Biology subjects

Bledsoe, R. B.

Publications and source records attributed to Bledsoe, R. B..

7 recordsLinked to original sources

bioRxiv2025

Rhizobia independently adapt to soil and legume host environments, but soil conditions influence the abundance of high-quality partners.

Rhizobia live as free-living microorganisms in the soil and in association with legume hosts. Both environments exert selective pressures on rhizobia, influencing the reproductive success of individual strains (e.g., fitness). The soil, a heterogeneous and fluctuating environment, is often overlooked, and little is known about whether selection in the soil influences the outcomes of the rhizobia-legume mutualism. We exposed a mixture of 68 Sinorhizobium meliloti strains to eight soil treatments (temperature, osmotic, and texture perturbations) and selection by two Medicago plant hosts. We found that cold (4{degrees}C) and warm (32{degrees}C) temperatures, as well as salt addition, had the strongest effects on diversity, community composition, or population size. Strain relative fitness was strongly positively correlated among soil treatments, except for cold. Genome-wide association analysis revealed a complex genetic architecture for soil fitness. In contrast, when comparing rhizobial fitness between soil and host environments, we found minimal strain fitness correlations, suggesting independent genetic bases and habitat-specific adaptations. Lastly, by examining the relationship between rhizobial fitness in the soil and their nitrogen-fixing plant benefits, we found that soil selection influenced the relative abundance of high- and low-quality strains; However, whether these effects were positive or negative for the plant was host dependent. Our results suggest that rhizobial evolution in soil and host are largely independent, but soil selection can alter mutualism benefits. IMPORTANCERhizobia-legume mutualism is crucial for introducing nitrogen into agricultural and natural ecosystems, and rhizobia persistence in the soil is an important component of agroecosystems. However, we know little about how individual strains of rhizobia persist and adapt to this environment, especially in the context of the soils spatial and temporal variations (temperature, moisture, and soil texture). We found that rhizobia similarly adapt to abiotic soil conditions but their reproductive success in the soil is independent from their reproductive success in the host. Intriguingly, we found that certain soil conditions increase (or decrease) the relative abundance of more effective nitrogen-fixing strains. Understanding how rhizobia adapt to diverse environments is crucial for developing effective bioinoculants that maintain high persistence in the soil while are also highly competitive to colonize the host and are beneficial to the plant.

ecology↗

bioRxiv2024

The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization

Plant-beneficial microbes have great potential to improve sustainability in agriculture. Still, managing beneficial microbes is challenging because the impact of microbial dormancy on community assembly across the soil, rhizosphere, and endosphere is poorly understood. We address this gap with the first documented use of Biorthogonal Non-Canonical Amino Acid Tagging (BONCAT) to probe active microbes in the soil-to-root gradient. Using nodule-forming legume Trifolium incarnatum, we confirmed that BONCAT is suitable for labeling endospheric microbes with microscopy. Next, we coupled BONCAT to Flow Cytometer Activated Cell Sorting (FACS) and 16S rRNA amplicon sequencing to probe patterns of microbial activity and the structure of the active microbial community across the soil, rhizosphere, root, and nodule with a native soil microbial community. As expected, we found x10 higher microbial activity in the endosphere than in the rhizosphere or bulk soil, likely due to increased plant resources. Finally, we revealed that microbial activity in the rhizosphere was significantly associated with successful endosphere colonization, more so than microbial abundance alone. This last finding has implications for the development of microbial inoculants, suggesting colonizing plant roots is linked to a microbes ability to overcome dormancy once deployed in the soil.

microbiology↗

bioRxiv2024

In multi-strain inoculations, mutation of Medicago symbiosis genes creates a complex selective landscape for naturally-occurring genetic variation in rhizobia

In the mutualism between leguminous plants and rhizobia bacteria, rhizobia live inside root nodules, creating potential for host genes to shape the rhizobial selective environment. Many host genes that affect symbiosis have been identified; however, the extent to which these genes affect selection acting on rhizobia is unknown. In this study, we inoculated 18 Medicago truncatula symbiotic mutants (including mutants that alter Nodule Cysteine-Rich (NCR) peptide production, plant defense, and nodule number regulation) with a mixture of 86 Sinorhizobium meliloti strains. Most mutations resulted in reduced host benefits, but the effects on rhizobial benefit (i.e., relative strain fitness) varied widely, revealing widespread host-by-strain fitness interactions. Genome-wide association analyses identified variants on rhizobial replicons pSymA and pSymB as important in mediating strain fitness responses to host mutations. Whereas most top variants affected rhizobial fitness with one host mutant (limited effect variants), nine affected fitness across six or more host mutations. These pervasive variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and some metabolic genes. In contrast to the limited effect variants, variants with pervasive positive effects on strain fitness when host genes were mutated tended to adversely affect fitness in wild-type hosts. Competition assays across Medicago genotypes confirmed a pervasive role for one candidate (malonyl-CoA synthase), and AlphaFold multimer modelling suggests that many rhizobial top candidates could interact with host NCR peptides. Our results reveal how host genetic variation affects rhizobial fitness, setting the stage for improving rhizobial inoculants and breeding legume hosts better adapted to multi-strain environments.

evolutionary biology↗

bioRxiv2020

Dynamic hydrology and plant-mediated effects reduce greenhouse gas emissions and alter wetland microbial communities

While wetlands represent a small fraction ([~]5-10%) of the worlds land surface, it is estimated that one-third of wetlands have been lost due to human activities. Wetland habitat loss decreases ecosystem benefits, including improved water quality and climate change mitigation. These microbially mediated functions are dependent on redox conditions, which are altered by soil hydrology and the presence of plants. We tested the overarching hypothesis that while microbial community composition would be resistant to change due to long-term hydrologic history, key functions like greenhouse gas production would remain plastic and responsive to short-term environmental shifts. Using a mesocosm design, we manipulated the duration of hydrologic conditions (i.e., stable dry, stable flooding, and alternating wet/dry) and the presence of plants to induce soil redox changes in wetland soils. We measured soil redox status, used targeted amplicon and shotgun metagenomic sequencing to characterize microbial communities, and measured greenhouse gas production to assess microbial function. The eight-week hydrologic treatment shifted community composition but did not override the stronger effects of long-term hydrologic history. Methane and carbon dioxide fluxes were altered by short-term hydrologic treatment, with methane production favored in the wet treatment and carbon dioxide production favored in the dry treatment. Plant presence versus absence manipulation had little impact on soil microbiome composition or soil greenhouse gas production. The results highlight the resistance of microbial community structure shaped by historical hydrologic regimes, and emphasize that hydrologic conditions exert a stronger influence than plant presence on microbial composition and function. Predicting the outcomes of wetland disturbance and restoration requires an enhanced understanding of community stability and functional plasticity. Our results suggest that wetland hydrologic restoration can establish a stable microbial community that is resistant to environmental shifts, but microbial functions such as greenhouse gas emissions remain responsive to hydrologic disturbances, including flooding and drought.

ecology↗

bioRxiv2020

A microbial perspective on balancing trade-offs in ecosystem functions in a constructed stormwater wetland

Green stormwater infrastructure, such as constructed wetlands (CWs), is a type of stormwater control measure that can decrease nutrient and pollutant loads from urban stormwater runoff. Wetland soil microorganisms provide nutrient and pollutant removal benefits which can also result in ecosystem disservices such as greenhouse gas (GHG) emissions and can inadvertently exacerbate climate change. Microbial respiration by facultative anaerobes in anoxic conditions is the primary pathway for nitrogen removal (benefit). Similar anoxic conditions that support denitrifying microorganisms can also support obligate anaerobes that produce methane (CH4) via methanogenesis (disservice). We examined nitrogen removal potential, GHG production, and microbial community structure within permanently flooded and shallow land or temporarily-flooded areas of a stormwater CW to identify zones for CW design optimization. Results indicate that permanently flooded zones compared to shallow land zones are greater sources of CH4 emissions (80.80 {+/-} 118.31, 2.32 {+/-} 9.33 mg CH4-C m-2 hr-1, respectively) and emit more carbon to the atmosphere (7161.27 kg CO2, 93.20 kg CO2 equivalents, respectively). However, nitrogen removal potential rates were similar across both flooded and shallow land zones (24.45 {+/-} 20.18, 20.29 {+/-} 15.14 ng N2O-N hr-1 g-1 dry soil, respectively). At this particular CW, reduction of permanently flooded zones within the wetland could decrease GHG emissions (disservice) without limiting nitrogen removal (benefit) potential of the wetland. Holistic development and design of stormwater control measures, which account for microbial activity, provides the opportunity to maximize benefits (i.e., nutrient and pollutant removal) and reduce disservices (i.e., GHG emissions) of green stormwater infrastructure.

ecology↗

bioRxiv2020

Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres

In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast growing copiotrophs, slow growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized vs. unfertilized) and plant association (bulk vs. rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass vs. forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease suppressive bacterial taxa and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. ImportanceOver the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorous deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline and bacterial communities are anticipated to increase in abundance of copiotrophic taxa. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly, of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter the metabolism of rhizosphere bacterial communities in unexpected ways.

microbiology↗

bioRxiv2019

Nutrient enrichment increases soil bacterial diversity and decomposition rates of different litter types in a coastal plain wetland

AO_SCPLOWBSTRACTC_SCPLOWHuman activities have led to increased deposition of nitrogen (N) and phosphorus (P) into soils. Nutrient enrichment of soils is known to increase plant biomass and rates of microbial litter decomposition. However, interacting effects of hydrologic position and associated changes to soil moisture can constrain microbial activity and lead to unexpected nutrient feedbacks on microbial community structure-function relationships. Examining how feedbacks of nutrient enrichment on decomposition rates is essential for predicting microbial contributions to carbon (C) cycling as atmospheric deposition of nutrients persists. This study explores how long-term nutrient addition and contrasting litter chemical quality influence soil bacterial community structure and function. We hypothesize that long-term nutrient enrichment of low fertility soils alters bacterial community structure and leads to higher rates of litter decomposition with decreasing C:N ratio of litter; but low nutrient and dry conditions limit constrain microbial decomposition of high C:N ratio litter. We leverage a long-term fertilization experiment to test how nutrient enrichment and hydrologic manipulation (due to ditches) affects decomposition and soil bacterial community structure in a nutrient poor coastal plain wetland. We conducted a litter bag experiment and characterized litter-associated and bulk soil microbiomes using 16S rRNA bacterial sequencing and quantified litter mass losses and soil physicochemical properties. Results revealed that distinct bacterial communities were involved in decomposing higher C:N ratio litter more quickly in fertilized compared to unfertilized especially under drier soil conditions, while decomposition rates of green tea litter (lower C:N ratio) were similar between fertilized and unfertilized plots. Bacterial community structure in part explained litter decomposition rates, and long-term fertilization and drier hydrologic status affected bacterial diversity and increased decomposition rates. However, community composition associated with high C:N litter was similar in wetter plots with available nitrate detected, regardless of fertilization treatment. This study provides insight into long-term fertilization effects on soil bacterial diversity and composition, decomposition, and the increased potential for soil C loss as nutrient enrichment and hydrology interact to affect historically low nutrient ecosystems.

ecology↗