20 Apr 2026

Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics

Abstract: Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess micro-biome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fun-gal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types. These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia—including bacteria, fungi, and protozoa—can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.

18 Apr 2024

Standardized NEON Organismal Data for Biodiversity Research

Abstract: Understanding patterns and drivers of species distribution and abundance, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is limited by a lack of standardized, high-quality, empirical data spanning large spatial scales and long time periods. The NEON fills this gap by providing freely available observational data generated during robust and consistent organismal sampling of several sentinel taxonomic groups within 81 sites distributed across the US and will be collected for at least 30 years. The breadth and scope of these data provide a unique resource for advancing biodiversity research. To maximize the potential of this opportunity, however, it is critical that NEON data be accessible and easily integrated into investigators’ workflows and analyses. To facilitate its use for biodiversity research and synthesis, we created a workflow to process and format NEON organismal data into the ecocomDP (ecological community data design pattern) format available through the ecocomDP R package; provided the standardized data as an R data package (neonDivData). We briefly summarize sampling designs and data wrangling decisions for the major taxonomic groups included. Our workflows are open-source so the biodiversity community may: add additional taxonomic groups; modify the workflow to produce datasets appropriate for their own analytical needs; and regularly update the data packages as more observations become available. Finally, we provide two simple examples of how the standardized data may be used for biodiversity research. By providing a standardized data package, we hope to enhance the utility of NEON organismal data in advancing biodiversity research and encourage the use of the harmonized ecocomDP data design pattern for community ecology data from other ecological observatory networks.

9 Apr 2024

Embracing Biodiversity on Engineered Coastal Infrastructure through Structured Decision-Making and Engineering With Nature

Abstract: Extreme weather variation, natural disasters, and anthropogenic actions negatively impact coastal communities through flooding and erosion. To safeguard coastal settlements, shorelines are frequently reinforced with seawalls and bulkheads. Hardened shorelines, however, result in biodiversity loss and environmental deterioration. The creation of sustainable solutions that engineer with nature is required to lessen natural and anthropogenic pressures. Nature-based solutions (NbS) are a means to enhance biodiversity and improve the environment while meeting engineering goals. To address this urgent need, the US Army Corps of Engineers (USACE) Engineering With Nature® (EWN) program balances economic, environmental, and social benefits through collaboration. This report presents how design and engineering practice can be enhanced through organized decision-making and landscape architectural renderings that integrate engineering, science, and NbS to increase biodiversity in coastal marine habitats. When developing new infrastructure or updating or repairing existing infrastructure, such integration can be greatly beneficial. Further, drawings and renderings exhibiting EWN concepts can assist in decision-making by aiding in the communication of NbS designs. Our practical experiences with the application of EWN have shown that involving landscape architects can play a critical role in effective collaboration and result in solutions that safeguard coastal communities while maintaining or enhancing biodiversity.