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

Abstract

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.

Sediment source and dose influence the larval performance of the threatened coralOrbicella faveolata

“…Finally, we showed that sediments collected near the Port contained higher abundances of potentially pathogenic bacteria compared to Reef sediments, aligning with previous work conducted in the vicinity of the Port Everglades inlet [65, 72]. These studies highlight the importance of monitoring for potential contaminants in sediments and changes in the microbiome which may result from dredging.…”

“…Relative abundance analysis of the most abundant taxa showed that Desulfobacterales were unique to the Port sediments (Fig 3C). These taxa have been found to be enriched in microbial communities from other inlets in southeast Florida [65] and have also been associated with black band disease [66], suggesting that this bacterial taxa may play a role in coral health and its enrichment in Port sediments may have contributed to the reduced survival and settlement in larvae exposed to both low- and high-doses of these sediments (Fig 2A). Moreover, Desulfobacterales are anaerobic sulfate-reducing bacteria [67] that reduce sulfate (SO 4 2− ) to hydrogen sulfide (H 2 S).…”

“…Sediments may also act as vectors for the transmission of diseases such as Stony Coral Tissue Loss Disease [22], which is documented to have appeared for the first time near Port Miami in 2014 [70, 71]. Also, bacteria genera from two common human pathogens, Staphylococcus and Streptococcus , have been found across multiple time points in surface water and sediment samples near Port Everglades [65, 72], another southeast Florida inlet subject to dredging impacts. Our findings add to these studies and also suggest that port inlets may carry potentially pathogenic bacteria which may be transported to nearby reefs through various sediment transport processes (natural or anthropogenic), resulting in potential exposure to coral larvae and other downstream health impacts.…”

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“…Relative abundance analysis of the most abundant taxa showed that Desulfobacterales were unique to the Port sediments (Fig 3C). These taxa have been enriched in microbial communities from other inlets in southeast Florida [71] and have also been associated with black band disease [72], suggesting a role in coral health. Moreover, Desulfobacterales are anaerobic sulfate-reducing bacteria [73] that reduce sulfate (SO 4 2−…”

“…Sediments may also act as vectors for the transmission of diseases such as Stony Coral Tissue Loss Disease [22], first reported in outbreak levels (>5% prevalence) in waters of Miami-Dade County around September 2014 ( [76,77] but see [78,79]), while the Port of Miami expansion dredging project was underway. Also, bacteria genera from two common human pathogens, Staphylococcus and Streptococcus, have been found across multiple time points in surface water and sediment samples near Port Everglades [71,80], another southeast Florida inlet subject to dredging impacts. Our findings add to these studies and also suggest that port inlets may carry potentially pathogenic bacteria which may be transported to nearby reefs through various sediment transport processes (natural or anthropogenic), resulting in potential exposure to coral larvae and other downstream health impacts.…”