Biology subjects

Gilbert, N. E.

Publications and source records attributed to Gilbert, N. E..

6 recordsLinked to original sources

bioRxiv2026

Iron limitation alters diatom carbon flow through shifts in microbiome exometabolite consumption

Iron is required for photosynthesis, and thus affects biogeochemical cycling in widespread regions where its availability is limited. Turnover of aquatic photosynthetically-derived carbon is largely constrained by bacterial activity, but we lack a mechanistic understanding of how iron limitation influences this activity. We examined a bacterial enrichment community dependent on carbon from the diatom Phaeodactylum tricornutum to investigate how iron limitation alters the flow of carbon to bacteria, and exometabolite and community composition. Using stable isotope tracing, we quantified diatom exudate incorporation with single-cell-resolution. We identified a population of bacteria under iron limitation with high metabolic activity yet low incorporation of newly-fixed diatom carbon, indicating a shift in metabolism relative to the iron-replete control. Ultra-high-resolution exometabolomics revealed bacterial consumption of aromatics, lipid-like compounds, and purines and pyrimidines occurred under iron-limitation, when these compounds also exhibited increased exudation. We identified gene pathways for utilization of these compounds in taxa with increased abundance under iron limitation which may be responsible for carbon flow shifts. These results provide a mechanistic link between iron-limitation driven shifts in exudate composition and flow of carbon to the microbiome. This has important implications for predicting carbon flow in surface oceans and manipulating algal-bacterial interactions in engineered systems.

microbiology↗

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

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↗

bioRxiv2024

An algicidal bacterium shapes the microbiome during outdoor diatom cultivation collapse

Biogeochemistry and productivity of algae-dominated environments is fundamentally influenced by the diversity and activity of bacteria. Namely, algicidal bacteria that prey on algal hosts can control elemental cycling and host populations within outdoor algal ponds used for biofuel production. In this study, we describe the genomic and proteomic signatures of a putative algicidal bacterium, Kordia sp. (family Flavobacteriaceae), that bloomed during a population-wide crash of the biofuel diatom, Phaeodactylum tricornutum. This Kordia sp. bloom occurred after 29 days of cultivation in outdoor algal raceway ponds inoculated with P. tricornutum, but not in parallel ponds inoculated with Microchloropsis salina. Several signatures of antagonism expressed by Kordia during diatom demise highlights previously unexplored mechanisms that may aid in algicidal activity or bacterial competition, including the type VI secretion system and hydrogen peroxide production. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provides evidence that cross-feeding is important in supporting microbial diversity during algal demise. Specifically, in situ and laboratory data suggest that Kordia acts as a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploit degradation molecules or scavenge metabolic byproducts for carbon. Further, targeted analysis of 30 Rhodobacteraceae metagenome assembled genomes suggest algal pond Rhodobacteraceae commonly harbor pathways for carbon monoxide oxidation, a potential strategy to persist under competition. Collectively, these observations further constrain the role of algicidal bacteria in the aquatic ecosystem.

microbiology↗

bioRxiv2024

Diel Partitioning in Microbial Phosphorus Acquisition in the Sargasso Sea

The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. According to temporal niche partitioning theory, competition for scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism structuring uptake of limiting nutrients and facilitating coexistence of diverse microbes in open ocean ecosystems.

ecology↗

bioRxiv2023

Declines in ice cover induce light limitation in freshwater diatoms

The rediscovery of diatom blooms embedded within and beneath Lake Erie ice cover (2007-2012) ignited an intense interest in psychrophilic adaptations and winter limnology. Subsequent studies determined ice plays a vital role in winter diatom ecophysiology, as diatoms partition to the underside of ice thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly ice-free state in several recent winters. It has been hypothesized the resultant turbid, isothermal water column will induce light limitation amongst winter diatoms, serving as a detrimental competitive disadvantage. Here, we conducted a physiochemical and metatranscriptomic survey of the winter Lake Erie water column (2019-2020) that spanned spatial, temporal, and climatic gradients to investigate this hypothesis. We determined ice-free conditions decreased diatom bloom magnitude and altered diatom community composition. Diatoms increased the expression of various photosynthetic genes and iron transporters, suggesting they are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). Notably, we identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a second means of light-driven energy acquisition) and fasciclins (a means to "raft" together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.

ecology↗