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

Abstract

Similar 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 and nutrients to surrounding beaches and offshore coral reefs.Understanding the composition and fluctuations of bacterioplankton communities ("microbiomes") in major port inlets is important due to their impacts on surrounding marine environments. We hypothesize annual microbial fluctuations based on seasons (wet vs dry), assessed by high throughput 16S rRNA amplicon library sequencing. Surface water samples were collected weekly for one year, creating a high sampling frequency and fine sampling scale. Over 1.4 million 16S rRNA V4 reads generated a total of 16,384 Operational Taxonomic Units (OTUs) from the PEI habitat. We observed Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria as the most dominant phyla. Analysis of potentially pathogenic genera show the presence of Staphylococcus and Bacillus, albeit at lower relative abundances during peak shipping and tourist months (November -April), thus underscoring their relatively low presence. Statistical analyses indicated significant alpha diversity differences when comparing microbial communities with respect to time.This observation probably stems from the low community richness and abundance in August, which had lower than average rainfall levels for Florida's wet season. The lower rainfall levels may have contributed to less runoff, and subsequently fewer bacterial groups being introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month and season. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages, which may have driven the significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were also observed in these months, possibly creating favorable bacterial growth conditions. To our knowledge, this study represents the first to sample a large port at this fine sampling 37 Analysis of potentially pathogenic genera show the presence of Staphylococcus and Bacillus, 38 albeit at lower relative abundances during peak shipping and tourist months (November -April), 39 thus underscoring their relatively low risk for public health concerns.40 Discussion. Statistical analyses indicated significant alpha diversity differences when comparing 41 microbial communities with respect to time. This observation probably stems from the low 42 community richness and abundance in August, which had lower than average rainfall levels for 43 Florida's wet season. The lower rainfall levels may have contributed to less runoff, and 44 subsequently fewer bacterial groups being introduced into the port surface waters.45 Bacterioplankton beta diversity differed significantly by month and season. The 2013-2014 dry 46 season (October-April), was warmer and wetter than historical averages, which may have driven 47 the significant differences in beta diversity. Increa...

Peer Review #1 of "Oceanographic habitat and the coral microbiomes of urban-impacted reefs (v0.1)"

“…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 (Sawstrom et al 2016), flushing times (Castelao et al 2010), and the availability of prey and nutrient inputs (Leichter et al 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.…”