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Certain species within the genus Pseudo-nitzschia are able to produce the neurotoxin domoic acid (DA), which can cause illness in humans, mass-mortality of marine animals, and closure of commercial and recreational shellfisheries during toxic events. Understanding and forecasting blooms of these harmful species is a primary management goal. However, accurately predicting the onset and severity of bloom events remains difficult, in part because the underlying drivers of bloom formation have not been fully resolved. Furthermore, Pseudo-nitzschia species often co-occur, and recent work suggests that the genetic composition of a Pseudo-nitzschia bloom may be a better predictor of toxicity than prevailing environmental conditions. We developed a novel next-generation sequencing assay using restriction site-associated DNA (2b-RAD) genotyping and applied it to mock Pseudo-nitzschia communities generated by mixing cultures of different species in known abundances. On average, 94% of the variance in observed species abundance was explained by the expected abundance. In addition, the false positive rate was low (0.45% on average) and unrelated to read depth, and false negatives were never observed. Application of this method to environmental DNA samples collected during natural Pseudo-nitzschia spp. bloom events in Southern California revealed that increases in DA were associated with increases in the relative abundance of P. australis. Although the absolute correlation across time-points was weak, an independent species fingerprinting assay (Automated Ribosomal Intergenic Spacer Analysis) supported this and identified other potentially toxic species. Finally, we assessed population-level genomic variation by mining SNPs from the environmental 2bRAD dataset. Consistent shifts in allele frequencies in P. pungens and P. subpacifica were detected between high and low DA years, suggesting that different intraspecific variants may be associated with prevailing environmental conditions or the presence of DA. Taken together, this method presents a potentially cost-effective and high-throughput approach for studies aiming to evaluate both population and species dynamics in mixed samples.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9869635 | PMC |
http://dx.doi.org/10.1016/j.hal.2022.102314 | DOI Listing |
Theor Appl Genet
December 2024
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China.
A dwarf mutant with short branches (csdf) was identified from EMS-induced mutagenesis. Bulked segregant analysis sequencing and map-based cloning revealed CsKAO encoding ent-kaurenoic acid oxidase as the causal gene. Plant architecture is the primary target of artificial selection during domestication and improvement based on the determinate function for fruit yield.
View Article and Find Full Text PDFMater Horiz
December 2024
Walter Schottky Institute, Technical University of Munich, 85748 Garching, Germany.
Semiconducting ternary nitrides are a promising class of materials that have received increasing attention in recent years, but often show high free electron concentrations due to the low defect formation energies of nitrogen vacancies and substitutional oxygen, leading to degenerate n-type doping. To achieve non-degenerate behavior, we now investigate a family of amorphous calcium-zinc nitride (Ca-Zn-N) thin films. By adjusting the metal cation ratios, we demonstrate band gap tunability between 1.
View Article and Find Full Text PDFEcol Evol
December 2024
Wildlife Conservation Society New York New York USA.
Population density is a valuable metric used to manage wildlife populations. In the Russian Far East, managers use the Formozov- Malyushev-Pereleshin (FMP) snow tracking method to estimate densities of ungulates for hunting management. The FMP also informs Amur tiger () conservation since estimates of prey density and biomass help inform conservation interventions.
View Article and Find Full Text PDFUnderstanding how ecological communities assemble in relation to natural and human-induced environmental changes is critical, particularly for communities of pollinators that deliver essential ecosystem services. Despite widespread attention to interactions between functional traits and community responses to environmental changes, the importance of sensory traits has received little attention. To address this, we asked whether visual traits of bumblebee communities varied at large geographical scales along a habitat gradient of increased tree cover.
View Article and Find Full Text PDFFront Microbiol
December 2024
VERO Program, Texas A&M University, Canyon, TX, United States.
Introduction: The gastrointestinal microbiota profoundly influences the health and productivity of animals. This study aimed to characterize microbial community structures of the mouth, gastrointestinal tract (GIT), and feces of cattle.
Methods: Samples were collected from 18 Akaushi crossbred steers at harvest from multiple locations, including the oral cavity, rumen, abomasum, duodenum, jejunum, ileum, cecum, spiral colon, distal colon, and feces.
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