Biology subjects

Gilbert, N. E.

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

3 recordsLinked to original sources

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↗