Miner, M. | bioRxiv Science

bioRxiv2026

Community assembly dynamics in a regulated stream: Insights from environmental DNA

Degradation of freshwater habitats, including the alteration of natural flow regimes by impoundment, is a major threat to native fishes. When dam removal is not possible, management actions to recover natural flow regimes can benefit native species, but monitoring community responses is crucial to show efficacy. We used eDNA metabarcoding to quantify spatiotemporal trends in fish assemblages along the longitudinal profile of a regulated stream where a court-ratified environmental flows framework is used to benefit native fishes. At a subset of sites, we also compared eDNA results with concurrent surveys conducted using long-term standardized fisheries monitoring techniques to evaluate concordance. From 59 eDNA samples collected over approximately 2 years, we detected 26 fish taxa, including 8 native species, with 25 taxa resolving to species level using a custom reference sequence database; one taxon could not be resolved between closely related species. Fish assemblages varied predictably along the longitudinal profile of the stream and by season (fall and spring). Diversity indices were higher at downstream sites and in fall, reflecting greater richness of warm-water non-native species. Evenness was similar among sites but shifts in species ranks suggests reordering processes drive spatiotemporal variation in assembly. Gradient forest analysis identified thirteen species associated with spatiotemporal gradients, including both native cold-water species and non-native warm-water species. Overall, eDNA results were concordant with conventional fisheries monitoring but eDNA detected significantly greater species richness through increased detection of rare species. eDNA results align with long-term monitoring that demonstrated assemblage shifts in upper, but not lower stream reaches, and extends the insights into spatial responses, species reordering, and ecology of rare species. These findings demonstrate the value of eDNA as a complementary tool for understanding community assembly dynamics, including responses to stream rehabilitation and ecosystem management.

ecology↗

bioRxiv2025

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the HIV antibody mediated prevention (AMP) trials, the broadly neutralizing antibody VRC01 demonstrated protective efficacy against new diagnoses with susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, we performed deep sequencing on 172 participants in the placebo and treatment arms, generating 63,444 gag-{Delta}pol (2.5 kb) and 53,088 rev-env-{Delta}nef (3 kb) sequences. Sequences were classified into transmitted founder lineages (TFLs), and infections with multiple distinct lineages were determined. Multilineage infections were detected in [~]38% of participants in both the African (HVTN 703/HPTN 081) and Americas/Europe (HVTN 704/HPTN 085) cohorts, regardless of placebo or treatment group, or cohort. The high levels of multilineage infections could be attributed to minor lineages (<5% abundance) identified in 20% of participants. Infection with VRC01 discordant viruses (IC80s >3-fold different) was observed in 40% of multilineage infections, with a trend toward greater intra-host neutralization differences with increasing VRC01 dose (Jonckheere-Terpstra test, p=0.072). In six VRC01 treated participants who acquired both sensitive (IC80<1{micro}g/ml) and resistant viruses (IC80>3{micro}g/ml), the sensitive lineages declined over time. Recombination was pervasive, observed in 63% of multilineage infections at the time of HIV diagnosis. In one treated participant infected with VRC01 discordant lineages, recombinant viruses preferentially inherited the resistance mutation (binomial p=0.004). In conclusion, our in-depth analysis of breakthrough viruses in the AMP trials revealed a high frequency of multilineage infections, including infections with viruses with different VRC01 sensitivities. This analysis also highlights the role of recombination in shaping intra-host viral evolution and facilitating escape from VRC01. SignificanceThis work advances our understanding of the diversity of initial viral infection and evolution and in vivo activity of broadly neutralizing antibodies (bNAbs). Deep sequencing revealed [~]38% of HIV acquisitions with multiple transmitted founder lineages, higher than previous studies. These occurrences were similar in the placebo and VRC01 groups. Viral recombination among post-acquisition variants was common under antibody selection and appeared to favor resistant sequences in the treatment group. These data suggest as with single antiviral therapy, passive and active immunization of bNAbs should be directed at multiple antigen targets of HIV-1.

molecular biology↗