Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages

Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments.     

Spatial and temporal variations in Caribbean zooplankton near Puerto Rico

Spatial and temporal patterns of abundance were examined inselected zooplankton categories sampled from oceanic surfacewaters (upper 100 m) south of Puerto Rico during 1980. In general,variations in abundances: (i) did not increase with spatialscales ranging from a few to –150 km; and (ii) were notcorrelated with geostrophic current patterns, These resultsimply a lack of zooplankton pattern characteristic of thesespatial scales, hence that corresponding physical processesdo not affect zooplankcton abundances in this region. Significantlyhigher abundances of zooplankton occurred during July in conjunctionwith peak chlorophyll a concentrations, the initial seasonaldecline in surface salinities and an eastward geostrophic flow.These observations are consistent with the hypothesis that upwellingat the edge of large low salinity lenses underlies increasedabundances of plankton. Because these variations in salinitiesresult from the annual pattern of rainfall in low latitude zonesof the Western Hemisphere, we conclude that the temporal patternof zooplankton abundance represents true seasonality and isassociated with large scale, regional processes occurring throughoutthe Eastern Caribbean.     

Cost-effectiveness of dengue vaccination in Puerto Rico

An effective and widely used vaccine could reduce the burden of dengue virus (DENV) around the world. DENV is endemic in Puerto Rico, where the dengue vaccine CYD-TDV is currently under consideration as a control measure. CYD-TDV has demonstrated efficacy in clinical trials in vaccinees who had prior dengue virus infection. However, in vaccinees who had no prior dengue virus infection, the vaccine had a modestly elevated risk of hospitalization and severe disease. The WHO therefore recommended a strategy of pre-vaccination screening and vaccination of seropositive persons. To estimate the cost-effectiveness and benefits of this intervention (i.e., screening and vaccination of seropositive persons) in Puerto Rico, we simulated 10 years of the intervention in 9-year-olds using an agent-based model. Across the entire population, we found that 5.5% (4.6%-6.3%) of dengue hospitalizations could be averted. However, we also found that 0.057 (0.045–0.073) additional hospitalizations could occur for every 1,000 people in Puerto Rico due to DENV-naïve children who were vaccinated following a false-positive test results for prior exposure. The ratio of the averted hospitalizations among all vaccinees to additional hospitalizations among DENV-naïve vaccinees was estimated to be 19 (13–24). At a base case cost of vaccination of 382 USD, we found an incremental cost-effectiveness ratio of 122,000 USD per QALY gained. Our estimates can provide information for considerations to introduce the CYD-TDV vaccine in Puerto Rico.     

Cecropia schreberiana in the Luquillo Mountains of Puerto Rico

Cecropia schreberiana Miq. (Cecropiaceae) is a common tree in the Luquillo Mountains of Puerto Rico because it is a pioneer that establishes abundantly after recurrent hurricanes that damage Luquillo forests. In these forestsC. schreberiana typically reaches about 20 m in height and 60 cm dbh and has few branches, these bearing large, deeply lobed leaves. The wood is light and weak. Unlike most of its congeners,C. schreberiana in Puerto Rico does not have symbiotic ants. It is dioecious and produces wind-pollinated flowers in spikes and abundant minute seeds broadly dispersed by birds and bats. Forest soils contain a high density of its seeds, which lie dormant until canopy opening stimulates germination. With adequate nutrientsC. schreberiana grows fast in high light, while nondominant individuals suffer heavy mortality. An individual of the species is thought to live 30 to 50 years. Cecropia schreberiana is uncommon in abandoned pastures in the Luquillo Mountains. It colonizes road cuts, landslides, and infrequent, large treefall gaps. Yet these disturbances provide only a limited “background regeneration,” which is not sufficient to maintain the species’ observed high abundance in Luquillo forests. However, there is widespread and abundantC. schreberiana regeneration after hurricane damage opens the forest canopy. Despite high mortality among these post-hurricane colonizers, enough survive and grow so thatC. schreberiana is generally among the ten most common canopy trees in the widespread “tabonuco” forest type. Post-hurricane colonizers mature, senesce, and decline in number, butC. schreberiana remains abundant as seeds in the soil ready to form tree cohorts after disturbance. The status of theC. schreberiana population indicates the developmental status of the forest as a whole. Moreover,C. schreberiana performs a key function in the reorganization of Luquillo forest ecosystems after disturbance, when its abundant regeneration and rapid growth capture and store nutrients. Also, its colonizing saplings may facilitate succession to mature forest by excluding grasses, herbs, and vines that hinder forest development. The biology of this species both reflects and helps drive the dynamics of forests in the Luquillo Mountains.     

Athecate hydroids from Puerto Rico and the virgin Islands

About 31 athecate hydroids collected from Puerto Rico and the vicinity are recorded, 9 for the first time in the Caribbean Sea. Two new genera, Heterocoryne and Millardiana, and four new species, Heterocoryne caribbensis, Millardiana longitentaculata, Silhouetta puertoricensis and Stylactis sandrae, are described.     

Urban influences on the nitrogen cycle in Puerto Rico

Anthropogenic actions are altering fluxes of nitrogen (N) in the biosphere at unprecedented rates. Efforts to study these impacts have concentrated in the Northern hemisphere, where experimental data are available. In tropical developing countries, however, experimental studies are lacking. This paper summarizes available data and assesses the impacts of human activities on N fluxes in Puerto Rico, a densely populated Caribbean island that has experienced drastic landscape transformations over the last century associated with rapid socioeconomic changes. N yield calculations conducted in several watersheds of different anthropogenic influences revealed that disturbed watersheds export more N per unit area than undisturbed forested watersheds. Export of N from urban watersheds ranged from 4.8 kg ha^?1 year^?1 in the Río Bayamón watershed to 32.9 kg ha^?1 year^?1 in the highly urbanized Río Piedras watershed and 33.3 kg ha^?1 year^?1 in the rural-agricultural Río Grande de Añasco watershed. Along with land use, mean annual runoff explained most of the variance in fluvial N yield. Wastewater generated in the San Juan Metropolitan Area receives primary treatment before it is discharged into the Atlantic Ocean. These discharges are N-rich and export large amounts of N to the ocean at a rate of about 140 kg ha^?1 year^?1. Data on wet deposition of inorganic N ( $\hbox{NH}_{4}^{+}+\hbox{NO}_{3}^{-}Anthropogenic actions are altering fluxes of nitrogen (N) in the biosphere at unprecedented rates. Efforts to study these impacts have concentrated in the Northern hemisphere, where experimental data are available. In tropical developing countries, however, experimental studies are lacking. This paper summarizes available data and assesses the impacts of human activities on N fluxes in Puerto Rico, a densely populated Caribbean island that has experienced drastic landscape transformations over the last century associated with rapid socioeconomic changes. N yield calculations conducted in several watersheds of different anthropogenic influences revealed that disturbed watersheds export more N per unit area than undisturbed forested watersheds. Export of N from urban watersheds ranged from 4.8 kg ha⁻¹ year⁻¹ in the Río Bayamón watershed to 32.9 kg ha⁻¹ year⁻¹ in the highly urbanized Río Piedras watershed and 33.3 kg ha⁻¹ year⁻¹ in the rural-agricultural Río Grande de A?asco watershed. Along with land use, mean annual runoff explained most of the variance in fluvial N yield. Wastewater generated in the San Juan Metropolitan Area receives primary treatment before it is discharged into the Atlantic Ocean. These discharges are N-rich and export large amounts of N to the ocean at a rate of about 140 kg ha⁻¹ year⁻¹. Data on wet deposition of inorganic N () suggest that rates of atmospheric N deposition are increasing in the pristine forests of Puerto Rico. Stationary and mobile sources of NO _x (NO+NO₂) and N₂O generated in the large urban centers may be responsible for this trend. Comprehensive measurements are required in Puerto Rico to quantitatively characterize the local N cycle. More research is required to assess rates of atmospheric N deposition, N fixation in natural and human-dominated landscapes, N-balance associated with food and feed trade, and denitrification.     

Antibacterial properties of tropical plants from Puerto Rico

In an effort to document the antibacterial properties of plants commonly used by the people of Puerto Rico, we studied the effects of 172 plant species, utilizing the disc diffusion method, against Escherichia coli and Staphylococcus aureus. The methanolic extracts of 14 species showed antibacterial activities during this preliminary screen. These positive plant extracts were tested successively over 15 additional species. The results showed that extracts from Citrus aurantifolia (Rutaceae), Citrus aurantium (Rutaceae), Punica granatum (Punicaceae), Phyllanthus acidus (Euphorbiaceae) and Tamarindus indica (Caesalpiniaceae) possess strong in vitro antibacterial activity against the bacteria tested.     

Novel Psychropiezophilic Oceanospirillales Species Profundimonas piezophila gen. nov., sp. nov., Isolated from the Deep-Sea Environment of the Puerto Rico Trench

The diversity of deep-sea high-pressure-adapted (piezophilic) microbes in isolated monoculture remains low. In this study, a novel obligately psychropiezophilic bacterium was isolated from seawater collected from the Puerto Rico Trench at a depth of ∼6,000 m. This isolate, designated YC-1, grew best in a nutrient-rich marine medium, with an optimal growth hydrostatic pressure of 50 MPa (range, 20 to 70 MPa) at 8°C. Under these conditions, the maximum growth rate was extremely slow, 0.017 h⁻¹, and the maximum yield was 3.51 × 10⁷ cells ml⁻¹. Cell size and shape changed with pressure, shifting from 4.0 to 5.0 μm in length and 0.5 to 0.8 μm in width at 60 MPa to 0.8- to 1.0-μm diameter coccoid cells under 20 MPa, the minimal pressure required for growth. YC-1 is a Gram-negative, facultatively anaerobic heterotroph. Its predominant cellular fatty acids are the monounsaturated fatty acids (MUFAs) C_16:1 and C_18:1. Unlike many other psychropiezophiles, YC-1 does not synthesize any polyunsaturated fatty acids (PUFAs). Phylogenetic analysis placed YC-1 within the family of Oceanospirillaceae, closely related to the uncultured symbiont of the deep-sea whale bone-eating worms of the genus Osedax. In common with some other members of the Oceanospirillales, including those enriched during the Deepwater Horizon oil spill, YC-1 is capable of hydrocarbon utilization. On the basis of its characteristics, YC-1 appears to represent both a new genus and a new species, which we name Profundimonas piezophila gen. nov., sp. nov.     

Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied.     

Regeneration filters in post-agricultural fields of Puerto Rico and Ecuador

To better understand how rainforest regenerates after agriculture I sampled the seed rain and seed bank, and set out seeds and seedlings, on microsites defined by distance to the forest in fields both in Puerto Rico and Ecuador. I found that (1) total seeds, species richness and life-form richness were twice as great in the Ecuador seed rain compared to Puerto Rico but Puerto Rico seeds were more evenly distributed among species and (2) total seedlings from the seed bank were similar between Puerto Rico and Ecuador, (3) the majority of seeds were lost to predation among all species and study sites, (4) seed disease was absent in P. aduncum and Miconia prasina, and no seeds germinated for Gonzalagunia spicata and P. riparia, (5) in Ecuador pathogenic disease claimed more seeds than germinated for all species, and Solanum ovalifolium was the only species that had seeds germinate but did not lose seeds to disease, (6) also in Ecuador, insect predation was significantly lower in the forest border for P. aduncum, and seed disease was significantly greater at the 10 m micro site for S. ovalifolium, (7) distance has a significant effect on seedling height and basal diameter, (8) losses of leaf area due to herbivory and pathogens were always low and (9) biomass and leaf specific mass were significantly reduced in the border and forest microsites. I conclude that Ecuador fields had more seeds, species, and life-forms than Puerto Rico fields, predation was the most severe post-dispersal seed filter in all fields, seeds that survived predation on Puerto Rico were lost either to disease or germination but to both mechanisms in Ecuador, all three seed mechanisms in Ecuador fields showed distance effects of seedling growth but not survivorship.