Oceanographic habitat and the coral microbiomes of urban-impacted reefs

Abstract

Coral reefs are in decline worldwide. In response to this habitat loss, there are efforts to grow, outplant, and restore corals in many regions. The physical oceanographic habitat of corals—such as sea temperature, waves, ocean currents, and available light—is spatially heterogeneous. We therefore hypothesize that outplant location may affect microbiomes, and ultimately, coral health and restoration success. We evaluated the influence of the physical oceanographic habitat on microbes in wild Porites astreoides and Siderastrea siderea. Tissue samples were collected at four Florida reefs in March, June, and September of 2015. We estimated oceanographic conditions from moored instruments, diver observations, remote sensing data, and numerical models. We analyzed microbiomes using amplicon 16S rRNA high-throughput sequencing data. We found microbial alpha-diversity negatively correlated with in situ sea temperature (which represented both the annual cycle and upwelling), as well as modeled alongshore currents, in situ sea-level, and modeled tide. Microbial beta-diversity correlated positively with significant wave height and alongshore currents from models, remotely-sensed relative turbidity, and in situ temperature. We found that archaea from the order Marine Group II decrease with increases in significant wave height, suggesting that this taxon may be influenced by waves. Also, during times of high wave activity, the relative abundance of bacteria from the order Flavobacteriales increases, which may be due to resuspension and cross-shelf transport of sediments. We also found that bacteria from the order SAR86 increase in relative abundance with increased temperature, which suggests that this taxon may play a role in the coral microbiome during periods of higher temperature. Overall, we find that physical oceanographic variability correlates with the structure of these coral microbiomes in ways that could be significant to coral health.

Rhodobacterales and Rhizobiales Are Associated With Stony Coral Tissue Loss Disease and Its Suspected Sources of Transmission

“…One study identified five bacteria families associated with SCTLD lesions, but none were found across all four coral species examined . Coincident with the initial outbreak of SCTLD, a dredging project at the Port of Miami in 2013-2015 increased sedimentation (Miller et al, 2016;Cunning et al, 2019) and relative turbidity (Rosales et al, 2019) in adjacent reefs. This has led to a controversial hypothesis that sediment is a potential source of transmission of the SCTLD pathogen(s) (Miller et al, 2016;Cunning et al, 2019;Gintert et al, 2019).…”

Considering Commercial Vessels as Potential Vectors of Stony Coral Tissue Loss Disease

“…While ships clearly have the potential to spread pathogens, understanding the likelihood of ship-mediated spread of SCTLD remains challenging given the unknown etiology of the disease. While successful treatment with antibiotics suggests the pathogen(s) may be bacterial ( Aeby et al, 2019 ; Neely et al, 2020 ), we cannot rule out a possible role of free-living or bacteria-infecting viruses, other microorganisms ( Rosales et al, 2020 ), or water quality ( Miller et al, 2016 ; Cunning et al, 2019 ; Rosales et al, 2019 ). Additionally, the potential that SCTLD is caused by a consortium of pathogens complicates development of targeted tests or treatments.…”

Coral persistence despite marginal conditions in the Port of Miami

“…In these areas, unique combinations of environmental factors can lead to outcomes that are difficult to predict using single-taxon, single-stressor studies. Particularly persistent coral species or genotypes may reveal mechanisms of resilience in the genetics of the coral host and/or the associated algal symbionts of the family Symbiodiniaceae 8 , as well as the wider microbiome 9 . These natural associations and molecular mechanisms may ultimately prove useful for increasing the efficacy and efficiency of restoration efforts and are likely critical for maintaining ecosystem function in a rapidly changing world.…”