Open Access
Communication
22 July 2025The Importance of Methods in Assessing Conservation Status of Abundant Fish Species through Genetic Diversity Estimates
This study compares the accuracy of two genomic approaches in estimating genetic diversity levels, which could be useful for informing species conservation assessments of abundant, exploited fish species. The first approach (SNP-calling-based) is the commonly used pipeline of SNP calling followed by SNP filtering at a determined Minor Allele Frequency (MAF). The second approach (genotype-likelihood-based) does not perform SNP calling but estimates the Site Spectrum Frequency (SFS) based on alignment quality and sample size. The results show up to two-fold differences in the magnitude of the estimated nucleotide diversities among the analyzed datasets. The SNP-calling-based approach produces overestimates when missing data are considered in the analysis and shows pronounced deviations of the SFS towards high-frequency SNPs when filtering by MAF > 5%. The genotype likelihood-based approach showed that nucleotide diversity estimates significantly deviated from neutral expectations, as expected based on the known history of the case-study fish population analyzed here, regardless of whether missing data were considered. In contrast, the SNP-calling-based approach only shows this expected difference when no missing data are included and no MAF filtering is performed. Overall, the results indicate that using the SNP-calling-based approach may hide the effects of population size declines in abundant exploited fish species, while genotype-likelihood-based estimates of nucleotide diversity can effectively contribute to informing conservation assessments.
Open Access
Article
14 August 2025Wood Chips Ameliorate the Negative Effects of LDPE Microplastic on Wheat Growth and Soil Microbial Community
As an emerging pollutant, microplastics (MPs) pose a potential risk to ecosystem health due to recycling technology’s limitations and long-term durability. Wood chip amendments can enhance the holding capacity of water and nutrients and improve the soil structure and quality of terrestrial ecosystems. However, the effects of wood chip amendments on MPs-contaminated soil-plant systems are still unclear. In this experiment, we employed a combination of field experiments, soil and plant measurements, molecular techniques (DNA extraction and sequencing), and advanced statistical analyses. A comprehensive assessment was conducted on the effects of Low-density polyethylene (LDPE) MPs on soil properties, wheat growth, and soil microbial communities, and the potential of wood chips as a mitigating agent was also evaluated. The results indicated that wood chips improved soil nutrient content, enhanced the activity of enzymes related to carbon, nitrogen, and phosphorus cycling, and promoted crop growth, all of which were negatively affected by LDPE. The effect of MPs on fungi was greater than that on bacterial communities, and adding wood chips could improve the α-diversity of fungal communities rather than bacteria. LDPE may increase the abundance of pathotrophic fungal groups, such as Stachybotrys and Alternaria. However, certain pathotrophic groups have been found to potentially facilitate the degradation of LDPE-MPs. LDPE reduced the symbiotroph groups and increased the competitiveness and complexity of the community in the microbial co-occurrence network. LDPE treatment inhibited the N-cycling bacteria group, while adding wood chips could promote most of the N-cycling bacteria groups. Wood chips increased saprotroph groups such as Trichoderma, which are able to degrade plastics. Wood chips emerge as a cost-effective and environmentally friendly solution to improve soil quality and mitigate the negative impacts of microplastics on crop growth.
