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61 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type locus. In vitro fruiting was obtained for 16 strains, enabling the definition of seven new species, namely Pseudorhypophila gallica, Pseudorhypophila guyanensis Rhypophila alpibus, Rhypophila brasiliensis, Rhypophila camarguensis, Rhypophila reunionensis and Rhypophila thailandica, as well as two new combinations, namely Pseudorhypophila latipes and Pseudorhypophila oryzae. Eight strains for which in vitro fruiting was not obtained may belong to additional new species. These results expand the known diversity of the Naviculisporaceae and greatly enlarge the genomic data available for the family.

Naviculisporaceae↗
DOE OSTI2024

Invasive wild pig ( Sus scrofa ) diets on barrier islands in the southeastern United States

BACKGROUND: Biological invasions are a leading cause of reductions in global biodiversity. Islands are particularly sensitive to invasions, which often result in cascading impacts throughout island communities. Wild pigs (Sus scrofa) are globally invasive and pose threats to numerous taxa and ecosystems, particularly for islands where they have contributed to declines of many endemic species. However, the impacts of wild pig diet on the flora and fauna remain understudied in many island systems. RESULTS: We used DNA metabarcoding of wild pig fecal samples to quantify the seasonal diet composition of wild pigs on three barrier islands in the southeastern United States. Wild pigs exhibited a diverse diet dominated by plants, but also including marine and terrestrial animals. The diet composition of plants varied seasonally and between islands. Consumption of invertebrates also changed seasonally, with a shift to coastal invertebrates, particularly crabs, in spring and summer. Vertebrates were found in <10% of samples, but spanned broad taxa including amphibians, fish, mammals, and reptiles. Species consumed by wild pigs indicate that wild pigs use a variety of habitats within barrier islands for foraging, including maritime forests, saltmarshes, and beaches. CONCLUSIONS: An observed shift to beach foraging during sea turtle nesting season suggests wild pigs have potential to hinder nesting success on islands without established management programs. These findings provide insight into the diverse diets of wild pigs on barrier islands and highlight the need for removal of wild pigs from sensitive island ecosystems because of their potential impacts to native plant and animal communities. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022

The Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 polymerase chain reaction testing and genomic sequencing into the influenza surveillance program that was established in 2007. A total of 7,698 nasopharyngeal/oropharyngeal (NP/OP) swab samples were collected and analyzed from ILI/SARI sentinel sites across the country from January to December 2022. All samples were tested for influenza and SARS-CoV-2. Of these, 252 (3.3%), 162 (2.1%), and 589 (7.7%) were positive for influenza A, influenza B, and SARS-CoV-2, respectively. Out of 414 influenza-positive samples, 122 (29.5%) were AH1pdm09, 130 (31.4%) were AH3, and 162 (39.1%) were B-Victoria. All SARS-CoV-2 sequenced samples were of the Omicron variant, with subvariants of concern known to evade the immune system being detected, such as BQ.1 and XBB.2. Other SARS-CoV-2 positive samples collected from other health centers in the community outside the surveillance sites were included into SARS-CoV-2 genomic sequencing with similar patterns with respect to variants. In all, the ILI/SARI surveillance system has shown to be an efficient, cost-effective, and sustainable program, providing a ready platform to monitor the circulation of SARS-CoV-2 in communities at the national level while remaining vigilant for the persistent threat of influenza. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will strengthen the laboratory response capacity, as well as facilitate the timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tris(isodecyl)guanidine Degradation in the MCU System

The current solvent blend consists of four components; an extractant, the modifier, a suppressor, and the diluent. Of the four components, only the suppressor – tris(isodecyl)guanidine (TiDG) has exhibited an appreciable depletion rate during facility operations. Using data derived from Modular Caustic-Side Solvent Extraction Unit (MCU) process samples, Savannah River National Lab (SRNL) derived a method to predict the TiDG depletion based upon time and volume of feed processed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Solvent Hold Tank Sample Results for MCU-19-569-571 (December 2019), MCU-20-1-28 (January 2020), and MCU-20-29-30-31 (June 2020) (Quarterly Report)

A trend summary of three Solvent Hold Tank (SHT) monthly samples MCU-19-569-570-571 (December 2019), MCU-20-1-28 (January 2020), and MCU-20-29-30-31 (June 2020) are reported. Most of the conclusions are based on the June 2020 SHT sample (MCU-20-29-30-31). Analyses of the June 2020 SHT sample indicated that the Modifier (Cs-7SB) and the Extractant (MaxCalix) concentrations were above their nominal recommended concentrations (169,000 mg/L and 46,900 mg/L respectively) by 6% and 7% respectively. The Suppressor (N,N’,N”–tris(3,7-dimethyloctyl)guanidine or TiDG) concentration has remained at 833 ± 16 mg/L, but it is above the minimum recommended concentration (479 mg/L). The Semi-Volatile Organic Analysis (SVOA) and FT-HNMR did not detect any organic impurities. Another impurity observed in the samples was mercury. Based on the June 2020 SHT sample, up to 23 ± 5 micrograms of mercury per gram of solvent (or 19 ± 4 mg/L) was detected. The mercury concentration steadily decreased from 34.8 ug/g solvent (or 21.9 mg/L) in the December 2019 SHT sample to 34.8 ug/g solvent (or 19 mg/L) in the June 2020 SHT sample. The gamma concentration (~3.33E4 dpm/mL) measured in the June 2020 SHT samples was consistent with previous values observed when MCU was idle (for example, between February 2017 and August 2017). If additional SHT samples become available, the laboratory will continue to monitor the quality of the solvent for any new impurities or degradation of the solvent components.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗