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

Abstract

BackgroundSimilar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis.Methods & ResultsSurface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus. However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons.DiscussionSignificant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013–2014 dry season (October–April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014–16 El Niño event.

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

“…All 240 sediment samples were processed for DNA analyses. Preparation of DNA samples from sediment and water acquired for high-throughput 16S rRNA gene sequencing were conducted as described in detail in previous studies ( Campbell et al, 2015 ; O’Connell et al, 2018 ; Easson & Lopez, 2019 ). Briefly, after pelleting 1–2 grams of sediment, genomic DNA was extracted using the DNeasy PowerLyzer Powersoil kit (12855; Qiagen, Hilden, Germany) following standard protocols.…”

“…These primers have been selected because they can amplify and provide the most comprehensive diversity of both Bacteria and Archaea. The resulting 16S rRNA gene libraries were purified with AMPure beads and prepared for sequencing on an Illumina MiSeq following the manufacturer’s protocol for library preparation and Miseq Reagent Kit v3 for 250 bp paired end reads and with custom indices needed for protocol outlined by the Earth Microbiome Project ( Thompson et al, 2017 ; O’Connell et al, 2018 ; Easson & Lopez, 2019 ).…”

“…For example, Peixoto et al (2021) have shown certain microbial symbionts positively affect and protect coral species. O’Connell et al (2018) provides a weekly sampling of PEI surface waters and found a fairly stable microbial composition, with increased microbial abundance and richness in the early spring and late summer months, most likely caused by increased temperatures, UV radiation, and precipitation. Thus, understanding microbial dynamics positively impacts the health of human and resident marine life.…”

Microscopic and Genetic Characterization of Bacterial Symbionts With Bioluminescent Potential in Pyrosoma atlanticum

“…The 16S rRNA gene fragment was the target for bacterial identification via high throughput DNA sequencing (O'Connell et al, 2018;Easson and Lopez, 2019). Samples were prepared for sequencing following the 16S Illumina Amplicon Protocol per the Earth Microbiome Project (Kuczynski et al, 2011;Thompson et al, 2017).…”

Oceanographic habitat and the coral microbiomes of urban-impacted reefs

“…Hence, any influence that sea-level (including tides) had on these microbiomes was more likely due to low-frequency variability in currents and/or transports forced by sea-level gradients, rather than to the sea-level variations themselves. In particular, low-frequency variability from both wind setup and tide can drive cross-shelf transport (Castelao et al, 2010; Lee & Smith, 2002; Leichter et al, 1996), affecting microbial connectivity (Säwström et al, 2016), flushing times (Castelao et al, 2010), and the availability of prey and nutrient inputs (Leichter, Stewart & Miller, 2003; Monismith et al, 2010; O’Connell et al, 2018). Such effects may serve to reduce microbial alpha-diversity on reefs (O’Connell et al, 2018) and may explain the correlations we observed.…”