Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO2 in northern peatlands

Warming and elevated CO2 (eCO2) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora

Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.

Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.

Shared governance in the plant holobiont and implications for one health

The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.

Climate warming and elevated CO2 alter peatland soil carbon sources and stability

Peatlands are an important carbon (C) reservoir storing one-third of global soil organic carbon (SOC), but little is known about the fate of these C stocks under climate change. Here, we examine the impact of warming and elevated atmospheric CO2 concentration (eCO2) on the molecular composition of SOC to infer SOC sources (microbe-, plant- and fire-derived) and stability in a boreal peatland. We show that while warming alone decreased plant- and microbe-derived SOC due to enhanced decomposition, warming combined with eCO2 increased plant-derived SOC compounds. We further observed increasing root-derived inputs (suberin) and declining leaf/needle-derived inputs (cutin) into SOC under warming and eCO2. The decline in SOC compounds with warming and gains from new root-derived C under eCO2, suggest that warming and eCO2 may shift peatland C budget towards pools with faster turnover. Together, our results indicate that climate change may increase inputs and enhance decomposition of SOC potentially destabilising C storage in peatlands.

Label-Free Functional Analysis of Root-Associated Microbes with Dynamic Quantitative Oblique Back-illumination Microscopy

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over five days, we observed increased dynamic activity in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize bacterial activity within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial activity and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog

Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Climate drivers alter nitrogen availability in surface peat and decouple N2 fixation from CH4 oxidation in the Sphagnum moss microbiome

Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N₂ -fixing (diazotrophic) and CH₄ -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO₂ (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH₄ , CO₂ ) and nitrogen (NH₄ -N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO₂ . Under ambient CO₂ , warming increased plant-available NH₄ -N in surface peat, excess N accumulated in Sphagnum tissue, and N₂ fixation activity decreased. Elevated CO₂ offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO₂ treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane-induced N₂ fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N-availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO₂ concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.

The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA

BACKGROUND

Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons.

RESULTS

A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora.

CONCLUSIONS

The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.

A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation

Alkanes are ubiquitous in marine ecosystems and originate from diverse sources ranging from natural oil seeps to anthropogenic inputs and biogenic production by cyanobacteria. Enzymes that degrade cyanobacterial alkanes (typically C15-C17 compounds) such as the alkane monooxygenase (AlkB) are widespread, but it remains unclear whether or not AlkB variants exist that specialize in degradation of crude oil from natural or accidental spills, a much more complex mixture of long-chain hydrocarbons. In the present study, large-scale analysis of available metagenomic and genomic data from the Gulf of Mexico (GoM) oil spill revealed a novel, divergent AlkB clade recovered from genomes with no cultured representatives that was dramatically increased in abundance in crude-oil impacted ecosystems. In contrast, the AlkB clades associated with biotransformation of cyanobacterial alkanes belonged to 'canonical' or hydrocarbonoclastic clades, and based on metatranscriptomics data and compared to the novel clade, were much more weakly expressed during crude oil biodegradation in laboratory mesocosms. The absence of this divergent AlkB clade in metagenomes of uncontaminated samples from the global ocean survey but not from the GoM as well as its frequent horizontal gene transfer indicated a priming effect of the Gulf for crude oil biodegradation likely driven by natural oil seeps.

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

BACKGROUND

Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.

RESULTS

Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH₄ and CO₂ concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.

CONCLUSIONS

Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.

Beach sand oil spills select for generalist microbial populations

The specialization-disturbance hypothesis predicts that, in the event of a disturbance, generalists are favored, while specialists are selected against. This hypothesis has not been rigorously tested in microbial systems and it remains unclear to what extent it could explain microbial community succession patterns following perturbations. Previous field observations of Pensacola Beach sands that were impacted by the Deepwater Horizon (DWH) oil spill provided evidence in support of the specialization-disturbance hypothesis. However, ecological drift as well as uncounted environmental fluctuations (e.g., storms) could not be ruled out as confounding factors driving these field results. In this study, the specialization-disturbance hypothesis was tested on beach sands, disturbed by DWH crude oil, ex situ in closed laboratory advective-flow chambers that mimic in situ conditions in saturated beach sediments. The chambers were inoculated with weathered DWH oil and unamended chambers served as controls. The time series of shotgun metagenomic and 16S rRNA gene amplicon sequence data from a two-month long incubation showed that functional diversity significantly increased while taxonomic diversity significantly declined, indicating a decrease in specialist taxa. Thus, results from this laboratory study corroborate field observations, providing verification that the specialization-disturbance hypothesis can explain microbial succession patterns in crude oil impacted beach sands.

Nitrogen and phosphorus cycling in an ombrotrophic peatland: a benchmark for assessing change

AIMS

Slow decomposition and isolation from groundwater mean that ombrotrophic peatlands store a large amount of soil carbon (C) but have low availability of nitrogen (N) and phosphorus (P). To better understand the role these limiting nutrients play in determining the C balance of peatland ecosystems, we compile comprehensive N and P budgets for a forested bog in northern Minnesota, USA.

METHODS

N and P within plants, soils, and water are quantified based on field measurements. The resulting empirical dataset are then compared to modern-day, site-level simulations from the peatland land surface version of the Energy Exascale Earth System Model (ELM-SPRUCE).

RESULTS

Our results reveal N is accumulating in the ecosystem at 0.2 ± 0.1 g N m^-2 year^-1 but annual P inputs to this ecosystem are balanced by losses. Biomass stoichiometry indicates that plant functional types differ in N versus P limitation, with trees exhibiting a stronger N limitation than ericaceous shrubs or Sphagnum moss. High biomass and productivity of Sphagnum results in the moss layer storing and cycling a large proportion of plant N and P. Comparing our empirically-derived nutrient budgets to ELM-SPRUCE shows the model captures N cycling within dominant plant functional types well.

CONCLUSIONS

The nutrient budgets and stoichiometry presented serve as a baseline for quantifying the nutrient cycling response of peatland ecosystems to both observed and simulated climate change. Our analysis improves our understanding of N and P dynamics within nutrient-limited peatlands and represents a crucial step toward improving C-cycle projections into the twenty-first century.

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.

Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA

Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.

Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles

Crude oil buried in intertidal sands may be exposed to alternating oxic and anoxic conditions but the effect of this tidally induced biogeochemical oscillation remains poorly understood, limiting the effectiveness of remediation and managing efforts after oil spills. Here, we used a combination of metatranscriptomics and genome-resolved metagenomics to study microbial activities in oil-contaminated sediments during oxic-anoxic cycles in laboratory chambers that closely emulated in situ conditions. Approximately 5-fold higher reductions in the total petroleum hydrocarbons were observed in the oxic as compared to the anoxic phases with a relatively constant ratio between aerobic and anaerobic oil decomposition rates even after prolonged anoxic conditions. Metatranscriptomics analysis indicated that the oxic phases promoted oil biodegradation in subsequent anoxic phases by microbially mediated reoxidation of alternative electron acceptors like sulfide and by providing degradation-limiting nitrogen through biological nitrogen fixation. Most population genomes reconstructed from the mesocosm samples represented uncultured taxa and were present typically as members of the rare biosphere in metagenomic data from uncontaminated field samples, implying that the intertidal communities are adapted to changes in redox conditions. Collectively, these results have important implications for enhancing oil spill remediation efforts in beach sands and coastal sediments and underscore the role of uncultured taxa in such efforts.

Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes

Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.

Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of Mexico

A new Rhodococcus strain, capable of degrading crude oil, was isolated from the Gulf of Mexico deep-sea sediment and was investigated for its biodegradation characteristics under atmospheric as well as under deep-sea pressure (1500 m = 15 MPa). Additionally, the effect of dispersant (Corexit EC9500A) addition was studied. Rhodococcus sp. PC20 was shown to degrade 60.5 ± 10.7% of the saturated and aromatic fraction of crude oil at atmospheric pressure and 74.2 ± 9.1% at deep-sea level pressure within 96 h. Degradation rates, especially for monoaromatic hydrocarbons, were significantly higher at elevated pressure compared to atmospheric pressure. This study found a growth inhibiting effect at a dispersant to oil ratio of 1:100 and higher. This effect of the dispersant was enhanced when elevated pressure was applied.

Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach

The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.

Dispersant Enhances Hydrocarbon Degradation and Alters the Structure of Metabolically Active Microbial Communities in Shallow Seawater From the Northeastern Gulf of Mexico

Dispersant application is a primary emergency oil spill response strategy and yet the efficacy and unintended consequences of this approach in marine ecosystems remain controversial. To address these uncertainties, ex situ incubations were conducted to quantify the impact of dispersant on petroleum hydrocarbon (PHC) biodegradation rates and microbial community structure at as close as realistically possible to approximated in situ conditions [2 ppm v/v oil with or without dispersant, at a dispersant to oil ratio (DOR) of 1:15] in surface seawater. Biodegradation rates were not substantially affected by dispersant application at low mixing conditions, while under completely dispersed conditions, biodegradation was substantially enhanced, decreasing the overall half-life of total PHC compounds from 15.4 to 8.8 days. While microbial respiration and growth were not substantially altered by dispersant treatment, RNA analysis revealed that dispersant application resulted in pronounced changes to the composition of metabolically active microbial communities, and the abundance of nitrogen-fixing prokaryotes, as determined by qPCR of nitrogenase (nifH) genes, showed a large increase. While the Gammaproteobacteria were enriched in all treatments, the Betaproteobacteria and different families of Alphaproteobacteria predominated in the oil and dispersant treatment, respectively. Results show that mixing conditions regulate the efficacy of dispersant application in an oil slick, and the quantitative increase in the nitrogen-fixing microbial community indicates a selection pressure for nitrogen fixation in response to a readily biodegradable, nitrogen-poor substrate.

The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills

The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.

Experimental warming alters the community composition, diversity, and N2 fixation activity of peat moss (Sphagnum fallax) microbiomes

Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.

Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States)

Climate warming is predicted to increase heterotrophic metabolism in northern peatland soils leading to enhanced greenhouse gas emissions. However, the specific relationships between temperature and the greenhouse gas producing microbial communities are poorly understood. Thus, in this study, the temperature dependence of carbon dioxide (CO2) and methane (CH4) production rates along with abundance and composition of microbial communities were investigated in peat from a Sphagnum-dominated peatland, S1 bog (Minnesota, United States). Whereas CH4 production rates increased with temperature up to 30°C, CO2 production did not, resulting in a lower CO2:CH4 ratio with increasing temperature. CO2 production showed both psychrophilic and mesophilic maxima at 4 and 20°C, respectively, and appears to be mediated by two anaerobic microbial communities, one that operates under psychrophilic conditions that predominate for much of the year, and another that is more active under warmer conditions during the growing season. In incubations at 10°C above the ambient range, members of the Clostridiaceae and hydrogenotrophic methanogens of the Methanobacteriaceae dominated. Moreover, a significant negative correlation between temperature and microbial diversity was observed. Results indicate that the potential consequences of warming surface peat in northern peatlands include a large stimulation in CH4 production and a significant loss of microbial diversity.