Biology subjects

Ndlovu, K. S.

Publications and source records attributed to Ndlovu, K. S..

3 recordsLinked to original sources

bioRxiv2025

Sub-daily Bermuda Atlantic Time Series virus sampling reveals taxonomy, host, and functional differences at the population, but not community level

Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4-(surface) or 12-(deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community-and population-scale short-time-frame observations relevant to future climate state modeling.

microbiology↗

bioRxiv2025

The cervicovaginal microbiome of pregnant people living with HIV on antiretroviral therapy in the Democratic Republic of Congo: A Pilot Study and Global Meta-analysis.

Recent studies are revealing that a suboptimal cervicovaginal microbiome (CVMB), including enrichment of anaerobic bacteria associated with multiple female genital disorders, and adverse pregnancy and birth outcomes in pregnant people. Problematically, however, the majority of the available data to date are biased towards highly developed, Global North countries, leaving underrepresented populations like the Democratic Republic of Congo (DRC) poorly characterised. Here, we investigate the CVMB from a cohort of 82 pregnant people living with HIV (PLWH) on antiretroviral therapy (ART) from the DRC. Specifically, we explore the associations between the CVMB via 16S rRNA gene sequencing and maternal peripheral immune factors. Additionally, we compare the CVMB of PLWH-ART from DRC to publicly available CVMB data (5 studies, 1861 samples) in a meta-analysis to elucidate the impact of HIV on the CVMB. Combined, these analyses revealed differences in community structure and predicted function of the microbiota between PLWH-ART and pregnant people without HIV (PWoH). Taxonomically, the CVMB of DRC PLWH-ART were enriched for Lactobacillus iners-dominated CVMBs (53%) or a diverse, polymicrobial CVMB, i.e., bacterial vaginosis (BV) (43%). Functional predictions made from these taxa suggested that protein-coupled receptors, amino sugar and nucleotide sugar metabolism, fatty acid metabolism, and polycyclic aromatic hydrocarbon degradation pathways were differentially abundant between communities. Correlation with host plasma immune factors revealed putative links between some CVMB metrics (e.g., alpha diversity and species abundance) that have been linked to adverse pregnancy and birth outcomes. ImportanceHIV remains prevalent in sub-Saharan Africa, where it has been linked to adverse birth outcomes. . Suboptimal CVMBs have shown similar links. This pilot study fills critical gaps in understanding how HIV interacts with the pregnant CVMB in populations underrepresented in microbiome research, like the Democratic Republic of Congo. We identified maternal systemic immune factors associated with suboptimal CVMBs that have been linked to poor birth outcomes. In a global meta-analysis, we found significant taxonomic and functional difference in the CVMBs between pregnant people living with and without HIV, revealing potential biomarkers that for increased risks for adverse birth outcomes. These findings provide crucial insights into CVMB features that may influence pregnancy health in pregnant people living with HIV, guiding future research and tailored interventions to support safer pregnancies in the DRC and similar populations.

microbiology↗

bioRxiv2025

Seasonal Enhancement of the Viral Shunt Catalyzes a Subsurface Oxygen Maximum in the Sargasso Sea

Subsurface oxygen maxima (SOMs) occur directly beneath the mixed layer of stratified water columns across oligotrophic open ocean basins. SOMs occur seasonally and are hypothesized to result from elevated microbial net primary productivity (NPP). Here, we set out to identify mechanistic drivers of the SOM near the Bermuda Atlantic Time Series (BATS) site in the Sargasso Sea in October 2019. Coupled time-series analysis of metatranscriptomics, flow cytometry, and family-specific cyanophage quantification revealed elevated Prochlorococcus abundances, cyanophage abundances, and cyanophage-specific transcriptional activity in the SOM. These findings spurred us to analyze historical oxygen saturation profiles at BATS - identifying a repeated, seasonal cycle in SOM emergence associated with elevated virus-like particles and Prochlorococcus numbers. Returning to the 2019 study site, we found that transcriptional markers for increased dissolved organic matter uptake by copiotrophic bacteria were enriched in the SOM, consistent with enhanced catabolic activity due to the viral shunt. In addition, Prochlorococcus exhibited enrichment in ammonium transport transcripts at the SOM, consistent with increased responsiveness to remineralization activity by heterotrophs. Altogether, these findings suggest that enhanced viral lysis leads to locally elevated nutrient recycling and oxygen production, further reinforcing hypotheses that viruses may play a critical role in the emergence of SOMs in the oligotrophic ocean.

ecology↗