Puerto Rico Luquillo Experimental Forest (LEF) soil metagenomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB26500 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background:The island of Puerto Rico supports a diverse assemblage of breeding birds, including 16 endemic species (Raffaele et al. 1998), and provides critical wintering habitat for many North American migratory birds (Wunderle and Waide 1994). Despite being a hotspot of avian biodiversity, spatially extensive data on the distribution and abundance of birds on the island are scarce. Breeding-bird assemblages were sampled by the North American Breeding Bird Survey from 1997-2007 (Sauer et al. 2013), but comparable primary data are not available for bird assemblages present during the boreal winter. New information:We provide data from one of the few spatially extensive surveys of forest birds on Puerto Rico. We sampled 211 locations in forests across the island during January-March 2015 using repeated point-count surveys. These data are suitable for use in estimating abundance, occupancy, and distribution of forest birds on Puerto Rico during the winter.
| S-EPMC5740410 | biostudies-literature
Project description:A number of recent studies have documented long-term declines in abundances of important arthropod groups, primarily in Europe and North America. These declines are generally attributed to habitat loss, but a recent study [B.C. Lister, A. Garcia, Proc. Natl. Acad. Sci. USA 115, E10397-E10406 (2018)] from the Luquillo Experimental Forest (LEF) in Puerto Rico attributed declines to global warming. We analyze arthropod data from the LEF to evaluate long-term trends within the context of hurricane-induced disturbance, secondary succession, and temporal variation in temperature. Our analyses demonstrate that responses to hurricane-induced disturbance and ensuing succession were the primary factors that affected total canopy arthropod abundances on host trees, as well as walkingstick abundance on understory shrubs. Ambient and understory temperatures played secondary roles for particular arthropod species, but populations were just as likely to increase as they were to decrease in abundance with increasing temperature. The LEF is a hurricane-mediated system, with major hurricanes effecting changes in temperature that are larger than those induced thus far by global climate change. To persist, arthropods in the LEF must contend with the considerable variation in abiotic conditions associated with repeated, large-scale, and increasingly frequent pulse disturbances. Consequently, they are likely to be well-adapted to the effects of climate change, at least over the short term. Total abundance of canopy arthropods after Hurricane Maria has risen to levels comparable to the peak after Hurricane Hugo. Although the abundances of some taxa have declined over the 29-y period, others have increased, reflecting species turnover in response to disturbance and secondary succession.
| S-EPMC7812834 | biostudies-literature
Project description:The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.
| S-EPMC8174771 | biostudies-literature
Project description:Guanica dry forest (GDF), located in the southwest area or region of Puerto Rico, is among the most preserved subtropical dry forests in the world [1]. To describe the taxonomic diversity and functional profiles of this environment, metagenomic DNA was extracted from a metagenomic library generated from the GDF. The DNA was shotgun-sequenced using Illumina and analyzed using the MG-RAST server. The diversity profile revealed that the most abundant domain was Bacteria (97.8%) followed by Archaea (1.12%), Eukaryota (1.02%) and Viruses (0.03%). Out of the 50 phyla present, the most abundant was Proteobacteria (41.6%) followed by Actinobacteria (18.7%) and Acidobacteria (7.06%). Moreover, a total of 213 orders, 384 families and 791 genus were identified. The functional profile showed abundance of genes related to Carbohydrates (13.16%), Clustering-based subsystems (13.0%), Amino Acids and Derivatives (9.9%) and Protein Metabolism (8.24%). Furthermore, more specific grouping showed that NULL (21.5%) was the most abundant function group, followed by Plant-Prokaryote DOE project (6.05%), Protein biosynthesis (4.82%), Central carbohydrate metabolism (3.98%), DNA repair (2.72%) and Resistance to antibiotics and toxic compounds (2.66%). This dataset is useful in bioprospecting studies with application in biomedical sciences, biotechnology and microbial, population and applied ecology fields.
| S-EPMC6926141 | biostudies-literature
Project description:We compared occupancy in local assemblages of birds in forested areas across Puerto Rico during a winter before (2015) and shortly after (2018) the passage of hurricanes Irma and Maria. Using dynamic community models analyzed within a Bayesian framework, we found significant changes in detectability, with some species becoming more readily detected after the storms and others becoming more difficult to detect during surveys. Changes in occupancy were equally mixed. Five species-mostly granivores and omnivores, but also Black-whiskered Vireo (Vireo altiloquus), a migratory insectivore-occupied more sites in 2018 than in 2015. Twelve species were less common after the hurricanes, including all of the obligate frugivores. Declines in site-occupancy rates were not only more common than increases, but tended to be of greater magnitude. Our results support the general conclusions that bird species respond largely independently to changes in forest structure caused by hurricanes, but that some dietary guilds, notably frugivores, are more sensitive and more likely to show changes in abundance or occupancy following strong storms.
| S-EPMC6559628 | biostudies-literature
Project description:Phosphate addition increases tropical forest soil respiration primarily by deconstraining microbial population growth. see doi: 10.1016/j.soilbio.2018.11.026.
Soil samples were collected from four locations in the El Yunque National Forest in Puerto Rico. Short-term laboratory incubation experiments were employed to relate soil respiration to phosphorus and oxygen and also to changes in microbial community structure and activity. Sequenced metagenomes and metatranscriptomes will be submitted under this project ID.
| PRJEB23349 | ENA
Project description:Puerto Ricans are a unique Hispanic population with European, Native American (Taino), and higher West African ancestral contributions than other non-Caribbean Hispanics. In admixed populations, such as Puerto Ricans, genetic variants can be found at different frequencies when compared to parental populations and uniquely combined and distributed. Therefore, in this review, we aimed to collect data from studies conducted in healthy Puerto Ricans and to report the frequencies of genetic polymorphisms with major relevance in drug response. Filtering for healthy volunteers or individuals, we performed a search of pharmacogenetic studies in academic literature databases without limiting the period of the results. The search was limited to Puerto Ricans living in the island, excluding those studies performed in mainland (United States). We found that the genetic markers impacting pharmacological therapy in the areas of cardiovascular, oncology, and neurology are the most frequently investigated. Coincidently, the top causes of mortality in the island are cardiovascular diseases, cancer, diabetes, Alzheimer's disease, and stroke. In addition, polymorphisms in genes that encode for members of the CYP450 family (CYP2C9, CYP2C19, and CYP2D6) are also available due to their relevance in the metabolism of drugs. The complex genetic background of Puerto Ricans is responsible for the divergence in the reported allele frequencies when compared to parental populations (Africans, East Asians, and Europeans). The importance of reporting the findings of pharmacogenetic studies conducted in Puerto Ricans is to identify genetic variants with potential utility among this genetically complex population and eventually move forward the adoption of personalized medicine in the island.
| S-EPMC4768757 | biostudies-literature
Project description:Projected increases in cyclonic storm intensity under a warming climate will have profound effects on forests, potentially changing these ecosystems from carbon sinks to sources. Forecasting storm impacts on these ecosystems requires consideration of risk factors associated with storm meteorology, landscape structure, and forest attributes. Here we evaluate risk factors associated with damage severity caused by Hurricanes María and Irma across Puerto Rican forests. Using field and remote sensing data, total forest aboveground biomass (AGB) lost to the storms was estimated at 10.44 (±2.33) Tg, ca. 23% of island-wide pre-hurricane forest AGB. Storm-related rainfall was a stronger predictor of forest damage than maximum wind speeds. Soil water storage capacity was also an important risk factor, corroborating the influence of rainfall on forest damage. Expected increases of 20% in hurricane-associated rainfall in the North Atlantic highlight the need to consider how such shifts, together with high speed winds, will affect terrestrial ecosystems.
| S-EPMC7062726 | biostudies-literature
Project description:PURPOSE:To identify rates of postoperative radiation therapy (RT) after breast conservation surgery (BCS) in women with stage I or II invasive breast cancer treated in Puerto Rico and to examine the sociodemographic and health services characteristics associated with variations in receipt of RT. METHODS:The Puerto Rico Central Cancer Registry-Health Insurance Linkage Database was used to identify patients diagnosed with invasive breast cancer between 2008 and 2012 in Puerto Rico. Claims codes identified the type of surgery and the use of RT. Logistic regression models were used to examine the independent association between sociodemographic and clinical covariates. RESULTS:Among women who received BCS as their primary definitive treatment, 64% received adjuvant RT. Significant predictors of RT after BCS included enrollment in Medicare (odds ratio [OR], 2.14; 95% CI, 1.46 to 3.13; P ? .01) and dual eligibility for Medicare and Medicaid (OR, 1.61; 95% CI, 1.14 to 2.27; P < .01). In addition, it was found that RT was more likely to have been received in certain geographic locations, including the Metro-North (OR, 2.20; 95% CI, 1.48 to 3.28; P < .01), North (OR, 1.78; 95% CI, 1.20 to 2.64; P < .01), West (OR, 4.04; 95% CI, 2.61 to 6.25; P < .01), and Southwest (OR, 2.79; 95% CI, 1.70 to 4.59; P < .01). Furthermore, patients with tumor size > 2.0 cm and ? 5.0 cm (OR, 0.61; 95% CI, 0.40 to 0.93; P = .02) and those with tumor size > 5.0 cm (OR, 0.37; 95% CI, 0.15 to 0.92; P = .03) were found to be significantly less likely to receive RT. CONCLUSION:Underuse of RT after BCS was identified in Puerto Rico. Patients enrolled in Medicare and those who were dually eligible for Medicaid and Medicare were more likely to receive RT after BCS compared with patients with Medicaid alone. There were geographic variations in the receipt of RT on the island.
| S-EPMC6180809 | biostudies-other
Project description:Tropical forests generally occur on highly weathered soils that, in combination with the immobility of phosphorus (P), often result in soils lacking orthophosphate, the form of P most easily metabolized by plants and microbes. In these soils, mineralization of organic P can be the major source for orthophosphate. Both plants and microbes encode for phosphatases capable of mineralizing a range of organic P compounds. However, the activity of these enzymes depends on several edaphic factors including P availability, tree species, and microbial communities. Thus, phosphatase activity in both roots and the root microbial community constitute an important role in P mineralization and P nutrient dynamics that are not well studied in tropical forests. To relate phosphatase activity of roots and bacteria in tropical forests, we measured phosphatase activity in roots and bacterial isolates as well as bacterial community composition from the rhizosphere. Three forests in the Luquillo Mountains of Puerto Rico were selected to represent a range of soil P availability as measured using the resin P method. Within each site, a minimum of three tree species were chosen to sample. Root and bacterial phosphatase activity were both measured using a colorimetric assay with para-nitrophenyl phosphate as a substrate for the phosphomonoesterase enzyme. Both root and bacterial phosphatase were chiefly influenced by tree species. Though tree species was the only significant factor in root phosphatase activity, there was a negative trend between soil P availability and phosphatase activity in linear regressions of average root phosphatase and resin P. Permutational multivariate analysis of variance of bacterial community composition based on 16S amplicon sequencing indicated that bacterial composition was strongly controlled by soil P availability (p-value < 0.05). These results indicate that although root and bacterial phosphatase activity were influenced by tree species; bacterial community composition was chiefly influenced by P availability. Although the sample size is limited given the tremendous diversity of tropical forests, our study indicates the importance of roots and bacterial function to understanding phosphatase activity. Future work will broaden the diversity of tree species and microbial members sampled to provide insight into P mineralization and model representation of tropical forests.
| S-EPMC5670114 | biostudies-literature