Biology subjects

Sharpe, G. C.

Publications and source records attributed to Sharpe, G. C..

5 recordsLinked to original sources

bioRxiv2024

Flagella are required to coordinately activate competition and host colonization factors in response to a mechanical signal

Bacteria employ antagonistic strategies to eliminate competitors of an ecological niche. Contact-dependent mechanisms, such as the type VI secretion system (T6SS), are prevalent in host-associated bacteria, yet we know relatively little about how T6SS+ strains make contact with competitors in highly viscous environments, such as host mucus. To better understand how cells respond to and contact one another in such environments, we performed a genome-wide transposon mutant screen of the T6SS-wielding beneficial bacterial symbiont, Vibrio fischeri, and identified two sets of genes that are conditionally required for killing. LPS/capsule and flagellar-associated genes do not affect T6SS directly and are therefore not required for interbacterial killing when cell contact is forced yet are necessary for killing in high-viscosity liquid (hydrogel) where cell-cell contact must be biologically mediated. Quantitative transcriptomics revealed that V. fischeri significantly increases expression of both T6SS genes and cell surface modification factors upon transition from low-to high-viscosity media. Consistent with coincubation and fluorescence microscopy data, flagella are not required for T6SS expression in hydrogel. However, flagella play a key role in responding to the physical environment by promoting expression of the surface modification genes identified in our screen, as well as additional functional pathways important for host colonization including uptake of host-relevant iron and carbon sources, and nitric oxide detoxification enzymes. Our findings suggest that flagella may act as a mechanosensor for V. fischeri to coordinately activate competitive strategies and host colonization factors, underscoring the significance of the physical environment in directing complex bacterial behaviors. SignificanceThe physical environment can have dramatic effects on bacterial behavior, but little is known about how mechanical signals impact antagonistic interactions. Symbiotic bacteria use molecular weapons to eliminate competitors for limited space within highly viscous host tissue and mucus. To better understand how the physical environment affects competition and adhesion within eukaryotic hosts, we used quantitative transcriptomics to reveal the flagella-dependent transcriptional response to bacterial transition from lower to a higher viscosity environment. This work revealed the T6SS interbacterial weapon is coordinately activated with host colonization factors, emphasizing the importance of integrating activation of interbacterial weapons into host colonization pathways to enhance a symbionts ability to successfully colonize the host while efficiently eliminating potential competitors from the host niche.

microbiology↗

bioRxiv2023

Microbial Respiration in Contrasting Ocean Provinces via High-Frequency Optical Assays

Microbial respiration plays a pivotal role in the marine carbon cycle, influencing the fraction of fixed carbon that undergoes remineralization versus export to depth. Despite its importance, methodological constraints have led to an inadequate understanding of this process, especially in low-activity oligotrophic and mesopelagic regions. Here, we quantify respiration rates as low as 0.2 {micro}mol O2 L-1 d-1 in contrasting ocean productivity provinces using optical oxygen sensors to identify size-fractionated respiration trends. At the low productivity North Pacific Ocean Station Papa, surface microbial respiration was relatively stable at 1.2 {micro}mol O2 L-1 d-1. Below the surface there was a decoupling of respiration and bacterial production potentially driven by phytodetritus remineralization. Size-fractionated rates showed cells <5 {micro}m contributed the most to Pacific respiration. At the North Atlantic Porcupine Abyssal Plain, the optode measurement frequency was drastically increased. Surface microbial respiration was higher (1.7 {micro}mol O2 L-1 d-1) and decreased by 3-fold below the euphotic zone. The Atlantic filtered fraction contributions to total respiration shifted with the phytoplankton bloom evolution. The high resolution optode method used in the Atlantic is consistent with coinciding in vivo 2-para-(iodophenyl)-3(nitrophenyl)-5(phenyl) tetrazolium chloride respiratory stain measurements and historical site estimates. We estimate that 58% of gross primary production was respired at the Pacific site and 34% at the Atlantic site, demonstrating that the Atlantic had a higher carbon export potential. This study highlights the dynamic nature of respiration across vertical, temporal, and size-fractionated factors, emphasizing the need for sensitive, high-throughput techniques to better understand ocean ecosystem metabolism.

microbiology↗

bioRxiv2023

Primary production dynamics during the decline phase of the North Atlantic annual spring bloom

The second field campaign of the NASA EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) program was conducted in the late spring of 2021 within the vicinity of the Porcupine Abyssal Plain (49.0{degrees}N, 16.5{degrees}W) in the North Atlantic Ocean. Observations from EXPORTS support previous characterizations of this system as highly productive and organic matter rich, with the majority of primary production occurring in large cells ([≥] 5 {micro}m) such as diatoms that are primarily utilizing nitrate. Rates of total euphotic zone depth-integrated net primary production ranged from 36.4 to 146.6 mmol C m- 2 d-1, with an observational period average f-ratio of 0.74, indicating predominantly new production. Substantial variability in the contribution of small (<5 {micro}m) and large cells occurred over the observation period, coinciding with the end of the annual spring phytoplankton bloom. Physical changes associated with storms appear to have impacted the integrated production rates substantially, enhancing rates by [~]10%. These disturbances altered the balance between contributions of the different phytoplankton size fractions, thus highlighting the important role of mixed layer variability in nutrient entrainment into the upper water column and production dynamics. In diatoms, inputs of silicic acid related to deepening of the mixed layer increased silicic acid uptake rates yet concomitant increases in NPP in large cells was not observed. This campaign serves as the high productivity endmember within the EXPORTS program and as such, elucidates how nutrient concentrations and size class play key roles in both low and high productivity systems, but in differing ways.

ecology↗

bioRxiv2023

The Vibrio fischeri type VI secretion system incurs a fitness cost under host-like conditions

The type VI secretion system (T6SS) is an interbacterial weapon composed of thousands of protein subunits and predicted to require significant cellular energy to deploy, yet a fitness cost from T6SS use is rarely observed. Here, we identify host-like conditions where the T6SS incurs a fitness cost using the beneficial symbiont, Vibrio fischeri, which uses its T6SS to eliminate competitors in the natural squid host. We hypothesized that a fitness cost for the T6SS could be dependent on the cellular energetic state and used theoretical ATP cost estimates to predict when a T6SS-dependent fitness cost may be apparent. Theoretical energetic cost estimates predicted a minor relative cost for T6SS use in fast-growing populations (0.4-0.45% of total ATP used cell-1), and a higher relative cost (3.1-13.6%) for stationary phase cells. Consistent with these predictions, we observed no significant T6SS-dependent fitness cost for fast-growing populations typically used for competition assays. However, the stationary phase cell density was significantly lower in the wild-type strain, compared to a regulator mutant that does not express the T6SS, and this T6SS-dependent fitness cost was between 11 and 23%. Such a fitness cost could influence the prevalence and biogeography of T6SSs in animal-associated bacteria. While the T6SS may be required in kill or be killed scenarios, once the competitor is eliminated there is no longer selective pressure to maintain the weapon. Our findings indicate an evolved genotype lacking the T6SS would have a growth advantage over its parent, resulting in the eventual dominance of the unarmed population.

microbiology↗

bioRxiv2022

Synechococcus nitrogen gene loss in iron-limited ocean regions

Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine primary productivity. Despite their biogeochemical importance, Synechococcus populations have been unevenly sampled across the ocean, with most studies focused on low-latitude strains. In particular, the near absence of Synechococcus genomes from high-latitude, High Nutrient Low Chlorophyll (HNLC) regions leaves a gap in our knowledge of picocyanobacterial adaptation to iron limitation and their influence on carbon, nitrogen, and iron cycles. We examined Synechococcus populations from the subarctic North Pacific, a well-characterized HNLC region, with quantitative metagenomics. Assembly with short and long reads produced two near complete Synechococcus metagenome-assembled genomes (MAGs). Quantitative metagenome-derived abundances of these populations matched well with flow cytometry counts, and the Synechococcus MAGs were estimated to comprise >99% of the Synechococcus at Station P. Whereas the Station P Synechococcus MAGs contained multiple genes for adaptation to iron limitation, both genomes lacked genes for uptake and assimilation of nitrate and nitrite, suggesting a dependence on ammonium, urea, and other forms of recycled nitrogen leading to reduced iron requirements. A global analysis of Synechococcus nitrate reductase abundance in the TARA Oceans dataset found nitrate assimilation genes are also lower in other HNLC regions. We propose nitrate and nitrite assimilation gene loss in Synechococcus represents an adaptation to severe iron limitation in high-latitude regions where ammonium availability is higher. Our findings have implications for models that quantify the contribution of cyanobacteria to primary production and subsequent carbon export. SignificanceThe cyanobacterium Synechococcus is a major contributor to ocean primary production and biogeochemistry. Here, we used quantitative metagenomics to assemble and enumerate two Synechococcus genomes from an iron-limited, High Nutrient Low Chlorophyll region. We show these genomes represent the majority of Synechococcus cells at the site and are the first known Synechococcus unable to assimilate either nitrate or nitrite. This gene loss is likely due to the high iron quota of these proteins and predominant availability of recycled forms of nitrogen. Synechococcus loss of nitrate assimilation affects their role in elemental cycles (e.g., carbon, nitrogen, and iron), limits their potential for carbon export, and enhances our understanding of Synechococcus evolution in response to nutrient limitation and competition.

ecology↗