeastern Atlantic with the high Rhodobacterales abundance found on the species. According to Neulinger et al. 21, the efficiency of the Rhodobacterales on white Lophelia allows it to adopt to areas of low organic materials in the deep-seas of the northeastern Atlantic and hence their dominance in this part of the ocean. Rhodobacterales are generally widespread in marine environments including on CWCs 25, 17. They have been described as sulfur-and metal-reducing bacterial taxon, are involved in carbon cycling and can be applied as probiotics 52. As this bacterial group occur in high abundance in the present study, it is likely they aid in growth and nutrition of the corals. Also, white Lophelia seems to be the dominant phenotype in the PBC, suggesting that Rhodobacterales may indeed be involved in Lophelia distribution in the northeast Atlantic
Members belonging to the order Rickettsiales have been described as opportunistic, facultative and pathogenic 53, 54, can be found in CWCs 34 and have been associated with hydrocarbon contamination 55. Rickettsiales have also been observed in tropical corals 56 and found in high abundance in healthy corals 57. It is interesting to note that even though the majority of bacterial groups that form the core microbiome in the present study have members which are pathogenic, only a few pathogenic members of Myxococcales have been characterised 58. This bacterial order is ubiquitous and can tolerate extreme environments. They can prey on bacteria and so have been applied as antibiotic, cytotoxic and antiviral compounds 59. Myxococcales are also involved in breakdown of organic carbon and nutrient cycling 60 and have been observed in coral species 61. Many of the bacterial groups identified in this study including Burkholderiales, Rhizobiales, Sphingobacterales, Flavobacteriales and Oceanospirillales have been described to be associated with petroleum hydrocarbons 55. However, there is no data from the upper PBC that suggest that petroleum exploration has been carried out in and around the canyon or that seabed pockmarks formed by hydrocarbon seepage are present. As such their presence may be related to a different function other than oil-degradation. Furthermore, the fact that many of these bacterial order occur in relatively low abundance seem not to be a petroleum degradation characteristic of corals from the upper PBC. It is probable that the dominant bacterial groups detected in the corals in this study are rather involved in the nutrition and growth of these species as suggested by other researchers 21, 16, 36. This claim can be substantiated from the actively growing and well developed CWCs, especially L. pertusa as observed in the upper PBC 19, 41.
Two commonly described bacterial genera Propionibacterium and Endozoicomonas in Lophelia from the Trondheimsfjord 21, Rockall Bank 35, Mediterranean 16 and western Atlantic 36 were not found in our samples. Also, Mycoplasma was reported to be part of L. pertusa microbiome 29, 25, 21 although not observed in this study nor in a study by Meistertzheim et al. 16. Also, Novosphingobium which was characterised to be part of L. pertusa core microbiome 36 was observed in only two sediment samples (SS2 and SS3) in this study while other studies on the same species failed to discover it, either on the coral or the surrounding environment 21, 35. Interestingly, we observed TM7, which was first recorded by Neulinger et al. 21 in CWCs from the Trondheimsfjord and later by Van Bleijswijk et al. 35 from the Rockall Bank. Neulinger et al. 21 noted the possible similarities in cross-taxa bacterial composition, as TM7 had previously been observed in the sponge Chondrilla nucula 62. Also, there seem to be a regional effect in the distribution of TM7 as it was observed in the northeastern Atlantic (this study; 21, 35), western Atlantic 25 but not the Mediterranean 16. That said, it is difficult to draw regional trends and patterns from host-bacterial composition. Meistertzheim et al. 16 and Kellogg et al. 36 have highlighted methodological variations in bacterial community profiling as possible reason for the compositional differences. For example, host-bacterial compositional disparities can arise from unique regions of the 16S RNA gene 63, microbial database used and/or number of sequences per sample 36, sampling technique 25 and sequencing platform and/or bioinformatic software 64, 65. We find that the cross-taxa phenomenon described by Neulinegr et al. 21 to be most likely the case. The dominant microbial groups associated with the CWCs L. pertusa and M. oculata were Proteobacteria, Acidobacteria, Gemmatimonadetes, Actinobacteria, Thaumarchaea, which have also been found in sponges from reef environments in the deep-sea 66, 21, 35, 36. Recently, Rix et al. 43 described how coral mucus nourishes different sponge species. The interaction between corals and sponges through mucus release demonstrates the importance of corals to the sponge-bacterial community and possibly other reef-associated organisms. For instance, the bacterium Tenacibaculum maritimum was represented in the corals in low abundance. This species can cause diseases in reef fishes 67.
Generally in the corals, relatively high abundances of bacteria belonging to the genera Pseudomonas, Pseudoalteromonas and Photobacterium were observed. They form part of the core microbiome (100% coral samples coverage). Species of Pseudoalteromonas are clinically relevant and perform probiotic functions 68. P. porphyrae has the potential to increase the growth of some marine species in a stressful environment while P. luteoviolacea is shown to produce antibacterial compounds 69, 70. P. luteoviolacea was observed in the scleractinian corals Porites. lutea 63, L. pertusa 33 and in the present study. Also, Pseudomonas has been observed in CWCs 3, 16. It is ubiquitous, possesses probiotic properties and has been reported in soft corals 71. Members of the genus Photobacterium are opportunistic with some holding probiotic properties 72. Photobacterium in a symbiotic relationship with host organism can aid chitin digestion 73. Röthig et al. 18 identified P. angustum as part of the core microbiome (100% coral samples coverage) whilst P. angustum and P. damselae were observed in a few samples in low abundances in the present study. P. angustum can suppress virulence genes 74 while P. damselae is pathogenic 75.
Also in this study, the genus Vibrio including V. shilonii (0.22%) were observed in a couple of coral samples, which contradicts the findings of researchers who have described Vibrio usually as part of the core microbiome 76. That said, both genera Vibrio and Photobacterium belong to the family Vibronaceae and have been characterised as opportunistic pathogens whose virulence is influenced by the environment 77, 21. For example P. damselae and V. shilonii can cause harm to their hosts in warm environments 77, suggesting that their pathogenic activities to the CWCs are somewhat being suppressed by the cold temperatures of the deep. Several members of Vibrio also have probiotic properties, digestive enzymes (e.g. amylase, lipase, cellulase and chitinase) that aid in digestion, fix nitrogen in anoxic or limiting oxygen conditions 73, and have been observed in healthy and/or diseased tropical corals 33 as well as CWCs 35, 17. It is thus more likely that the bacterial species P. damselae, Tenacibaculum maritimum and V. shilonii observed in the present study (where only healthy corals were collected) are opportunistic pathogens that only contribute to the overall health of the corals. Other recognised important pathogenic species represented in a few samples in low abundance include Flexispiras rappini, Serratia mercens, Helicobacter cinaedi and Salmonella enterica, Cardiobacterium valvarum. Nevetheless, the relatively low abundant pathogenic bacterial species render them less important to the general health and functioning of the corals compared to the more abundant and dominant probiotic bacterial groups which play a major role in disease-prevention, nutition, and growth of the corals in the PBC.
Many archaeal taxa have been identified in CWCs (this study; 35). Thaumarchaeota was represented in high abundance in all the coral samples except HF5 while Thermoplasmata was the only taxon present in sample FF3 (Madrepora sample). Both Thaumarchaeota and Thermoplasmata were identified in Lophelia samples from the Rockall Bank 35. Members of this taxon can extract and metabolise amino acids from the water column as well as reduce sulfur 78. Lophelia as an opportunistic feeder can take up dissolved amino acids from the water column and incorporate them into its cells 79, 80. Thus, the dominance of Thaumarchaeota on the coral samples could be a selective mechanism which parallels with the feeding strategy of Lophelia. Our work corroborates with Van Bleijswijk et al. 35 who identified Thaumarchaeota as the single most important dominant archaeal taxa of CWCs (e.g. L. pertusa). Also, Parvarchaea has been described to be associated with petroleum hydrocarbon 55. Interestingly, we note that all archaea in FF3 (Madrepora coral sample) from the flank are Thermoplasmata which is absent from SF2 (Madrepora coral sample), but highly abundant in only SS2 (sediment sample) which is also from the flank, suggesting that Thermoplasmata could be more associated with location in the canyon rather than the corals.
The current trends of deep-sea warming due to climate change and anthropogenic activities (e.g. deep-sea mining and bottom-fishing 81) put the corals in a vulnerable state, considering that most of the pathogenic microbes observed can cause disease in warmer and polluted environments. Although the coral microbiome suggests the coral are healthy with low abundances of pathogen, higher abundances of pathogens observed in the surrounding water and sediment suggest that this may change if corals become stressed. Appropriate measures ought to be implemented to reverse the current trends of climate change to protect the teeming corals of the deep or risk losing them, a situation that can arise from a shift from a generally benign and useful host-associated microbial community to pathogenic and disease-causing microbes as have been described for tropical corals elsewhere 9, 46.