Biology subjects

Peralta, A. L.

Publications and source records attributed to Peralta, A. L..

12 recordsLinked to original sources

bioRxiv2026

Which, when and where traits matter: functional trait-mediated species associations shift with microenvironmental and climatic variation

O_LIPredicting coexistence in species-rich plant communities requires understanding the role of functional traits in species interactions and their resilience to environmental variation. C_LIO_LIIn a manipulative factorial field experiment in an annual community (>45,000 individuals and 45 species), we followed plant associations from seedling to adult on both preserved and altered biological soil crust over two years with contrasting weather conditions. Neighborhood models quantified how among-species differences in key functional traits affected coexistence and how these effects varied in response to ontogenetic stage, environmental variation and spatial scale. C_LIO_LITrait-based models revealed a prevalent negative relationship between functional differences and species associations, but these relationships varied predictively with stage, environment and spatial scale. Functional dissimilarity in traits such as specific leaf area, seed mass, and reproductive-to-vegetative biomass ratio consistently mediated species segregation, especially during wet years and among seedlings, while biological soil crust disturbance altered trait-mediated associations differently at fine and coarse spatial scales. C_LIO_LITrait-mediated species associations shift predictably with environmental variation, suggesting that coexistence reflects a dynamic balance between environmental filtering and competitive interactions. This work provides novel experimental evidence of when, where, and which traits predict community assembly, which has implications for forecasting biodiversity responses to global environmental change. C_LI

ecology↗

bioRxiv2025

Hydrologic history and flooding pulses control iron and sulfur metabolic composition with variable associations to greenhouse gas production in a coastal wetland mesocosm experiment

Coastal wetlands store carbon, but compound stressors, including saltwater intrusion, sea level rise, and precipitation extremes, threaten this benefit by altering microbial communities and influencing greenhouse gas emissions. Mediating soil gas exchange, nutrient and carbon availability, and soil moisture, wetland vegetation interacts with these compound stressors. However, the exclusion of plant-driven redox shifts from many mesocosm studies limits our understanding of their role in shaping microbial responses to hydrologic conditions. This study employed a soil mesocosm approach to investigate the impact of hydrology (wet, dry, and interim) and plant presence on microbial communities and greenhouse gas fluxes in coastal freshwater wetland soils with varying past hydrologic regimes (i.e., soil history) and salinity stress. We used shotgun metagenomic sequencing to characterize the functional potential of soil microbes, measured in situ greenhouse gas fluxes, and characterized soil physicochemistry. Results showed that contemporary hydrology and soil history significantly impacted microbial gene composition related to sulfate and iron reduction. The compositions of genes for sulfate and iron reduction were correlated, and dissimilatory sulfate reduction genes influenced methane emissions. Findings highlight the roles of historical hydrology, potential saltwater exposure, and soil iron in shaping microbial responses to future changes in soil moisture, plant cover, and salinity. While plants did not significantly influence sulfur or iron metabolism, plant presence did impact green-house gas fluxes. We found a strong relationship between sulfate reduction and methanogenesis, which complements previous studies that have shown enhanced methanogenesis with seawater amendment. These results indicate that flooding without salinity is sufficient for coupled sulfate reduction and methanogenesis, provided that a legacy of saltwater intrusion has altered soil sulfate concentrations and sulfate-reducing microbial communities. Understanding microbial community metabolism in coastal wetlands is crucial for predicting their role in carbon sequestration and greenhouse gas emissions under future climate scenarios, developing effective management strategies to mitigate climate change impacts, and preserving these vital wetland ecosystems.

ecology↗

bioRxiv2024

Evaluating Plant-Microbe Associations in Response to Environmental Stressors to Enhance Salt Marsh Restoration

Despite substantial contributions of ecosystem services, mutualistic plant-microbe associations in wetlands are severely threatened by human activities. Therefore, promoting positive plant-microbe associations underpins coastal wetland restoration, where human stressors and climate change challenge successful outcomes. This study examined how salinity stressors influence plant-microbe relationships, where we hypothesized that the presence of microbes would provide a rescue effect by buffering abiotic stressors and yielding higher plant biomass. We used a whole sediment inocula approach and exposed marsh cordgrass (Sporobolus alterniflorus) plugs to a factorial experiment with three levels of microbiome addition (microbial inocula, autoclaved microbial inocula, no microbe control) and two levels of salinity (<0.5 psu, 20 psu), replicated ten times. We added marsh-site microbial inocula with autoclaved peat-based greenhouse soil and exposed half the plugs to saltwater (20 psu) and half to freshwater (<0.5 psu). Results revealed that marsh microbial inocula additions during early plant development may ameliorate salinity stressors. Plants treated with microbial inocula and salinity stress exhibited greater aboveground biomass (P < 0.09) than those under freshwater conditions. With live microbial inocula, the median of aboveground biomass and change in plant height were higher in saltwater compared to freshwater conditions. Change in plant height, belowground biomass, root-to-shoot ratio, soil bacterial diversity H, and evenness J were similar across microbial and salinity treatments. However, salinity (P < 0.001) and microbial treatments (P < 0.001) significantly influenced the bacterial community composition, with distinct assemblages under salinity conditions. This work supports microbiome stewardship enhancing plant resiliency, improving future wetland restoration outcomes.

ecology↗

bioRxiv2024

Predation by a ciliate community mediates temperature and nutrient effects on a peatland prey prokaryotic community.

Temperature significantly impacts microbial communities composition and function, which plays a vital role in the global carbon cycle that determines climate change. Nutrient influxes often accompany rising temperatures due to human activity. While ecological interactions between different microorganisms could shape their response to environmental change, we do not understand how predation may influence these responses in a warmer and increasingly nutrient-rich world. Here, we assess whether predation by a ciliate community of bacterial consumers influences changes in the diversity, biomass, and function of a freshwater prokaryotic community under different temperature and nutrient conditions. We found that predator presence mediates the effects of temperature and nutrients on total prokaryotic community biomass and composition through various mechanisms, including direct and indirect effects. However, the total community function was resilient. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community composition and function but also demonstrates how predation can mediate these effects, indicating that the biotic context is as important as the abiotic context to understanding microbial responses to novel climates. ImportanceWhile the importance of the abiotic environment in microbial communities has long been acknowledged, how prevalent ecological interactions like predation may influence these microbial community responses to shifting abiotic conditions is largely unknown. Our study addresses the complex interplay between temperature, nutrients, predation, and their joint effects on microbial community diversity and function. Our findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly alters these responses. Our study underscores the impact of abiotic factors on microbial communities and the importance of accounting for the biotic context in which these occur to understand, let alone predict, these responses properly.

ecology↗

bioRxiv2023

The effects of social experience on host gut microbiome in male zebrafish (Danio rerio)

Although the gut and the brain vastly differ in physiological function, they have been interlinked in a variety of different neurological and behavioral disorders. The bacteria that comprise the gut microbiome communicate and influence the function of various physiological processes within the body including nervous system function. However, the effects of social experience in the context of dominance and chronic stress on gut microbiome remain poorly understood. Here, we examined whether social experience impacts the host zebrafish (Danio rerio) gut microbiome. We studied how social dominance during the first two weeks of social interactions changed the composition of zebrafish gut microbiome by comparing gut bacterial composition, diversity and relative abundance among socially dominant, submissive, social isolates, and control group-housed communal fish. Using amplicon sequencing of the 16S rRNA gene, we report that social dominance significantly affects host gut bacterial community composition but not bacterial diversity. At the genus-level, Aeromonas and unclassified Enterobacteriaceae relative abundance decreased in dominant individuals while commensal bacteria (e.g., Exiguobacterium and Cetobacterium) increased in relative abundance. Conversely, the relative abundance of Psychrobacter and Acinetobacter was increased in subordinates, isolates, and communal fish compared to dominant fish. The shift in commensal and pathogenic bacteria highlights the impact of social experience and the accompanying stress on gut microbiome with potentially similar effects in other social organisms. IMPORTANCEDisruptions in the gut microbiome negatively impact various systems in the body. Recently, the gut microbiome has been associated with neurological deficits in both behavioral and neurodegenerative disorders. Given the increasing prevalence in diagnosis of both neurological disease and behavioral disorders, researching the link between social behaviors and the gut microbiome is critical to better understand how the gut and the brain communicate during healthy and diseased states. Our research findings demonstrate the effects of social dominance and chronic stress on host gut microbiome composition. By identifying variations in bacterial relative abundance based on social experience and associated stress, a broader understanding of pathogenic (e.g., Enterobacteriaceae, Aeromonas) versus commensal communities (e.g., Exiguobacterium, Cetobacterium) and related host physiology can be inferred.

microbiology↗

bioRxiv2022

Long-term fertilization modifies the composition of slow-growing oligotrophs more than fast-growing copiotrophs in a nutrient poor coastal plain wetland

Wetland ecosystems are known for their carbon storage potential due to slow decomposition rates and high carbon fixation rates. However, nutrient addition from human activities affects this carbon storage capacity as the balance of fixed and respired carbon shifts due to plant and microbial communities. Ongoing atmospheric deposition of nutrients could be changing wetland plant-microbe interactions in ways that tip the balance from carbon storage to loss. Therefore, examining microbial community patterns in response to nutrient enrichment is important to understanding nutrient effects on carbon storage potential. In this study, we hypothesized that fertilization of a low nutrient ecosystem leads to increased organic carbon input from plant biomass into the soil and results in increased soil bacterial diversity and modifications to soil bacterial community composition. As such, increased soil nutrients and carbon resources provide more energy to support increased microbial growth rates, which can result in wetland carbon losses. To test this hypothesis, we used bacterial community-level and soil chemical data from the long-term wetland ecology experiment at East Carolina Universitys West Research Campus (established in 2003). Specifically, we examined the extent that long-term effects of nutrient enrichment affect wetland microbial communities and plant biomass, which are factors that can affect carbon storage. We collected soil cores from fertilized and unfertilized test plots. We extracted genomic DNA from soil samples and conducted 16S rRNA targeted amplicon sequencing to characterize the bacterial community composition. In addition, we measured plant above and belowground biomass and soil carbon content. Results revealed an increase in aboveground plant biomass, soil carbon, and bacterial diversity. In contrast, belowground plant biomass and microbial biomass were similar in fertilized and unfertilized plots. To further examine bacterial community changes to nutrient enrichment, we compared the relative abundance of fast growing copiotrophic and slow growing oligotrophic bacteria of a subset of taxa putatively identified as belonging to either life history strategy. These taxa-level results revealed a decrease in oligotroph relative abundance and little to no change in copiotroph relative abundance of a subset of bacterial taxa. If there is a community-wide shift in the proportion of oligotroph to copiotroph life history strategies, this would have a negative impact on organic carbon storage since oligotrophic bacteria respire less carbon than copiotrophic bacteria over the same amount of time. Taken together, this study provided evidence that long-term nutrient enrichment influences wetland soils in ways that decrease their carbon storage potential of important carbon sinks.

ecology↗

bioRxiv2021

Bacterial composition reflects fine-scale salinity changes while phylogenetic diversity exhibits a strong salt divide

Climate change induced salinization events are predicted to intensify and lead to increased salt stress in freshwater aquatic ecosystems. As a consequence, formerly distinct abiotic conditions and associated biotic communities merge, and the emergence, loss, and persistence of microbial taxa modify the types and rates of ecosystem processes. This study examined how bacterial taxonomic and phylogenetic diversity and ecosystem function respond to acute salinization events where freshwater and estuarine communities and environments coalesce. We hypothesized that when the salinity change outpaces microbial adaptation or saline microbial populations are not yet established in formerly freshwater conditions, then these aquatic communities will exhibit diminished carbon cycling rates, decreased microbial diversity, and altered composition of microbial communities compared to historically freshwater communities. We used an experimental mesocosm approach to determine how salinity and the merging of distinct communities influenced resultant bacterial community structure and function. Each mesocosm represented different salinities (0, 5, 9, 13 psu). Two dispersal treatments, representing aquatic communities sourced from brackish 13 psu ponds and a mix of 13 psu and freshwater ponds, were added to all salinity levels and replicated four times. Results revealed that salinity, but not dispersal, decreased bacterial taxonomic and phylogenetic diversity. Carbon mineralization rates were highest in freshwater conditions and associated to bacterial taxa represented in low relative abundance. Acute salinity changes, such as localized flooding due to storm surge, will more negatively affect freshwater aquatic communities compared to chronic exposure to salinization where the communities have had time to adapt or turnover. IMPORTANCE STATEMENTClimate change induced salinization results in the mixing of formerly distinct environmental conditions and aquatic communities. This study examined the consequence of short-term, acute salinity stress on aquatic bacterial taxonomic and phylogenetic diversity and ecosystem function using an experimental approach. Results revealed that salinity, but not the source of aquatic communities, decreased bacterial taxonomic and phylogenetic diversity. Carbon mineralization rates, which represented ecosystem function, were highest in freshwater conditions and also associated with indicator bacterial taxa in low abundance relative to the total microbial community. Taken together, acute salinity changes will more negatively affect freshwater aquatic communities compared to chronic exposure to salinization where the communities have had time to adapt or turnover resulting in recovered biogeochemical functions.

ecology↗

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

Metabolic insight into bacterial community assembly across ecosystem boundaries

The movement of organisms across habitat boundaries has important consequences for populations, communities, and ecosystems. However, because most species are not well adapted to all habitat types, dispersal into suboptimal habitats could induce physiological changes associated with persistence strategies that influence community assembly. For example, high rates of cross-boundary dispersal are thought to maintain sink populations of terrestrial bacteria in aquatic habitats, but these bacteria may also persist by lowering their metabolic activity, introducing metabolic heterogeneity that buffers the population against niche selection. To differentiate between these assembly processes, we analyzed bacterial composition along a hydrological flow path from terrestrial soils through an aquatic reservoir by sequencing the active and total (active + inactive) portions of the community. When metabolic heterogeneity was ignored, our data were consistent with views that cross-boundary dispersal is important for structuring aquatic bacterial communities. In contrast, we found evidence for strong niche selection when metabolic heterogeneity was explicitly considered, suggesting that, relative to persistence strategies, dispersal may have a weaker effect on aquatic community assembly than previously thought. By accounting for metabolic heterogeneity in complex communities, our findings clarify the roles of local- and regional-scale assembly processes in terrestrial-aquatic meta-ecosystems.

ecology↗

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↗