Fluoroalkylether compounds affect microbial community structures and abundance of nitrogen cycle-related genes in soil-microbe-plant systems
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59 BASIC BIOLOGICAL SCIENCES↗
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Results for “Soil microbial community”
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Switchgrass ( Panicum virgatum L.) cultivars have similar impacts on soil carbon and nitrogen stocks and microbial function
Abstract Switchgrass ( Panicum virgatum L.) production for biofuel has the potential to produce reasonable yields on lands not suited for conventional agriculture. We assessed nine switchgrass cultivars representing lowland and upland ecotypes grown for 11 years at a site in the upper Midwest USA for belowground differences in soil carbon and nitrogen stocks, soil organic matter fractions, and standing root biomass to 1 m depth. We also compared potential nitrogen mineralization and carbon substrate use through community‐level physiological profiling in surface soils (0–10 cm depth). Average yields and standing root biomass differed among cultivars and between ecotypes, but we found no significant cultivar‐related impacts on soil carbon and nitrogen stocks, on the distribution of particulate and mineral‐associated soil organic matter fractions, nor on potential nitrogen mineralization or microbial community‐level physiological profiles. That these traits did not differ among cultivars suggests that soil carbon and nitrogen gains under switchgrass are likely to be robust with respect to cultivar differences, and to this point not much affected by breeding efforts.
Agriculture↗
Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification
Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO 2 -derived 13 C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of 13 C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of 13 C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in 13 C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.
59 BASIC BIOLOGICAL SCIENCES↗
Plastispheres as hotspots of microbially-driven methylmercury production in paddy soils
Microplastics (MPs) as emerging contaminants have accumulated extensively in agricultural ecosystems and are known to exert important effects on biogeochemical processes. However, how MPs in paddy soils influence the conversion of mercury (Hg) to neurotoxic methylmercury (MeHg) remains poorly understood. Here, in this study, we evaluated the effects of MPs on Hg methylation and associated microbial communities in microcosms using two typical paddy soils in China (i.e., yellow and red soils). Results showed that the addition of MPs significantly increased MeHg production in both soils, which could be related to higher Hg methylation potential in the plastisphere than in the bulk soil. We found significant divergences in the community composition of Hg methylators between the plastisphere and the bulk soil. In addition, the plastisphere had higher proportions of Geobacterales in the yellow soil and Methanomicrobia in the red soil compared with the bulk soil, respectively; and plastisphere also had more densely connected microbial groups between non-Hg methylators and Hg methylators. These microbiota in the plastisphere are different from those in the bulk soil, which could partially account for their distinct MeHg production ability. Our findings suggest plastisphere as a unique biotope for MeHg production and provide new insights into the environment risks of MP accumulation in agricultural soils.
54 ENVIRONMENTAL SCIENCES↗
Postfire Biogeochemical Processes: Implications to Source Water Quality in Fire-Influenced Watersheds
Forested watersheds are instrumental in providing purified and reliable water to millions of people worldwide. The changing climate has increased the frequency and severity of global fire events. Forested watersheds and their ecosystem functions are greatly disrupted during fire activity. Postfire concerns in forested watersheds include unpredictable and potentially simultaneous alterations in source water quality and hydro-biogeochemical processes. Here, the degree of fire severity can complexly modify water quality through the production of fire-transformed constituents on the burned forest floor (i.e., nutrients, metal(loid)s, dissolved organic matter, and the formation of disinfection byproducts). Correspondingly, fire severity and postfire rainfall patterns can refine hydro-biogeochemical processes that influence the transport of the fire-transformed constituents (i.e., vegetation function, soil structure, hydrological pathways, and microbial communities). Postfire alterations to water quality and hydro-biogeochemical processes introduce further complexity with varying temporal influence, which ranges from months to decades. As postfire water quality and watershed response research progresses, it is essential to homogenize interdisciplinary expertise to bridge knowledge gaps between fields ranging from forest ecology, hydrology, microbiology, and geochemistry. A multidisciplinary approach in wildfire research will facilitate a comprehensive perception of the diverse water quality risks associated with fire activity and mitigate fire concerns on a global level.
Disinfection Byproducts↗
An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments
Abstract Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa . Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.
59 BASIC BIOLOGICAL SCIENCES↗
Pine‐fungal co‐invasion alters whole‐ecosystem properties of a native eucalypt forest
Summary Pine‐fungal co‐invasions into native ecosystems are increasingly prevalent across the southern hemisphere. In Australia, invasive pines slowly spread into native eucalypt forests, creating novel mixed forests. We sought to understand how pine‐fungal co‐invasions impact interconnected above‐ and belowground ecosystem characteristics. We sampled beneath maturePinus radiataandEucalyptus racemosain a pine‐invaded eucalypt forest in New South Wales, Australia. We measured microbial community composition via amplicon sequencing of 16S, ITS2, and 18S rDNA regions, microbial metabolic activity via Biolog plate substrate utilization, and soil, leaf litter, and understory plant characteristics. Pines were associated with decreased topsoil moisture, increased pine litter, and decreased eucalypt litter total phosphorus content. Soils and roots beneath pines had distinct microbial community composition and activity relative to eucalypts, including decreased bacterial diversity, decreased microbial utilization of several C‐ and N‐rich substrates, and enrichment of pine‐associated ectomycorrhizae. Introduced suilloid fungi were abundant across both pine and eucalypt soils and roots. Many ecosystem impacts increased with pine size. Invasive pines and their ectomycorrhizae have significant impacts on eucalypt forest properties as they grow. Interconnected impacts at the scale of individual trees should be considered when managing invaded forests and predicting effects of pine invasions.
Plant Sciences↗
Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning
Abstract Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.
59 BASIC BIOLOGICAL SCIENCES↗
Experimentally determined traits shape bacterial community composition one and five years following wildfire
Abstract Wildfires represent major ecological disturbances, burning 2–3% of Earth’s terrestrial area each year with sometimes drastic effects above- and belowground. Soil bacteria offer an ideal, yet understudied system within which to explore fundamental principles of fire ecology. To understand how wildfires restructure soil bacterial communities and alter their functioning, we sought to translate aboveground fire ecology to belowground systems by determining which microbial traits are important post-fire and whether changes in bacterial communities affect carbon cycling. We employed an uncommon approach to assigning bacterial traits, by first running three laboratory experiments to directly determine which microbes survive fires, grow quickly post-fire and/or thrive in the post-fire environment, while tracking CO 2 emissions. We then quantified the abundance of taxa assigned to each trait in a large field dataset of soils one and five years after wildfires in the boreal forest of northern Canada. We found that fast-growing bacteria rapidly dominate post-fire soils but return to pre-burn relative abundances by five years post-fire. Although both fire survival and affinity for the post-fire environment were statistically significant predictors of post-fire community composition, neither are particularly influential. Our results from the incubation trials indicate that soil carbon fluxes post-wildfire are not likely limited by microbial communities, suggesting strong functional resilience. From these findings, we offer a traits-based framework of bacterial responses to wildfire.
54 ENVIRONMENTAL SCIENCES↗
Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics
Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes than with “narrow” functions in which specific microorganisms specialize. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with broad and narrow functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five broad and the five narrow functions that we chose. Our results revealed that, compared with the five broad functions, soil microbes capable of performing the five narrow functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in narrow functions. Co-occurrence networks indicated that microorganisms conducting broad functions were positively related, but microbes specializing in narrow functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between broad and narrow functions in soil microbes, as the association of functional diversity with taxonomy was greater in the five narrow than in the five broad functions.
54 ENVIRONMENTAL SCIENCES↗
Peatland microbial community responses to plant functional group and drought are depth-dependent
Peatlands store one-third of Earth's soil carbon, the stability of which is uncertain due to climate change-driven shifts in hydrology and vegetation, and consequent impacts on microbial communities that mediate decomposition. Peatland carbon cycling varies over steep physicochemical gradients characterizing vertical peat profiles. However, it is unclear how drought-mediated changes in plant functional groups (PFGs) and water table (WT) levels affect microbial communities at different depths. We combined a multiyear mesocosm experiment with community sequencing across a 70-cm depth gradient, to test the hypotheses that vascular PFGs (Ericaceae vs. sedges) and WT (high vs. low) structure peatland microbial communities in depth-dependent ways. Several key results emerged. (i) Both fungal and prokaryote (bacteria and archaea) community structure shifted with WT and PFG manipulation, but fungi were much more sensitive to PFG whereas prokaryotes were much more sensitive to WT. (ii) PFG effects were largely driven by Ericaceae, although sedge effects were evident in specific cases (e.g., methanotrophs). (iii) Treatment effects varied with depth: the influence of PFG was strongest in shallow peat (0-10, 10-20 cm), whereas WT effects were strongest at the surface and middle depths (0-10, 30-40 cm), and all treatment effects waned in the deepest peat (60-70 cm). Furthermore, our results underline the depth-dependent and taxon-specific ways that plant communities and hydrologic variability shape peatland microbial communities, pointing to the importance of understanding how these factors integrate across soil profiles when examining peatland responses to climate change.
59 BASIC BIOLOGICAL SCIENCES↗
A soil-inspired dynamically responsive chemical system for microbial modulation
Interactions between the microbiota and their colonized environments mediate critical pathways from biogeochemical cycles to homeostasis in human health. Here, in this study, we report a soil-inspired chemical system that consists of nanostructured minerals, starch granules and liquid metals. Fabricated via a bottom-up synthesis, the soil-inspired chemical system can enable chemical redistribution and modulation of microbial communities. We characterize the composite, confirming its structural similarity to the soil, with three-dimensional X-ray fluorescence and ptychographic tomography and electron microscopy imaging. We also demonstrate that post-synthetic modifications formed by laser irradiation led to chemical heterogeneities from the atomic to the macroscopic level. The soil-inspired material possesses chemical, optical and mechanical responsiveness to yield write-erase functions in electrical performance. The composite can also enhance microbial culture/biofilm growth and biofuel production in vitro. Finally, we show that the soil-inspired system enriches gut bacteria diversity, rectifies tetracycline-induced gut microbiome dysbiosis and ameliorates dextran sulfate sodium-induced rodent colitis symptoms within in vivo rodent models.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Distribution and speciation of Sb and toxic metal(loid)s near an antimony refinery and their effects on indigenous microorganisms
Although several studies have investigated the effects of Sb contamination on surrounding environments and indigenous microorganisms, little is known about the effect of co-contamination of Sb and toxic metal(loid)s. In this study, the occurrence of Sb and other toxic metal(loid)s near an operating Sb refinery and near-field landfill site were investigated. Topsoil samples near the refinery had high Sb levels (~3250 mg kg -1 ) but relatively low concentrations of other toxic metal(loid)s. However, several soil samples taken at greater depth from the near-field landfill site contained high concentrations of As and Pb, as well as extremely high Sb contents (~21,400 mg kg -1 ). X-ray absorption fine structure analysis showed that Sb in the soils from both sites was present as Sb(V) in the form of tripuhyite (FeSbO 4 ), a stable mineral. Three-dimensional principal coordinate analysis showed that microbial community compositions in samples with high toxic metal(loid)s concentrations were significantly different from other samples and had lower microbial populations (~10 4 MPN g -1 ). Sequential extraction results revealed that Sb is present primarily in the stable residual fraction (~99 %), suggesting low Sb bioavailability. Finally, however, microbial redundancy analysis suggested that the more easily extractable Pb might be the major factor controlling microbial community compositions at the site.
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)
ABSTRACT 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.
59 BASIC BIOLOGICAL SCIENCES↗
Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production
Abstract Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.
09 BIOMASS FUELS↗
Phosphate-modulated transformation of Sb(V)-bearing ferrihydrite under microbial iron- and sulfate-reducing conditions
Antimony (Sb) is a toxic metalloid that poses environmental risks in terrestrial and aquatic systems. The fate of the Sb(V) oxyanion, Sb(OH) 6 − , is governed by complex biogeochemical processes, including immobilization by ferric (Fe(III)) oxides, reduction by sulfide, and the less-explored competitive adsorption with other anions such as phosphate (PO 4 3− ). Here, this study investigates the interplay between such mechanisms in controlling the behavior of Sb(V) associated with ferrihydrite (Fh) under Fe(III)- and sulfate-reducing conditions, with a particular emphasis on the role of phosphate in influencing Sb(V) mobility and transformation. Anoxic reactors that contained Sb(V)-coprecipitated Fh, varying PO 4 3− concentrations (0, 0.2, and 2 mM), and sulfate, were inoculated with a microbial community sourced from Sb-contaminated soil. Additionally, abiotic reactors with either Sb(V)-adsorbed or Sb(V)-coprecipitated Fh and different PO 4 3− loadings (0–100 mM) were created to investigate the competitive adsorption mechanisms in the absence of microbial activity. Results from the abiotic reactors suggest that Sb(V) is likely incorporated into the Fh structure, with only minor amounts remaining surface-bound and extractable by PO 4 3− . In the biotic reactors, microbial Fe(III) and sulfate reduction were more extensive in the presence of PO 4 3− . At 0.2 mM PO 4 3− , microbial activity transformed Fh into siderite and led to the complete reduction of Sb(V) to Sb(III) as stibnite (Sb 2 S 3 ). At 2 mM PO 4 3− , the greater coverage by PO 4 3− stabilized Fh and decreased the extent of both Fe(III) and Sb(V) reduction, and shifted the reduced products to mackinawite and Sb(III) adsorbed onto Fh, in addition to stibnite formation. This study demonstrates that while PO 4 3− may not directly compete with Sb(V) for sorption sites, it can influence Sb mobility in Fe(III)- and sulfate-reducing environments by enhancing microbial activity and altering the mineralization pathways.
Microbial Fe(III) and sulfate reduction↗
Disturbance legacies regulate coastal forest soil stability to changing salinity and inundation: A soil transplant experiment
Coastal forests worldwide are vulnerable to a dramatic transition from upland to wetland as sea-level rise accelerates and regimes of precipitation and storms change. However, the biogeochemical impacts of shifting salinity and inundation disturbance that foreshadow forest to wetland state transitions are largely unknown. This experiment used a natural salinity gradient in a tidal creek in eastern Maryland, U.S.A., to examine how soil respiration and chemistry may change under novel salinity and inundation disturbance regimes. Soil monoliths were transplanted in a reciprocal design among plots varying in seawater exposure and elevation above the creek. We monitored the monoliths’ carbon dioxide (CO 2 ) flux for two years and performed soil chemical analyses at the end of the experiment. Soil CO 2 flux was affected by changing disturbance regimes and responses were dependent upon the salinity and inundation legacies associated with each study location. Lowland soil CO 2 flux was resistant to changing salinity and inundation disturbance, with transplanted soil monolith chemistry composition in between that of its origin and destination. Conversely, upland soil CO 2 flux was sensitive to changing salinity and inundation disturbance and remained suppressed throughout the 2-year study when exposed to wetter, saline conditions. Additionally, transplanted upland soil chemistry composition was like that of its destination, rather than origin, with upland soils displaying higher pH, base saturation, and nutrient availability relative to lowland soils. Here, we hypothesize that reductions in soil respiration rates were driven by loss of soil nutrients and osmotic and redox stress on microbial communities following exposure to seawater. Together, our results suggest that disturbance legacies shape coastal forest soil responses to changing salinity and inundation disturbance regimes. However, fully understanding the dependence of system responses on disturbance legacies requires future study across a variety of systems and spatial and temporal scales.
54 ENVIRONMENTAL SCIENCES↗