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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Abstract Background and aim Rice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored. Methods We compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants. Results Our data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields. Conclusions Results from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

Agriculture↗
DOE OSTI2022

Latitudinal shifts of soil microbial biomass seasonality

Soil microbes ultimately drive the mineralization of soil organic carbon and thus ecosystem functions. We compiled a dataset of the seasonality of microbial biomass carbon (MBC) and developed a semi-mechanistic model to map monthly MBC across the globe. MBC exhibits an equatorially symmetric seasonality between the Northern and Southern Hemispheres. In the Northern Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes (<25°N), peaks in the spring and is minimal in autumn at mid-latitudes (25°N to 50°N), while peaks in autumn and is minimal in spring at high latitudes (>50°N). This latitudinal shift of MBC seasonality is attributed to an interaction of soil temperature, soil moisture, and substrate availability. The MBC seasonality is inconsistent with patterns of heterotrophic respiration, indicating that MBC as a proxy for microbial activity is inappropriate at this resolution. This study highlights the need to explicitly represent microbial physiology in microbial models. The interactive controls of environments and substrate on microbial seasonality provide insights for better representing microbial mechanisms in simulating ecosystem functions at the seasonal scale.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy

Abstract In studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula × alba

Trees depend on beneficial interactions between roots and soil microbes for their nutrition and protection against stresses. The soil microbiome provides the main reservoir of microbes for root colonization and is subject to natural variations that can affect its composition. It is not clear whether the tree’s root system is able to buffer the natural variations occurring in the soil microbiome to capture a stable and effective microbiome or whether these variations affect its microbiome to impact its physiology. To address this question, we planted cuttings of Gray Poplar (Populus tremula × alba clone 717-1B4) in natural soil taken from a poplar stand under the same tree over two consecutive years and grew them in a greenhouse. We analyzed the soil and root microbiomes by high throughput Illumina MiSeq sequencing of fungal rDNA internal transcribed spacer and bacterial 16S rRNA amplicons and we characterized the root metabolome by gas chromatography-mass spectrometry. Soil and root microbial communities significantly shifted over the 2 years. A modification of the balance between endophytes, saprophytes, and mycorrhizal fungi occurred in the roots as well as a replacement of some dominant operational taxonomic units by others. These modifications were correlated with a significant alteration of the levels of about 10% of primary and secondary metabolites, suggesting that natural fluctuations in soil microbial communities can have a profound impact on tree root metabolism and physiology. Tree roots functioning may thus be indirectly strongly affected by the effects of future extreme climatic variations on the soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Plant Roots and the Fate of Mineral-Associated Soil Carbon (Final Report)

Atmospheric CO 2 concentrations continue to rise due to human activities, but there are also natural mechanisms operating in ecosystems that can store carbon in soil long-term. The organic carbon derived from organisms in soil becomes associated with minerals, where it can be protected for thousands of years. Plants are particularly important contributors of carbon belowground, via their roots. The long-term protection of carbon contributed to soil has great value to humans as climate change looms. But, to keep growing, living plants and soil microbes also need to be able to access and recycle soil nutrients that are stored along with the carbon. In this DOE-funded work, Cardon (MBL), Keiluweit (UMass Amherst/University of Lausanne), Malmstrom (MSU), and Riley (LBNL) used lab and greenhouse experiments coupled with mathematical modeling to determine mechanisms by which plant roots and their associated microbes can dislodge organic matter from soil minerals, making its components available for recycling, but also making its carbon vulnerable to re-release to the atmosphere as CO 2 .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Short-term warming increased soil heterotrophic respiration due to enhanced active microbial community

Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50% of global soil organic carbon. Nevertheless, the response mechanisms of active microbial community to climate warming and their subsequent impacts on soil heterotrophic respiration (Rh) remain insufficiently understood. To resolve this mechanistic uncertainty, we implemented a 3-year soil translocation experiment to investigate soil warming effects on active microbial community and Rh. We used 16S rRNA gene amplicon sequencing, Metatranscriptomics sequencing, coupled with correlation analyses to explore the linkages between warming-induced shifts in Rh and the active microbial community. Our results demonstrated that warming of soil induced a 55% enhancement in Rh. Concurrently, the Shannon index and Richness of active microbial community increased by 20% and 117%, respectively. Warming significantly altered active microbial community composition, inducing a compositional shift characterized by 0.5-to 2-fold increases in the abundances of Proteobacteria, Chloroflexi, and Actinobacteria. Our study also revealed 92–100% increases in the abundance of C-degradation functional genes encoding starch, cellulose, and lignin decomposition pathways within active microbial community under warming. Statistical analyses identified significant positive correlations between Rh and the abundance of Proteobacteria and Actinobacteria, as well as expression levels of functional genes associated with lignin and cellulose decomposition pathways. Furthermore, our results suggested that short-term warming increased Rh through altering diversity, species composition, and C degradation functional genes of active microbial community providing insights into the influence of microbial communities on soil C-climate feedbacks under climate warming.

Active microbial community↗
DOE OSTI2024

Field experiments show no consistent reductions in soil microbial carbon in response to warming

Soil microbes play an essential role in maintaining soil functions and services, but the dynamics of soil microbial biomass carbon (MBC) under global climate change remain unclear. Recently, Patoine et al. combined a global MBC data set with Random Forest modeling and reported that global MBC decreased over 1992–2013, mainly driven by increasing temperatures. Contrarily, using MBC field observations from soil warming manipulation experiments and in-situ long-term measurements across the globe, we found that MBC showed no significant changes under soil warming. Our findings indicate that soil MBC is unlikely to have decreased significantly due to the global warming of 0.28 °C during 1992–2013, and that further mechanistic studies are needed to understand potential changes in MBC under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Microbial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite Composition

Rapid microbial growth in the early phase of plant litter decomposition is viewed as an important component of soil organic matter (SOM) formation. However, the microbial taxa and chemical substrates that correlate with carbon storage are not well resolved. The complexity of microbial communities and diverse substrate chemistries that occur in natural soils make it difficult to identify links between community membership and decomposition processes in the soil environment. To identify potential relationships between microbes, soil organic matter, and their impact on carbon storage, we used sand microcosms to control for external environmental factors such as changes in temperature and moisture as well as the variability in available carbon that exist in soil cores. Using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) on microcosm samples from early phase litter decomposition, we found that protein- and tannin-like compounds exhibited the strongest correlation to dissolved organic carbon (DOC) concentration. Proteins correlated positively with DOC concentration, while tannins correlated negatively with DOC. Through random forest, neural network, and indicator species analyses, we identified 42 bacterial and 9 fungal taxa associated with DOC concentration. The majority of bacterial taxa (26 out of 42 taxa) belonged to the phylum Proteobacteria while all fungal taxa belonged to the phylum Ascomycota. Additionally, we identified significant connections between microorganisms and protein-like compounds and found that most taxa (12/14) correlated negatively with proteins indicating that microbial consumption of proteins is likely a significant driver of DOC concentration. This research links DOC concentration with microbial production and/or decomposition of specific metabolites to improve our understanding of microbial metabolism and carbon persistence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Microbial O 2 consumption as a function of pore structure in soils of sorghum, switchgrass, and prairie vegetation systems

Abstract Microscale O 2 availability in soil, a main factor influencing microbial processing of soil carbon and nitrogen, is a function of O 2 diffusion and microbial O 2 consumption. While O 2 diffusivity is widely studied, it is difficult to quantify the rate of microbial O 2 consumption ( MO ). In this study, we quantified the MO using O 2 microsensor profiling to compare MO in different soils and vegetation systems while manipulating the soil pore structure. Soil samples were collected from three bioenergy vegetation systems, sorghum ( Sorghum bicolor L. Moench), switchgrass ( Panicum virgatum L.), and prairie, at an experimental site in Southeast Michigan, and from switchgrass and prairie systems at two sites in South and North Wisconsin. We prepared soil cores with two contrasting pore structures, that is, large (>30 µm Ø) pore‐dominated soil (LP) and small (<10 µm Ø) pore‐dominated soil (SP), from the same 1‐ to 2‐mm soil size fraction. We quantified MO (nmol O 2 cm −3 s −1 ) using a microprofiler with an oxygen (OX‐100 µm) microsensor (Unisense) pre‐ and post‐38‐day incubation. Across all studied systems, there was a trend for a decrease in SP MO post‐incubation, suggesting a change in microbial metabolism to lower O 2 utilization. However, sizeable microbial O 2 consumption continued in the LP soils, further corroborated by a positive correlation between the C‐CO 2 emission rate and the post‐incubation MO , highlighting that LP provided a better physical microenvironment for the soil microbes.

Chakraborty, Poulamee [Department of Plant Soil an↗
DOE OSTI2021

Soil gas probes for monitoring trace gas messengers of microbial activity

Abstract Soil microbes vigorously produce and consume gases that reflect active soil biogeochemical processes. Soil gas measurements are therefore a powerful tool to monitor microbial activity. Yet, the majority of soil gases lack non-disruptive subsurface measurement methods at spatiotemporal scales relevant to microbial processes and soil structure. To address this need, we developed a soil gas sampling system that uses novel diffusive soil probes and sample transfer approaches for high-resolution sampling from discrete subsurface regions. Probe sampling requires transferring soil gas samples to above-ground gas analyzers where concentrations and isotopologues are measured. Obtaining representative soil gas samples has historically required balancing disruption to soil gas composition with measurement frequency and analyzer volume demand. These considerations have limited attempts to quantify trace gas spatial concentration gradients and heterogeneity at scales relevant to the soil microbiome. Here, we describe our new flexible diffusive probe sampling system integrated with a modified, reduced volume trace gas analyzer and demonstrate its application for subsurface monitoring of biogeochemical cycling of nitrous oxide (N 2 O) and its site-specific isotopologues, methane, carbon dioxide, and nitric oxide in controlled soil columns. The sampling system observed reproducible responses of soil gas concentrations to manipulations of soil nutrients and redox state, providing a new window into the microbial response to these key environmental forcings. Using site-specific N 2 O isotopologues as indicators of microbial processes, we constrain the dynamics of in situ microbial activity. Unlocking trace gas messengers of microbial activity will complement -omics approaches, challenge subsurface models, and improve understanding of soil heterogeneity to disentangle interactive processes in the subsurface biome.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2022

Exploring the roles of microbes in facilitating plant adaptation to climate change

Plants benefit from their close association with soil microbes which assist in their response to abiotic and biotic stressors. Yet much of what we know about plant stress responses is based on studies where the microbial partners were uncontrolled and unknown. Under climate change, the soil microbial community will also be sensitive to and respond to abiotic and biotic stressors. Thus, facilitating plant adaptation to climate change will require a systems-based approach that accounts for the multi-dimensional nature of plant–microbe–environment interactions. In this perspective, we highlight some of the key factors influencing plant–microbe interactions under stress as well as new tools to facilitate the controlled study of their molecular complexity, such as fabricated ecosystems and synthetic communities. When paired with genomic and biochemical methods, these tools provide researchers with more precision, reproducibility, and manipulability for exploring plant–microbe–environment interactions under a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ectomycorrhizal fungal diversity interacts with soil nutrients to predict plant growth despite weak plant-soil feedbacks

Background and aims Plant-soil feedbacks are the result of multiple abiotic and biotic mechanisms. However, few studies have addressed how feedbacks vary based on abiotic context or attempted to identify microbiota responsible for feedbacks. In this work, we investigated whether plant-soil feedbacks of an ectomycorrhizal tree (Quercus macrocarpa) varied based on soil nutrient status and whether fungal community composition and diversity could explain feedback patterns. Furthermore, we inoculated Q. macrocarpa seedlings with field-sampled soils taken from five soil origins – including heterospecific and conspecific trees and an old field – which were profiled using fungal DNA metabarcoding.Results Despite finding that soils associated with different hosts harbored distinct fungal communities and that fungal communities were predictive of plant growth, we did not find any significant plant-soil feedbacks regardless of fertilization status. We did find that the growth promotive effect associated with ectomycorrhizal OTU diversity was weakened with fertilization, suggesting context-dependent relations between plant growth and a guild of fungal mutualists. Our results demonstrate that the host-specific accumulation of functionally important soil microbes is not always sufficient to drive observable plant-soil feedbacks. Our data provide support for a role for ECM fungal diversity in mediating plant growth responses, though it is unclear whether this effect is direct or indirect.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Abstract Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

Environmental Sciences & Ecology↗
DOE OSTI2020

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Ectomycorrhizal effects on decomposition are highly dependent on fungal traits, climate, and litter properties: A model-based assessment. Dataset.

To simulate the effects of mycorrhizal fungi on soil organic matter cycling, we incorporated mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model to develop a new soil model Myco-CORPSE. The new model was calibrated and evaluated against soil measurements taken at temperate forests in New Hampshire (NH) and Georgia (GA). A series of scenario analysis were also conducted to explore the conditions under which ectomycorrhizal (ECM) N acquisition processes can induce different soil C accumulation in ECM systems compared to arbuscular (AM) systems.In this data package, we included:-The Python codes of the standard Myco-CORPSE model we developed: "Standard Myco_CORPSE python codes.zip". The main program is the "gradient_sim.py" which calculates the bulk soil microbes and CN content along a user defined gradient of clay, soil temperature, soil moisture and mycorrhizal dominance, and relies on two subprograms "CORPSE_deriv.py" and "CORPSE_integrate.py". "CORPSE_deriv.py" calculated the changes in all simulated soil stock within every time step and "CORPSE_integrate.py" integrate the changes in all simulated soil stock within simulated time period. The program "Plot.py" is used to plot the major outputs produced by the main program "gradient_sim.py".-The modified Python codes of Myco-CORPSE models with site-level environmental inputs (in NH and GA) used to conduct simulations in NH and GA sites: "NH_GA model simulations.zip". -The Python codes used to evaluate the Myco-CORPSE simulation outputs in NH and GA sites against site-level measurements: "Plot NH_GA simulation against measurements.zip". It includes both the evaluation Python code, the model outputs on NH and GA sites, and the measured soil properties in both sites.-The modified Python codes of Myco-CORPSE models "Scenario analysis_model simulations.zip" that is used to conduct scenario analysis of how different litter properties, mycorrhizal fungal traits, climate, and seasonal variation in temperature and vegetation phenology impact the mycorrhizal effects on soil CN properties. The sub file folder "Scenario analysis_litter traits" contains the codes for scenario analysis of different litter properties; The sub file folder "Scenario analysis_ECM types" contains the codes for scenario analysis of different ECM fungal traits; The sub file folder "Scenario analysis_climate&seasonality" contains the codes for scenario analysis of different climate and seasonalities;-"Scenario analysis_model results and plotting codes.zip" contains all the output files from the the scenario analysis of Myco-CORPSE model as described above and the plotting codes used to the generate the heatmaps and scatterplots shown in the manuscript "Ectomycorrhizal effects on decomposition are highly dependent on fungal traits, climate, and litter properties: A model-based assessment"The majority of the model outputs did not have specific geographic information or temporal coverage because the analysis we conducted are mainly hypothetical model simulations. We only provided geographic description, coordinates and temporal coverage for those soil measurements which we used for model evaluations (included in the "Plot NH_GA simulation against measurements.zip").

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g −1 , which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant ( p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes . Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Shen, Qihui↗