Biology subjects

Larson, E. R.

Publications and source records attributed to Larson, E. R..

3 recordsLinked to original sources

bioRxiv2025

Applying environmental DNA metabarcoding to calculate an index of biotic integrity for freshwater fish

Multi-metric indices like the Index of Biotic Integrity (IBI) are important biomonitoring tools for Clean Water Act compliance in the United States (US) but have also been implemented worldwide across many taxonomic groups. Environmental DNA (eDNA) metabarcoding could complement IBIs by increasing detection sensitivity for rare taxa while also reducing monitoring costs. To date, no studies have examined the efficacy of using eDNA metabarcoding to calculate IBIs in the US. Here, we used eDNA metabarcoding to calculate a fish-based IBI for streams and rivers of the Tennessee River Basin in northern Alabama, US. We collected water samples from 50 stream and river sites across a gradient of land use intensity, extracted eDNA from these samples, and sequenced the eDNA using vertebrate-specific primers. We compared our eDNA-IBI to a previous fish-IBI implemented by the state of Alabama using conventional sampling, as well as predicted biological condition of these streams from the US Environmental Protection Agency (EPA) based on a benthic macroinvertebrate multi-metric index (BMMI). We found a highly significant, positive relationship between the eDNA-IBI and fish-IBI for the same streams but a weaker, non-significant positive relationship between the eDNA-IBI and BMMI. Notably, the former was recovered despite eDNA-IBI sampling being conducted nine years after the conventional fish sampling at slightly different locations, the fish-IBI having used greater sampling effort throughout the year (including spring and autumn rather than only summer sampling), and a lack of reference DNA sequences that prevented eDNA detection for some species detected by conventional fish sampling. Accordingly, our study provides a baseline for how an eDNA-IBI may work relative to multi-metric indices calculated from conventional sampling, which can be improved through future directions identified and discussed in our paper.

molecular biology↗

bioRxiv2023

Paraburkholderia bonniea symbiont strain identity impacts amoeba host fitness and rate of horizontal transmission

In facultative symbioses, only a fraction of hosts are associated with a symbiont. Understanding why specific host and symbiont strains are associated can inform us of the evolutionary forces affecting facultative symbioses. Possibilities include ongoing host-symbiont coevolution driven by reciprocal selection, or priority effects that are neutral in respect to the host-symbiont interaction. We hypothesized that ongoing host-symbiont coevolution would lead to higher fitness estimates for naturally co-occurring (native) host and symbiont combinations compared to nonnative combinations. We used the Dictyostelium discoideum - Paraburkholderia bonniea system to test this hypothesis. P. bonniea features a reduced genome size relative to another Paraburkholderia symbiont of D. discoideum, indicating a significant history of coevolution with its host. Facultative symbionts may experience continued genome reduction if coevolution is ongoing, or their genome size may have reached a stable state if the symbiosis has also stabilized. Our work demonstrates that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead represents a stable facultative symbiosis. Specifically associated host and symbiont strains in this system are the result of priority effects, and presently unassociated hosts are simply uncolonized. We find evidence for a virulence-transmission trade-off without host strain specificity, and identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in benevolence. Lay summarySymbiotic relationships between hosts and their microbial partners are prolonged and intimate associations. Some of these relationships are obligatory for both a host and symbiont to survive, while others are facultative and each partner can survive without the other. In the latter case, some host individuals may be associated with a symbiont while others are not. Specific host and symbiont combinations can be the result of reciprocal adaptation between host and symbiont partners so that naturally co-occurring combinations are best suited for each other in terms of their biological fitness. On the other hand, the symbiont that a host is associated with may simply be the symbiont that arrived first, in what is called a priority effect. We sought to determine which possibility best explained naturally co-occurring combinations of host and symbiont strains of the social amoeba Dictyostelium discoideum and its symbiont Paraburkholderia bonniea. Our work demonstrates that D. discoideum and P. bonniea are in a stable facultative relationship. Specifically associated host and symbiont combinations are the result of priority effects, and D. discoideum hosts without symbionts are simply uncolonized. This work fills a gap in our understanding of the evolutionary forces affecting facultative symbiotic relationships. We also show for the first time that P. bonniea symbionts can spread among amoeba hosts when they aggregate together during the social stage of their life cycle.

evolutionary biology↗

bioRxiv2020

Identifying root traits affecting root-substrate adhesion in Arabidopsis using a novel centrifugation technique

The physical presence of roots and the compounds they release affect the cohesion between roots and their environment. However, the plant traits that are important for these interactions are unknown and most methods that quantify the contributions of these traits are time-intensive and require specialist equipment and complex substrates. Our lab developed an inexpensive, high-throughput phenotyping assay that quantifies root-substrate adhesion in Arabidopsis thaliana. We now report that this method has high sensitivity and versatility for identifying different types of traits affecting root-substrate adhesion including root hair morphology, vesicle trafficking pathways and root exudate composition. We describe a practical protocol for conducting this assay and introduce its use in a forward genetic screen to identify novel genes affecting root-substrate interactions. This assay is a powerful tool for identifying and quantifying genetic contributions to cohesion between roots and their environment.

plant biology↗