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The Indian River Lagoon (IRL), located on Florida, USA’s east coast, is an Estuary of National Significance and is an important economic and ecological resource. The IRL faces several environmental pressures from freshwater discharges through the St. Lucie Estuary, the accumulation of a fine-grained, highly organic sediment known as “IRL muck”, and metal contamination from agriculture or marinas. Although the IRL has been well studied, little is known about its prokaryotic communities, thus a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial/archaeal communities. It was found that there are statistically different communities present between the IRL and St. Lucie Estuary with the latter exhibiting more obvious microbial seasonality, such as higher Betaproteobacteriales in wet season samples, due to larger changes in porewater salinity. The other most common orders associated with these estuaries were Desulfobacterales, Flavobacteriales, Anaerolineales, and Steroidobacteriales. These communities were more affected by changes in total organic matter and copper than changes in temperature despite the IRL’s unique location along the temperate/subtropical climate transition. This study provides a first look at the prokaryotic communities of sediments in the IRL, allowing it to act as comparision data for future studies.
Bradshaw DJ II, Dickens NJ, Trefry JH, McCarthy PJ (2020) Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance. PLoS ONE 15(10): e0236305. https://doi.org/10.1371/journal.pone.0236305
Clone this repository. You will need a conda environment with Snakemake and Qiime2 installed.