Jonathan Lopez Duran | USGS Science

USGS2023

A nitrifier-enriched microbial community contributes to the degradation of environmental DNA

Environmental DNA (eDNA) surveys are a promising alternative to traditional monitoring of invasive species, rare species, and biodiversity. Detecting organism-specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with species abundance can be difficult due to the many abiotic and biotic factors that influence eDNA persistence and degradation. Here, we assessed the impact of a nitrifier-enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt eDNA using experimental aquatic mesocosms and a quantitative PCR approach. The NEM community was cultured from combined sediment and water samples collected from a golf course pond in Columbia, Missouri (USA), and experiments were conducted in the dark at 22°C. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, both in the presence and absence of ammonia nitrogen. Additionally, regardless of ammonia availability, milt eDNA followed a one-phase exponential decay pattern after an initial 24-h plateau in the presence of the NEM community. However, milt eDNA had a shorter half-life (12.5 h) in the absence of exogenous ammonia compared to when ammonia was present (15 h). In sterile mesocosms, eDNA was stable during the 72-h experiment. Together, these results suggest that the presence of microorganisms is necessary for short-term degradation of eDNA. Furthermore, nitrifying microbial communities, which are ubiquitous in most soil and water environments, could limit eDNA persistence in the environment. Understanding the contributions of environmental microbial communities will allow more confidence in sampling design and eDNA result interpretations for biodiversity management applications.

Environmental DNA↗

USGS2023

Ammonia and aquatic ecosystems – A review of global sources, biogeochemical cycling, and effects on fish

The purpose of this review is to better understand the full life cycle and influence of ammonia from an aquatic biology perspective. While ammonia has toxic properties in water and air, it also plays a central role in the biogeochemical nitrogen (N) cycle and regulates mechanisms of normal and abnormal fish physiology. Additionally, as the second most synthesized chemical on Earth, ammonia contributes economic value to many sectors, particularly fertilizers, energy storage, explosives, refrigerants, and plastics. But, with so many uses, industrial N 2 -fixation effectively doubles natural reactive N concentrations in the environment. The consequence is global, with excess fixed nitrogen driving degradation of soils, water, and air; intensifying eutrophication, biodiversity loss, and climate change; and creating health risks for humans, wildlife, and fisheries. Thus, the need for ammonia research in aquatic systems is growing. In response, we prepared this review to better understand the complexities and connectedness of environmental ammonia. Even the term “ammonia” has multiple meanings. So, we have clarified the nomenclature, identified units of measurement, and summarized methods to measure ammonia in water. We then discuss ammonia in the context of the N-cycle, review its role in fish physiology and mechanisms of toxicity, and integrate the effects of human N-fixation, which continuously expands ammonia's sources and uses. Ammonia is being developed as a carbon-free energy carrier with potential to increase reactive nitrogen in the environment. With this in mind, we review the global impacts of excess reactive nitrogen and consider the current monitoring and regulatory frameworks for ammonia. The presented synthesis illustrates the complex and interactive dynamics of ammonia as a plant nutrient, energy molecule, feedstock, waste product, contaminant, N-cycle participant, regulator of animal physiology, toxicant, and agent of environmental change. Few molecules are as influential as ammonia in the management and resilience of Earth's resources.

Science of the Total Environment↗