Analysis of Sediments from Port Everglades Inlet (PEI) for Microbiome Characterization, Phase II

EXECUTIVE SUMMARY

Our laboratory was funded for two years to conduct a study of microbial communities (“microbiomes”) to characterize Port Everglades Inlet (PEI) and reef microbiomes with the standard 16S rRNA gene marker (CRCP Project 13). Phase I was completed in June 2020 (Lopez et al, 2020). This report summarizes Phase II (which we may refer to as 2021 herein) of the same CRCP project that began in 2020, using essentially the same exact collection and laboratory methods, sampling sites and computational analyses. The latter combines DNA sequencing with traditional and novel water chemistry analyses (ion chromatography, high resolution mass spectrometry) to determine the following overarching goals: i) a comprehensive spatial profile of the microbial communities (and potential pathogens) present in PEI sediments (P) and adjacent Florida’s Coral Reef sediments (R); and ii) begin cursory analyses that may link sediment parameters with microbiome profiles.

We realize that the port must be periodically dredged in order to accommodate ship traffic, and so part of the Phase II project design was to characterize PEI microbes after regular operations and maintenance dredging (OED) was carried out. This activity necessarily disturbs bottom sediment which can be resuspended and transported to the reef and other natural habitats. Therefore, we have used state of the art microbial genetics methods, such as high throughput sequencing (HTS) of 16S rRNA amplicon variants, in order to profile the alpha and beta diversity of sediment microbiomes found within Port Everglades Inlet (PEI) and the adjacent Florida’s Coral Reef. This method provides one of the most reliable and fastest ways to obtain a comprehensive profiling of bacterial diversity, including the majority of unculturable taxa.

We have thus expanded analyses by combining the 2020 and 2021 microbiome datasets in order to determine any temporal based changes over the one-year time period. Having two years of microbiome data now increases the power of our analyses and allows us to focus on specific taxa that may have been significantly affected by an operations and maintenance dredging (OED) in 2021.

The CRCP Project 13 Phase II results now provide two time points, and the ability to compare four cohorts of environmental data: 2020 port (P) and reef (R), and 2021 port and reef communities. A large 2021 dataset of over 14 million sequence reads was generated by HTS. This data translates to at least 1097 identified bacterial families in the port and 960 families in the reef. The results indicate several similar findings in microbiomes from last year, as similar microbial taxa can be identified across all four datasets, but with varying relative abundances, dependent on time and location. Again, the most dominant phyla at both site types (P and R) was Proteobacteria, although reef sediments continued to show greater abundances of cyanobacterial taxa. The strongest differences were between 2021 port and reef communities, with the former providing the greatest significant differences in any pairwise comparison of alpha diversity. Port microbiomes also changed between 2020 and 2021 but with weak significance. The taxa contributing to changes in 2021 port communities were mostly anaerobic Archaea and in the Phylum Chloroflexi. The increase of Chloroflexi could be associated with sites P13, P16, P17 in 2021.

Moreover, R communities shifted to appear less structured than 2021 P communities compared to 2020 in beta diversity analyses. In general, the R communities between 2020 and 2021 had an increase of Thaumarchaeota (Archaea), Rhodospirillaceae, and Saprospiraceae (Bacteroidetes). An increase of Chloroflexi could be associated with sites P13, P16, P17 in 2021. Concomitant increases in the Archaeal phyla Euryarchaeota and Crenarchaeota also appeared at these same port sites. Site P14 was the only port site with elevated Chloroflexi in 2020. When chemical profiles were analyzed in the context of the microbiome data, we find less influence of Cd, while total Phosphorus (TP) affected port communities similar to 2020. Potential pathogenic bacterial taxa were once again identified in port and reef communities, but as in 2020 and most cases, they appear as part of the natural community.

Taking both Phase I and II together, the CRCP Project 13 provides an interesting comparison and contrast of microbiomes in a human “built” environment (P) adjacent to nearby “natural” reef environments (R). The two year dataset indicates that microbiomes at most sites are dynamic and can be affected by a temporal gradient. There is evidence of possible acute disturbances via the O&M dredging within the port which could have affected its microbial communities. However, the once a year annual sampling provided by this study cannot account for other possible factors which could have also affected both P and R microbiomes. To determine these factors further, we recommend more frequent sampling, and the application of other informatics tools which can track the transfer of discrete taxa from various locales.