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This project aims to study the microbial structure and potential functions of bacterial and fungal microbiomes in leaves, stems, roots, rhizospheres, and bulk soils of energy crops (oilcane) grown in greenhouses.
Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset from 2,953 soils that comprises 616,935 uncultivated virus genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents the most extensive characterization of soil viral diversity to date and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
ABSTRACT Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications. IMPORTANCE Although soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction—less than 1%—can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from anin situsoil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.
Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes.
Soil organic matter (SOM) is comprised of a diverse array of reactive carbon molecules, including hydrophilic and hydrophobic compounds, that impact rates of SOM formation and persistence. Despite clear importance to ecosystem science, little is known about broad-scale controls on SOM diversity and variability in soil. Here, we show that microbial decomposition drives significant variability in the molecular richness and diversity of SOM between soil horizons and across a continental-scale gradient in climate and ecosystem type (arid shrubs, coniferous, deciduous, and mixed forests, grasslands, and tundra sedges). The molecular dissimilarity of SOM was strongly influenced by ecosystem type (hydrophilic compounds: 17%, P < 0.001; hydrophobic compounds: 10% P < 0.001) and soil horizon (hydrophilic compounds: 17%, P < 0.001; hydrophobic compounds: 21%, P < 0.001), as assessed using metabolomic analysis of hydrophilic and hydrophobic metabolites. While the proportion of shared molecular features was significantly higher in the litter layer than subsoil C horizons across ecosystems (12 times and 4 times higher for hydrophilic and hydrophobic compounds, respectively), the proportion of site-specific molecular features nearly doubled from the litter layer to the subsoil horizon, suggesting greater differentiation of compounds after microbial decomposition within each ecosystem. Together, these results suggest that microbial decomposition of plant litter leads to a decrease in SOM α-molecular diversity, yet an increase in β-molecular diversity across ecosystems. The degree of microbial degradation, determined by the position in the soil profile, exerts a greater control on SOM molecular diversity than environmental factors, such as soil texture, moisture, and ecosystem type.
Data collected at Council, AK (64°51’35.0”N 163°41’59.1”W) during a summer campaign in 2023. Water data consists of soil porewater collected by centrifuging soil cores and also by field collection with porewater samplers (rhizons). Gas data consists of CO2, CH4 and N2O surface soil fluxes measured with a portable FTIR analyzer. Plant and root data consists of biomass, root length, diameter and mass. Soil data consists of total C and N. Air, water and soil samples span two main locations: a thermokarst wetland and an upland tussock. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).This dataset was generated to broadly address the following research question: how will climate change (i.e., thawing permafrost, landscape change) alter the ecosystem flux (sink versus source) of important greenhouse gases such as CO2, CH4 and N2O?Description of the contents of this data package: This dataset contains 5 different individual .csv files containing plant, soil, water and gas data. No software is needed to utilize them. PFTCover: Plant functional type ground cover in 1x1 meter plots. SoilCores: Solidphase and porewater phase soil biogeochemical variablesPlantData: Above and belowground plant traits. GasFlux: Surface plant-soil gas measurementsFieldPorewater: Field collected porewater biogeochemical variables
The accumulation of dust on the surface of photovoltaic modules can reduce their performance and affect the cost competitiveness of this technology. This phenomenon is known as soiling and can be mitigated through appropriate corrective and/or preventive actions. In order to maximize its effectiveness, it is important to plan the soiling mitigation strategy even before the PV system is operational. This is typically done through a nearest neighbor approach, by estimating soiling using data from the nearest operational photovoltaic system. This work focuses on understanding the uncertainty related to this practice. For this purpose, the semi-variance function is used to study the dissimilarity between the soiling losses of two locations in California depending on their distance. The results show that, when the soiling loss at a nearby system is used to estimate soiling of a site, the uncertainty can be approximated to increase linearly at a rate of 0.08-0.10%/km up to 60 or 80 km. After this distance, the use of a nearest neighbor approach is no longer justified, as it produces an uncertainty as big as the average soiling loss of the sites in the dataset used in this study. In some conditions, uncertainties > 0% are found also for sites located within 25 km, meaning that even close-by systems might soil differently.
Rare biosphere represents the majority of Earth's biodiversity and performs vital ecological functions, yet little is known about its biogeographical patterns and community assembly processes in terrestrial ecosystems. Herein, we investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundant (>1%) bacteria in dryland grassland soils on the Tibetan Plateau. Results revealed similar biogeographical patterns of rare and abundant bacteria at both compositional and phylogenetic levels, but rare subcommunity was more heavily influenced by stochasticity (72%) than the abundant (57%). The compositional variation of rare bacteria was less explained by environmental factors (41%) than that of the abundant (80%), while the phylogeny of rare bacteria (36%) was more explained than that of the abundant (29%). The phylogeny of rare bacteria was equally explained by local factors (soil and vegetation) and geospatial distance (11.5% and 11.9% respectively), while that of the abundant was more explained by geospatial distance (22.1%) than local factors (11.3%). Furthermore, a substantially tighter connection between the community phylogeny and composition was observed in rare (R(2) = 0.65) than in abundant bacteria (R(2) = 0.08). Our study provides novel insights into the assembly processes and biographical patterns of rare and abundant bacteria in dryland soils.
Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
Soils represent the largest terrestrial carbon (C) pool, and the flux of carbon dioxide (CO 2 ) from soils to the atmosphere is ~ 6-10 times more than anthropogenic emissions. Understanding responses of soil CO 2 emissions to warming is crucial for evaluating feedback to ongoing environmental changes. The relationship between microbial respiration and temperature is typically modeled using a Q 10 function. Generally, observations of the apparent Q 10 of soil respiration are higher for cold vs. warm ecosystems, reflecting expected biophysical controls of Arrhenius kinetics. However, results from two field warming experiments in the tropics contradict this expectation, both observing extraordinarily high soil respiration responses to in situ warming. Our overall objective for the proposed work is to reduce uncertainty in temperature sensitivity of soil C loss by systematically synthesizing underlying mechanisms related to soil C turnover and stabilization. We are evaluating the temperature sensitivity of soil respiration in ecosystems across temperature extremes (e.g., arctic/boreal and tropical systems) by integrating data collected from field warming experiments with machine learning and biogeochemical models.
Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress—such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.
Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirk) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.
Linkages between aboveground and belowground communities are a key but globally under-researched component of responses to environmental change. Given the logistical complications to studying these relationships, much of our knowledge derives from laboratory experiments and localized field studies which have so far yielded inconsistent results. Because environmental factors may alter relationships between above- and belowground communities, there is a need for broad-scale field studies testing these interactions. The Antarctic Peninsula provides an ideal test setting, given the relatively simple communities both above- and belowground. The Peninsula is also experiencing rapid environmental changes, including alterations in species diversity and distribution both above- and belowground. Thus, an improved understanding of the broad-scale consequences of altered environments and vegetation communities for the soil microbiome is of high priority. To determine the nature and strength of the relationship between in situ plant and soil communities across a broad spatial scale and range of environmental conditions, we sampled soil communities at 9 locations (spanning 60–72°S along the Scotia Arc and Antarctic Peninsula) beneath the major aboveground habitats (moss, grass, lichen, algae and bare soil). We measured a comprehensive suite of soil physicochemical properties, microbial (bacterial and fungal) diversity and composition, and invertebrate abundance and community composition to determine the relationships between plant and soil communities. Furthermore, our results suggest that, with increased environmental severity, plant cover types become more important for influencing the physicochemical soil environment, and therefore the soil microbial communities. Although we found site-specific relationships, broad-scale patterns reveal significant differences among bare soils and vegetated soils, particularly soils beneath grass and moss. This suggests that expansion of vegetation communities under current climate warming projections will be accompanied by shifts in the soil microbiome, with important implications for the ecosystem functioning with which they are associated.
Atmospheric CO 2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO 2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO 2 (eCO 2 ) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO 2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO 2 , especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO 2 . A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO 2 environment.
Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Abstract Sea-level rise is causing widespread tree mortality of coastal forests, with large consequences on the Earth system as a result of these forests’ importance in carbon and nutrient export. The mechanisms of mortality under these conditions are, however, poorly tested. We used wood anatomy traits, wood δ 13 C, and tree radial growth to retrospectively assess the physiological process of seawater effects on whole tree xylem hydraulic capacity, gas exchange, and radial growth. During the latter stages of mortality (2018–2019), we directly measured metrics of water use and carbon metabolism across trees having crowns ranging from fully foliated to completely defoliated to investigate mortality processes at the sub-annual scale. Upon seawater exposure, soil salinity increased and allocation to hydraulic function declined, resulting in a dramatic reduction in water supply to the crown, increased crown-level water stress, and subsequent crown foliage loss. Simultaneously, leaf-level photosynthetic capacity declined steeply with increasing salinity. The combined loss of crown foliage area and photosynthetic rates per unit leaf area promoted carbon starvation, while no evidence of hydraulic failure was observed. These results elucidate mechanisms of coastal forest death under seawater exposure, enabling more accurate modeling in the future.
In high-level radioactive waste geological repositories, compacted bentonite undergoes coupled thermo-hydraulic processes due to heat released from a central waste canister and groundwater imbibition from the surrounding host rock. An understanding of these processes is essential for long-term simulations of radionuclide migration and canister corrosion, which requires an understanding of temperature effects on the coupled thermo-hydraulic properties governing these processes. In this study, a tank-scale radial infiltration test was used to investigate water imbibition processes in compacted bentonite under a central heater temperature of 200 °C that simulates high thermal gradients in a repository. Interpretation of this test focuses on evaluation of the liquid water wetting front during hydration and the interpretation of the temperature-dependent transient soil water retention curve (SWRC), thermal conductivity function (TCF), and hydraulic conductivity function (HCF). The SWRC during imbibition follows a temperature-dependent wetting path. Temperature effects on the hydraulic conductivity of bentonite in saturated conditions had the greatest effect on the shape of the HCF, with minimal temperature effects at higher suctions. The transient thermal conductivity data matched well with a new TCF linked with the SWRC shape. Although the bentonite layer was restrained, local deformations during hydration may have affected the shapes of the TCF and HCF.
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We also demonstrate the utility of this collection for secondary metabolite biosynthetic potential and predicting host-virus linkage, which can provide a view into the global distribution of lysogenic viruses. This resource underscores the value of leveraging genome-centric approaches to reveal genomic properties of uncultivated microbes that impact on ecosystem processes.