Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms.

Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.

A methodological framework for assessing sea level rise impacts on nitrate loading in coastal agricultural watersheds using SWAT+: A case study of the Tar-Pamlico River basin, North Carolina, USA.

This study addresses the urgent need to understand the impacts of climate change on coastal ecosystems by demonstrating how to use the SWAT+ model to assess the effects of sea level rise (SLR) on agricultural nitrate export in a coastal watershed. Our framework for incorporating SLR in the SWAT+ model includes: (1) reclassifying current land uses to water for areas with elevations below 0.3 m based on SLR projections for mid-century; (2) creating new SLR-influenced land uses, SLR-influenced crop database, and hydrological response units for areas with elevations below 2.4 m; and (3) adjusting SWAT+ parameters for the SLR-influenced areas to simulate the effects of saltwater intrusion on processes such as plant yield and denitrification. We demonstrate this approach in the Tar-Pamlico River basin, a coastal watershed in eastern North Carolina, USA. We calibrated the model for monthly nitrate load at Washington, NC, achieving a Nash-Sutcliffe Efficiency (NSE) of 0.61. Our findings show that SLR substantially alters nitrate delivery to the estuary, with increased nitrate loads observed in all seasons. Higher load increases were noted in winter and spring due to elevated flows, while higher percentage increases occurred in summer and fall, attributed to reduced plant uptake and disrupted nitrogen cycle transformations. Overall, we observed an increase in mean annual nitrate loads from 155,000 kg NO3-N under baseline conditions to 157,000 kg NO3-N under SLR scenarios, confirmed by a statistically significant paired t-test (p = 2.16 × 10-10). This pioneering framework sets the stage for more sophisticated and accurate modeling of SLR impacts in diverse hydrological scenarios, offering a vital tool for hydrological modelers.

The Effects of Social Experience on Host Gut Microbiome in Male Zebrafish (Danio rerio).

AbstractAlthough 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 social 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 2 weeks of social interactions changed the composition of zebrafish gut microbiome by comparing gut bacterial composition, diversity, and relative abundance between 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.

Air temperature spikes increase bacteria presence in drinking water wells downstream of hog lagoons.

>44 million United States residents depend on private drinking water wells that are federally unregulated. Maintaining a clean groundwater supply for populations without access to public water systems is essential to supporting public health and falls to state regulators and private well owners. Yet, monitoring practices do not reflect the fact that groundwater pollution risk varies seasonally and with proximity to nearby surface-contaminated sites. Examination of nearly 50,000 well water samples across North Carolina, ranked second nationally in domestic well dependence and swine production, from 2013 to 2018 reveals a uniform sampling schedule but a variable risk of bacterial contamination within each calendar year. We document a threshold of 32.2 °C (90 °F) where total coliform bacteria and Escherichia coli (E. coli) detection in private well water spikes near swine lagoons but is absent from "upstream" wells and otherwise unexplained by a variety of other known contamination sites. Closing the gap between perceived and actual risks of drinking water contamination has potential to improve public health. State regulations and federal guidelines should consider coordinating domestic well sampling with seasonally and spatially fluctuating risks of groundwater contamination. Findings from this study are generalizable, having implications for other parts of the world with water sources that have the potential to get contaminated by nearby surface sources of human and animal waste, such as manure applications and leaching septic systems.

Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering.

Every seed germinating in soils, wastewater treatment, and stream confluence exemplify microbial community coalescence-the blending of previously isolated communities. Here, we present theoretical and experimental knowledge on how separated microbial communities mix, with particular focus on managed ecosystems. We adopt the community coalescence framework, which integrates metacommunity theory and meta-ecosystem dynamics, and highlight the prevalence of these coalescence events within microbial systems. Specifically, we (i) describe fundamental types of community coalescences using naturally occurring and managed examples, (ii) offer ways forward to leverage community coalescence in managed systems, and (iii) emphasize the importance of microbial ecological theory to achieving desired coalescence outcomes. Further, considering the massive dispersal events of microbiomes and their coalescences is pivotal to better predict microbial community dynamics and responses to disturbances. We conclude our piece by highlighting some challenges and unanswered question yet to be tackled.

Microbial community structure and denitrification in a wetland mitigation bank.

Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.

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 versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus 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.IMPORTANCE Over 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 phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. 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 diversity and metabolism of rhizosphere bacterial communities in unexpected ways.

Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift.

Sea level rise is mixing formerly isolated freshwater communities with saltwater communities. The structure of these new aquatic communities is jointly controlled by pre- and post-colonization processes. Similarly, since salinity is a strong abiotic determinant of post-colonization survival in coastal systems, changes in salinity will likely impact community composition. In this study, we examine how a strong abiotic gradient affects the diversity and structure of bacterial and zooplankton communities and associated ecosystem functions (decomposition and carbon mineralization). We ran a six week dispersal experiment using mesocosm ponds with four distinct salinity profiles (0, 5, 9, and 13 psu). We find that salinity is the primary driver of both bacterial and zooplankton community composition. We find evidence that as bacterial richness increases so does the amount of decomposition. A phenomenological model suggests carbon mineralization may decrease at mid-salinities; this warrants future work into possible mechanisms for this apparent loss of function. Understanding how salinization changes community structure and ecosystem function may be paramount for managing and conserving coastal plain ecosystems where salinity is increasing due to sea level rise, saltwater intrusion, storm surges, and drought.

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 species sorting. 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 species sorting in the active portion of the aquatic community, suggesting that dispersal may have a weaker effect than persistence strategies on aquatic community assembly. 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.

Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina).

Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity.

Relative influence of landscape vs. local factors on plant community assembly in restored wetlands.

Ecological restoration often involves only the manipulation of abiotic factors at the local scale. However, processes external to a restoration site determine the range of local conditions within the site, constraining the level of restoration progress that can be achieved by on-site manipulations. We examined the relationship of landscape and local explanatory variables to plant species composition in 28 restored wetlands in Illinois, USA. Using constrained ordination combined with variation partitioning, we determined the independent and joint effects of three spatially hierarchical sets of variables: (1) macroscale landscape features reflecting site setting within regional landscapes, (2) mesoscale landscape features reflecting nearby propagule sources and buffers from disturbances, and (3) local environmental factors. Because the relative influence of landscape- vs. local-scale factors on restoration success may depend on particular restoration goals, we repeated the analyses using three multivariate plant community responses that represented three frequently stated goals: (1) replicating species composition, (2) restoring a particular wetland community type, and (3) constructing sites with high value for plant conservation. Explanatory variables at landscape and local scales had independent and nearly equally strong relationships to plant species composition. In contrast, when species were aggregated based on plant traits, the independent contribution of local predictors was greater than the independent contributions of macroscale or mesoscale landscape predictors, reflecting convergence of plant trait composition in sites with similar local conditions. Local predictors explained a significant amount of variation in plant conservation value among sites, but much of the variation could be explained by large-scale landscape setting, indicating that landscape constraints on local environmental conditions limited the level of floristic conservation value achievable. The appropriate scale at which to focus restoration efforts will vary depending upon restoration objectives. Restoration of particular wetland community types might be successfully achieved through manipulation of local abiotic factors. In contrast, restoration of a particular species assemblage or reconstruction of wetlands with high value for conservation requires consideration of landscape processes and available species pools.