Characterization of the microbial communities in paddy soils in Lajas, Puerto Rico using 16S rRNA gene.

The microbiota in the paddy soils of the Lajas Agricultural Experimental Station at the University of Puerto Rico (LAES-UPR) plays a crucial role in agricultural ecosystems. Despite being at an experimental station, these soils represent natural environments supporting rice cultivation. Microbial diversity was evaluated during pre-harvest and post-harvest periods.

Sea cucumber () intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.

The sea cucumber () is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.

Chemical sensing of common microorganisms found in biopharmaceutical industries using MIR laser spectroscopy and multivariate analysis.

Mid-infrared laser spectroscopy was used to investigate common bacteria encountered in biopharmaceutical industries. The study involved the detection of bacteria using quantum cascade laser spectroscopy coupled to a grazing angle probe (QCL-GAP). Substrates similar to surfaces commonly used in biopharmaceutical industries were used as support media for the samples.

RING Program: The CFAR Diversity, Equity, and Inclusion Pathway Initiative.

Background: Case Western Reserve University (CWRU)/University Hospitals Cleveland Medical Center in Cleveland, OH, and the University of Pittsburgh (Pitt) in Pittsburgh, PA, forged a strategic alliance to form the Rustbelt Center for AIDS Research. The Rustbelt Center for AIDS Research developed a National Institutes of Health-supported diversity, equity, and inclusion pathway initiative termed the "Rustbelt Investigators for the Next Generation (RING) Program" that provides research training experiences for Puerto Rican students that will help them pursue a biomedical research career in HIV.

Setting: The RING Program provides 10-week research training experiences in different disciplines of HIV/AIDS for under-represented minority undergraduate and masters students from 4 campuses (Río Piedras, Mayagüez, Humacao, and Cayey) at the University of Puerto Rico.

Microbial Model Construction Activity for Introducing Students to Microbiome and Metagenomic Fields.

Educational activities in biology teaching focused on model construction allow students to make the invisible evident. The development and integration of these pedagogical strategies in emerging sciences is essential and necessary in the classroom of noncollege academia. A two-component pedagogical activity was developed to expose high school students to the emerging disciplines of microbiomes and metagenomics.

Stool microbiome dataset of the critically endangered Puerto Rican parrot ().

The Puerto Rican parrot (), endemic to Puerto Rico, is the only native parrot in the United States and is classified as a critically endangered species. There are two captive populations of in Puerto Rico located in the Iguaca Aviary in El Yunque National Rainforest and the José L. Vivaldi Aviary in the Río Abajo Forest.

Soil microbiome dataset from Guanica dry forest in Puerto Rico generated by shotgun sequencing.

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.

Soil metagenome datasets underneath the Arecibo Observatory reflector dish.

The Arecibo Observatory (AO) located in Arecibo, Puerto Rico, is the most sensitive, powerful and active planetary radar system in the world [1]. One of its principal components is the 305 m-diameter spherical reflector dish (AORD), which is exposed to high frequency electromagnetic waves. To unravel the microbial communities that inhabit this environment, soil samples from underneath the AORD were collected, DNA extracted, and sequenced using Illumina MiSeq.

Datasets generated by shotgun sequencing of metagenomic libraries of the guajataca water reservoir.

The Guajataca Water Reservoir (GWR) was constructed for irrigation and to bring potable water to the northwestern region of Puerto Rico. The generation of DNA sequencing data from aquatic bodies (AB) using culture-independent approaches allows the investigation of the total microbial diversity as well as the potential anthropogenic impact. Metagenomic libraries were constructed for two GWR sampling sites and genomic information access through shotgun sequencing.

Microbiome dataset from Clara Cave and Empalme Sinkhole waters in Puerto Rico.

Camuy River Cave Park (CRCP) is an underground cave system located at the subtropical karst carved by the Camuy River in the subtropical moist forest of northern Puerto Rico (Nieves-Rivera, 2003) [1]. This article contains a metagenomic dataset from the microbial and functional diversity of Clara Cave and Empalme Sinkhole water samples. The environmental DNA (eDNA) from the samples was extracted following direct Metagenomic DNA Isolation method, followed by Next-Generation-Sequencing technology (Illumina MiSeq).

The metagenome of gut microbiome using culture independent approaches and shotgun sequencing.

Studies underestimate the microbial diversity and genotypic traits in the snails' microbiome. a land snail native to Caribbean islands, can adapt to different environments. Our research focused on the generation of a metagenomic library from gut, to further explore the diversity and functional traits.

The metagenome of bromeliads phytotelma in Puerto Rico.

Bromeliads tank water or phytotelma is an eutrophic microenvironment where microorganisms have evolved to resist sudden changes in pH and nutritional competition. Metagenomics studies have been poorly studied in bromeliads and environmental DNA (eDNA) characterization for its microenvironment is deficient in Puerto Rico. Therefore, the data represents the microbial communities inhabiting bromeliads phytotelma.

Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing.

In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation.

Profiling lethal factor interacting proteins from human stomach using T7 phage display screening.

The anthrax lethal factor (LF) is a zinc dependent metalloproteinase that cleaves the majority of mitogen-activated protein kinase kinases and a member of NOD-like receptor proteins, inducing cell apoptosis. Despite efforts to fully understand the Bacillus anthracis toxin components, the gastrointestinal (GI) anthrax mechanisms have not been fully elucidated. Previous studies demonstrated gastric ulceration, and a substantial bacterial growth rate in Peyer's patches.

Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater.

To evaluate the efficacy of bioimmobilization of Cr(VI) in groundwater at the Department of Energy Hanford site, we conducted a series of microcosm experiments using a range of commercial electron donors with varying degrees of lactate polymerization (polylactate). These experiments were conducted using Hanford Formation sediments (coarse sand and gravel) immersed in Hanford groundwater, which were amended with Cr(VI) and several types of lactate-based electron donors (Hydrogen Release Compound, HRC; primer-HRC, pHRC; extended release HRC) and the polylactate-cysteine form (Metal Remediation Compound, MRC). The results showed that polylactate compounds stimulated an increase in bacterial biomass and activity to a greater extent than sodium lactate when applied at equivalent carbon concentrations.

Summer workshop in metagenomics: one week plus eight students equals gigabases of cloned DNA.

We designed a week-long laboratory workshop in metagenomics for a cohort of undergraduate student researchers. During this course, students learned and utilized molecular biology and microbiology techniques to construct a metagenomic library from Puerto Rican soil. Pre-and postworkshop assessments indicated student learning gains in technical knowledge, skills, and confidence in a research environment.

Genotypic characterization of environmental isolates of Cryptococcus gattii from Puerto Rico.

Cryptococcus neoformans and Cryptococcus gattii are found in distinct environments with some overlap around different parts of the world. However, no systematic surveys of these two pathogens have been reported from Puerto Rico, a tropical island uniquely situated between mainland USA and countries in South America. We carried out an exhaustive environmental survey in southwestern Puerto Rico for pathogenic Cryptococcus species.

Miniprimer PCR, a new lens for viewing the microbial world.

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide "miniprimers" expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers.

Learning geomicrobiology as a team using microbial mats, a multidisciplinary approach.

Microbial mats are one of the best suited laminar organo-sedimentary ecosystems for students from different educational backgrounds to visualize the direct relationship between microbes and minerals. We have used tropical hypersaline microbial mats from Puerto Rico as educational tools to promote active learning of geomicrobiology introductory concepts for undergraduate students organized in multidisciplinary teams with biological and geological backgrounds. Besides field trips and independent research projects focused on microbial mats, four intensive workshops and one capstone activity were designed to expose students to the different geomicrobiology subdisciplines (microbiology, molecular biology, geology, and geochemistry).

The delta cooperative model: a dynamic and innovative team-work activity to develop research skills in microbiology.

The Delta Cooperative Model (DCM) is a dynamic and innovative teamwork design created to develop fundamentals in research skills. High school students in the DCM belong to the Upward Bound Science and Math (UBSM) program at the Inter American University, Ponce Campus. After workshops on using the scientific method, students were organized into groups of three students with similar research interests.

Features of Rhodobacter sphaeroides CcmFH.

In this study, the in vivo function and properties of two cytochrome c maturation proteins, CcmF and CcmH from Rhodobacter sphaeroides, were analyzed. Strains lacking CcmH or both CcmF and CcmH are unable to grow under anaerobic conditions where c-type cytochromes are required, demonstrating their critical role in the assembly of these electron carriers. Consistent with this observation, strains lacking both CcmF and CcmH are deficient in c-type cytochromes when assayed under permissive growth conditions.