Metagenomic Survey of a Military-Impacted Lagoon in Puerto Rico

Military practices have left a legacy of contamination worldwide. In Puerto Rico, the east part of the populated Vieques Island was used for over fifty years as a bombing range by the Navy. A year after the base was closed in 2003, the impacted area was designated as a Superfund site. Previous studies have shown elevated levels of heavy metals, explosives (e.g. RDX, TNT, HMX), and other toxic chemicals at the site. The Anones Lagoon, located in the middle of the bombing range is one of the most polluted spots within the site. Intermittently, the lagoon is connected through a channel to the Caribbean Sea. In order to describe the microbial diversity and its potential contribution to natural attenuation of explosives, sediment samples have been collected since 2005. Sediment from reference lagoons (San Juan and Cabo Rojo) have also been sampled and analyzed in parallel for comparisons. Total DNA was extracted and sequenced using Ilumina My-Seq platform. Results indicate that Gammaproteobacteria were abundant in all lagoons samples but the Vieques lagoon harbors overall different microbial taxa. Alpha diversity analysis showed that Anones was less diverse compared to the pristine Cabo Rojo lagoon. Importantly, a clear shift was seen in the Anones Lagoon in 2013 compared to 2005, were Halomonas spp. became dominant (up to 25%) while other groups like Marinobacter showed signs of enrichment as well. Interestingly, these groups have been shown to degrade explosive-related chemicals in tropical sediments. Functional gene annotation of the Anones metagenome showed the presence of RDX degradation genes such as cytochrome p450. This study is the first comparative metagenomic survey of lagoons in Puerto Rico that explored the microbial diversity and biodegradation potential at Vieques.