Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing

Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs

Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S rRNA ahead of a large-scale port deepening event. For the first time, this study established baseline bacterial community characterizations and their patterns of diversity prior to and after a maintenance dredging event. PEI samples were collected for two consecutive years 2020 (Phase I, before maintenance dredging) and 2021 (Phase II, after maintenance dredging) from PEI sediments and adjacent coral reef sediments. In spite of their proximity and tidal connections through the PEI, reef and PEI sediment microbial communities were distinct. Changes in microbial diversity within the intracoastal waterway (ICW), a route for community exchange or transfers, were the greatest after maintenance dredging occurred. Microbial diversity in reef sediments also changed after dredging, indicating potential influence from resuspended sediments due to an associated increase in trace metals and decrease in cyanobacterial diversity. Sediments were identified as a possible source of human and coral pathogens, although dredging did not affect the relative abundances of these indicator microorganisms. This study highlighted the utility and relative ease of applying current molecular ecology methods to address macroscale questions with environmental management ramifications.

Oceanographic habitat and the coral microbiomes of urban-impacted reefs

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.