Publicaciones Científicas

Abstract: The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0–5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR’s capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as “Candidatus Biekeibacterium resiliens” gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.

Abstract: The unique microbial communities present on fruit surfaces significantly influence the fermentation process and product quality of artisanal cider production, constituting a microbial terroir analogous to that recognized in viticulture. In this study, we investigated the microbial composition and diversity associated with the apple varietals (Empire, Golden Delicious, and Idared) cultivated by two different orchard producers in the Hudson River Valley of New York. Using 16S rRNA and ITS amplicon sequencing, we identified distinct bacterial and fungal communities that varied significantly according to the apple varietal and orchard location. Notably, the orchard was the dominant factor shaping both the bacterial and fungal communities on the apples’ surfaces, with the varietal differences also playing a significant, albeit secondary, role. For example, we found that the bacterial genera Acidophilim sp. and 1174-901-12 sp., as well as the fungus Sporobolmyces patagonicus, were important markers of the orchard in which the apples were cultivated. These microbial signatures persisted into the early stages of cider fermentation, suggesting their potential influence on the cider quality and flavor profile. Our findings underscore the critical importance of the microbial terroir in cider production, and suggest that targeted management practices can leverage regional microbial diversity to enhance the distinctiveness and marketability of artisanal cider products.

Abstract: The genus Halorubrum is a member of the family Halobacteriaceae which currently has the highest number of described species (31) of all the haloarchaea. Here we report the draft genome sequence of strain V5, a new species within this genus that was isolated from the solar salterns of Cabo Rojo, Puerto Rico. Assembly was performed and rendered the genome into 17 contigs (N50 = 515,834 bp), the largest of which contains 1,031,026 bp. The genome consists of 3.57 MB in length with G + C content of 67.6%. In general, the genome includes 4 rRNAs, 52 tRNAs, and 3246 protein-coding sequences. The NCBI accession number for this genome is LIST00000000 and the strain deposit number is CECT9000.

Abstract: The genus Haloarcula belongs to the family Halobacteriaceae which currently has 10 valid species. Here we report the draft genome sequence of strain SL3, a new species within this genus, isolated from the Solar Salterns of Cabo Rojo, Puerto Rico. Genome assembly performed using NGEN Assembler resulted in 18 contigs (N50 = 601,911 bp), the largest of which contains 1,023,775 bp. The genome consists of 3.97 MB and has a GC content of 61.97%. Like all species of Haloarcula, the genome encodes heterogeneous copies of the small subunit ribosomal RNA. In addition, the genome includes 6 rRNAs, 48 tRNAs, and 3797 protein coding sequences. Several carbohydrate-active enzymes genes were found, as well as enzymes involved in the dihydroxyacetone processing pathway which are not found in other Haloarcula species. The NCBI accession number for this genome is LIUF00000000 and the strain deposit number is CECT9001.

The composition and seasonal patterns of airborne bacterial and fungal communities and how these are affected by atmospheric conditions (e.g., dry vs. rain), origin of air masses, and presence of air pollutants remain understudied, despite their obvious importance for public health. To provide insights into these questions, monthly dry air and rain samples were collected at the Environmental Science and Technology building rooftop on Georgia Tech’s campus (Metro Atlanta) between June 2017 and November 2019. The sampling included the remnants of Hurricane Irma and a Saharan dust event in 2020. Amplicon sequencing of the V4 region of the 16S rRNA gene and the fungal nuclear ribosomal internal transcribed spacer (ITS) region showed that spore-forming bacteria and widespread fungi were enriched in dry samples, while photosynthetic bacteria and wood-decaying fungi were more abundant in rain samples, demonstrating the effect of sample type on bioaerosol composition. Further, higher relative abundance of fungal human pathogens and allergens were identified in the dry-air and Saharan dust samples, including Alternaria alternata and Cladosporium cladosporioides. Bacterial and fungal species richness and composition appeared to be relatively consistent between seasons for both sample types. Accordingly, sample type and seasonality explained ∼14% and ∼8.5% of the microbial diversity between samples, respectively, while presence of air pollutants and three-day back trajectory data were not significant. Collectively, our data indicates that dry air might represent a higher public health risk and provides a reference point for the long-term monitoring of airborne microbial communities in an urban Southeast US setting.