Biology subjects

Stuart, R.

Publications and source records attributed to Stuart, R..

6 recordsLinked to original sources

bioRxiv2026

Oxidative stress reshapes diatom-microbiome interactions by shifting benefits from mutualistic to opportunistic bacteria

The roles of reactive oxygen species (ROS) as signaling molecules and inhibitors of phytoplankton growth are well documented. While phytoplankton physiological mechanisms for ROS detoxification are well characterized, the role of heterotrophic bacterial partners in ROS alleviation and outcomes for these bacteria remain poorly understood. Here, we examined how extracellular hydrogen peroxide (H2O2) shapes nutrient exchange between the diatom Phaeodactylum tricornutum and two phycosphere bacteria. From an initial screen of 20 bacteria, we identified a "helper" (Muricauda sp.) that enabled P. tricornutum to survive acute H2O2 stress and a "non-helper" (Algoriphagus sp.) that did not. Using nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked diatom-derived carbon and nitrogen (13C and 15N) transfer to each bacterial partner under ROS stress. Oxidative stress disrupted diatom metabolism and altered nutrient transfer: diatom-derived carbon and nitrogen incorporation was significantly reduced in the helper but increased in the non-helper under H2O2 stress. Growth assays revealed that the helper preferentially utilized exudates from healthy, intact hosts, whereas the non-helper did not grow on exudates but thrived on lysates from damaged or lysed cells. Together, these findings indicate the helper was better adapted to accessing resources from living hosts, while the non-helper relied on nutrients released through ROS-induced host damage. Our results highlight oxidative stress as a key driver of algal-bacterial interactions and suggest that bacterial resource-acquisition strategy underlies host protection: bacteria utilizing healthy-host exudates are more likely to protect hosts from oxidative stress, while those benefiting from host damage are not, despite retaining ROS detoxification capacity.

microbiology↗

bioRxiv2025

Direct and diffuse cross-kingdom interactions in plant microbiome assembly

Studies of plant-associated microbial communities consistently indicate a role for classic assembly mechanisms, such as environmental and host filters, but often leave substantial unexplained variation. Biotic interactions within microbial communities may help to fill this gap, specifically cross-kingdom interactions between fungi and bacteria, as these are increasingly found to be important to both assembly and function. We hypothesized that direct interactions between bacteria and fungi are an important driver of composition in low-diversity leaf habitats, where pairwise interactions are more likely. In high-diversity root habitats, we expected diffuse, indirect interactions to be more relevant to composition. To test these hypotheses, we characterized bacterial and fungal communities of switchgrass (Panicum virgatum L.) leaves and roots at 14 sites spanning mountain to coastal ecoregions of North Carolina, USA. We analyzed putative direct and diffuse interactions using ecological network inference and partitioned variance explained in microbial community composition by spatial, environmental, and biotic interactions. We found that cross-kingdom biotic interactions contributed to microbial community structure. The largest improvements to variance explained (5-11%) were from direct interactions, except for root fungal communities where diffuse interactions (7.5%) explained more than double that of direct interactions (2.8%). These contributions were comparable to those from environmental and spatial factors. The joint effects of putative biotic interactions and environmental conditions also contributed to the explained variation, highlighting the importance of environmental tracking in microbes. These findings suggest that using network inference for identifying cross-kingdom ecological interactions can improve our fundamental understanding of how plant-associated microbiomes assemble, which is also directly relevant to applied efforts such as the effective development of synthetic communities.

ecology↗

bioRxiv2024

Spatially structured competition and cooperation alters algal carbon flow to bacteria

Microbial communities regulate the transformations of carbon in aquatic systems through metabolic interactions and food-web dynamics that can alter the balance of photosynthesis and respiration. Direct competition for resources is thought to drive microbial community assembly in algal systems, but other interaction modes that may shape communities are more challenging to isolate. Through untargeted metabolomics and metabolic modeling, we predicted the degree of resource competition between bacterial pairs when growing on model diatom Phaeodactylum tricornutum-derived substrates. In a subsequent sequential media experiment, we found that pairwise interactions were consistently more cooperative than predicted based on resource competition alone, indicating an unexpected role for cooperation in algal carbon processing. To link this directly to algal carbon fate, we chose a representative cooperative and competitive influencer isolate and a model recipient and applied single-cell isotope tracing in a custom porous microplate cultivation system. In the presence of live algae, the recipient drew down more algal carbon in the presence of the cooperative influencer compared to the competitive influencer, supporting the sequential experiment results. We also found that total carbon assimilation into bacterial biomass, integrated over influencer and recipient, was significantly higher for the cooperative interaction. Our findings support the notion that non-competitive interactions are critical for predicting algal carbon fate. Significance StatementMicrobial interactions have widely been studied in the context of host resources but testing and measuring direct interactions in a lab has been particularly challenging. By combining untargeted metabolomics, sequential/(co-)culture, and metabolic modeling, we demonstrate that the presence of an unexpected interaction mode in a live system and show how it impacts the flow of host-derived resources. This top-down approach can help identify novel bacterial interactions that play a crucial role in microbial community-host ecosystems, which may have an impact in holobiont phenotypes including alga, fungal, or plant systems.

microbiology↗

bioRxiv2024

Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction

Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtiis capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum, a vitamin B12-producing -proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the algas fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15NH4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide - a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B12 and supported the growth of a B12-dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.

microbiology↗

bioRxiv2022

Single cell carbon and nitrogen incorporation and remineralization profiles are uncoupled from phylogenetic groupings of diatom-associated bacteria

Bacterial remineralization of algal organic matter is thought to fuel algal growth, but this has not been quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others, nor whether this is linked their incorporation. We quantified bacterial incorporation of algal-derived complex dissolved organic C (DOC) and N (DON) and net algal incorporation of remineralized C and N at the single cell level using isotope tracing and NanoSIMS for fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum. We found unexpected variability in the net C and N fluxes between algae and bacteria, including non-ubiquitous complex DON utilization and remineralization. We identified three distinct functional categories of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional categories were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics. Using comparative proteogenomic analyses, we show that a complex DON incorporating strain expressed proteins related to growth and peptide transport, and a non-incorporator prioritized reactive oxygen species scavenging and inorganic nutrient uptake. Our analysis suggests that phylogeny does not predict the extent of algae-bacteria metabolite exchange, and activity-based measurements are indispensable to classify the high diversity of microbes into functional groups. These categorizations are useful for conceptual understanding and mechanistic numerical modeling to ultimately predict the fate of elemental cycles in response to environmental change.

microbiology↗

bioRxiv2022

Mycorrhizal fungi stabilize bacterial growth and diversity in water-limited soils

Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H 18O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis- compared in S. bescii- inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought-susceptible. Overall, H 18O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.

ecology↗