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Application of inorganic nitrogen (N) fertilizers in agriculture can increase emissions of nitrous oxide, a potent greenhouse gas, leaching of nitrate (NO 3 ), a groundwater contaminant hazardous to human health, and soil acidification. Soil amendment with biochar potentially mitigates these losses and undesirable outcomes. However, there have been considerable inconsistencies in reported impacts, likely owing to variable physiochemical characteristics of the biochar materials and/or the soil environment. This study methodically evaluated the impact of biochar soil incorporation on N transformation and underlying microbial processes using soils with varying biochar types, soil texture, soil moisture, and manure compost co- amendments. Laboratory incubations were conducted to monitor the fate of urea fertilizer N spiked in biochar amended and unamended soils by assaying soil ammonium (NH - ), a groundwater contaminant hazardous to human health, and soil acidification. Soil amendment with biochar potentially mitigates these losses and undesirable outcomes. However, there have been considerable inconsistencies in reported impacts, likely owing to variable physiochemical characteristics of the biochar materials and/or the soil environment. This study methodically evaluated the impact of biochar soil incorporation on N transformation and underlying microbial processes using soils with varying biochar types, soil texture, soil moisture, and manure compost co- amendments. Laboratory incubations were conducted to monitor the fate of urea fertilizer N spiked in biochar amended and unamended soils by assaying soil ammonium (NH 4 + concentrations, pH, and abundances of soil nitrifiers; ammonia oxidizing bacteria and archaea (AOB and AOA) and Nitrospira with the capacity to perform complete ammonia oxidation (comammox). Soil moisture was a critical factor affecting N transformation processes, more so than biochar, but biochar did result in significantly different concentrations of N species in response to urea application. Biochar enhanced nitrification, more significantly in drier conditions and in sandy soil. Biochar offered some buffering potential in the neutral-alkaline, unsaturated soils, preventing >1 unit drop in pH compared to unamended soils. Co-application of biochar with manure composts enhanced nitrification slightly, which was evidenced by higher abundances of some soil nitrifiers at 4 weeks, although increases in nitrification rates were not statistically significant. Soil nitrifier populations tended to increase in response to a pinewood biochar, but trends differed for saturated soil, in soils of differing textures, or when different biochar materials were evaluated. Thus, when evaluating implications of biochar on the fate of mineral N fertilizer, soil moisture and other environment conditions should be considered.2 - ), and NO 3 - concentrations, pH, and abundances of soil nitrifiers; ammonia oxidizing bacteria and archaea (AOB and AOA) and Nitrospira with the capacity to perform complete ammonia oxidation (comammox). Soil moisture was a critical factor affecting N transformation processes, more so than biochar, but biochar did result in significantly different concentrations of N species in response to urea application. Biochar enhanced nitrification, more significantly in drier conditions and in sandy soil. Biochar offered some buffering potential in the neutral-alkaline, unsaturated soils, preventing >1 unit drop in pH compared to unamended soils. Co-application of biochar with manure composts enhanced nitrification slightly, which was evidenced by higher abundances of some soil nitrifiers at 4 weeks, although increases in nitrification rates were not statistically significant. Soil nitrifier populations tended to increase in response to a pinewood biochar, but trends differed for saturated soil, in soils of differing textures, or when different biochar materials were evaluated. Thus, when evaluating implications of biochar on the fate of mineral N fertilizer, soil moisture and other environment conditions should be considered., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Suduan Gao reports financial support was provided by United States Department of Agriculture Agricultural Research Service., (Published by Elsevier B.V.)

Switchgrass is a deep-rooted perennial native to the US prairies and an attractive feedstock for bioenergy production; when cultivated on marginal soils it can provide a potential mechanism to sequester and accumulate soil carbon (C). However, the impacts of switchgrass establishment on soil biotic/abiotic properties are poorly understood. Additionally, few studies have reported the effects of switchgrass cultivation on marginal lands that have low soil nutrient quality (N/P) or in areas that have experienced high rates of soil erosion. Here, we report a comparative analyses of soil greenhouse gases (GHG), soil chemistry, and microbial communities in two contrasting soil types (with or without switchgrass) over 17 months (1428 soil samples). These soils are highly eroded, 'Dust Bowl' remnant field sites in southern Oklahoma, USA. Our results revealed that soil C significantly increased at the sandy-loam (SL) site, but not at the clay-loam (CL) site. Significantly higher CO 2 flux was observed from the CL switchgrass site, along with reduced microbial diversity (both alpha and beta). Strikingly, methane (CH 4 ) consumption was significantly reduced by an estimated 39 and 47% at the SL and CL switchgrass sites, respectively. Together, our results suggest that soil C stocks and GHG fluxes are distinctly different at highly degraded sites when switchgrass has been cultivated, implying that carbon balance considerations should be accounted for to fully evaluate the sustainability of deep-rooted perennial grass cultivation in marginal lands., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Although interactions between plants and microbes at the plant-soil interface are known to be important for plant nutrient acquisition, relatively little is known about how root exudates contribute to nutrient exchange over the course of plant development. In this study, root exudates from slow- and fast-growing stages of Arabidopsis thaliana plants were collected, chemically analysed and then applied to a sandy nutrient-depleted soil. We then tracked the impacts of these exudates on soil bacterial communities, soil nutrients (ammonium, nitrate, available phosphorus and potassium) and plant growth. Both pools of exudates shifted bacterial community structure. GeoChip analyses revealed increases in the functional gene potential of both exudate-treated soils, with similar responses observed for slow-growing and fast-growing plant exudate treatments. The fast-growing stage root exudates induced higher nutrient mineralization and enhanced plant growth as compared to treatments with slow-growing stage exudates and the control. These results suggest that plants may adjust their exudation patterns over the course of their different growth phases to help tailor microbial recruitment to meet increased nutrient demands during periods demanding faster growth., (© 2020 John Wiley & Sons Ltd.)

We examined the effect of a labile soil amendment, compost, and recalcitrant biochar on soil microbial community structure, diversity, and activity during turfgrass establishment. Two application rates of biochar (B1 at 12.5 t ha-1and B2 at 25 t ha-1), a 5 centimeter (cm) green waste compost treatment (CM) in top soil, a treatment with 12.5 t ha-1 biochar and 5 cm compost (B1+CM), and an unamended control (CK) treatment were prepared and seeded with tall fescue. Overall, results of phospholipid fatty acid analysis (PLFA) profiling and Illumina high-throughput sequencing of 16S rRNA genes amplified from soil DNA revealed significant shifts in microbial community structures in the compost amended soils whereas in biochar amended soils communities were more similar to the control, unamended soil. Similarly, increases in enzymatic rates (6-56%) and nitrogen-induced respiration (94%) were all largest in compost amended soils, with biochar amended soils exhibiting similar patterns to the control soils. Both biochar and compost amendments impacted microbial community structures and functions, but compost amendment, whether applied alone or co-applied with biochar, exhibited the strongest shifts in the microbial community metrics examined. Our results suggest application of compost to soils in need of microbiome change (reclamation projects) or biochar when the microbiome is functioning and long-term goals such as carbon sequestration are more desirable., Competing Interests: The authors have declared that no competing interests exist.

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q 10 ) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.

Invasive plant species may alter soil nutrient availability to facilitate their growth and competitiveness. However, the roles and functional mechanisms of plant-associated microbes that mediate these soil biogeochemical cycles remain elusive. Here, we studied how soil microorganisms and their functional processes differed between soils invaded by Ageratina adenophora and adjacent non-invaded soils in a region of China with heavy invasion. Our results indicated that soil nitrogen contents were over 4.32 mg/kg higher (p < 0.05) in both rhizosphere soils and bulk soils dominated by A. adenophora as compared with those in soils dominated by non-invaded plants. Concurrently, soil microbial-mediated functional processes, i.e. nitrogen fixation rate, nitrification rate and ammonification rate, were also significantly (p < 0.05) higher in either rhizosphere soils or bulk soils of invasive A. adenophora. Using a functional gene microarray, we found higher relative abundances of soil microbial genes involved in N cycling processes in A. adenophora soils, e.g. nifH, required for nitrogen fixation, which significantly correlated with ammonia contents (r = 0.35 in bulk soils, r = 0.37 in rhizosphere soils, p < 0.05) and the nitrogen fixation rate (r = 0.44, p < 0.05). We also found that the relative abundances of labile carbon decomposition genes were higher in invasive A. adenophora soils, implying a potential higher availability of carbon. These results suggest that the soil surrounding the invasive plant A. adenophora is a self-reinforcing environment. The plant litter and rhizosphere environment of the invasive may influence soil microbial communities, promoting self-supporting soil processes. Alternatively, the regions invaded by A. adenophora may have already had properties that facilitated these beneficial microbial community traits, allowing easier invasion by the exotics. Both scenarios offer important insights for the mitigation of plant invasion and provide an ecosystem-level understanding of the invasive mechanisms utilized by alien plants., (Copyright © 2019. Published by Elsevier B.V.)

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon-climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming. Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change., (© 2017 John Wiley & Sons Ltd.)

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling., (© 2017 John Wiley & Sons Ltd.)

BackgroundFor achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability.ResultsWe found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass.ConclusionsOur results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.

BackgroundIn a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.ResultsThe β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.ConclusionsOur findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.

The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.

Mild disturbances are prevalent in the environment, which may not be easily notable but could have considerable ecological consequences over prolonged periods. To evaluate this, a field study was designed to examine the effects of very light-intensity lamb grazing on grassland soil microbiomes with different soil backgrounds. No significant change (P > 0.05) was observed in any vegetation and soil variables. Nonetheless, hundreds of microbial functional gene families, but not bacterial taxonomy, were significantly (P

As climate cooling is increasingly regarded as important natural variability of long-term global warming trends, there is a resurging interest in understanding its impact on biodiversity and ecosystem functioning. Here, we report a soil transplant experiment from lower to higher elevations in a Tibetan alpine grassland to simulate the impact of cooling on ecosystem community structure and function. Three years of cooling resulted in reduced plant productivity and microbial functional potential (for example, carbon respiration and nutrient cycling). Microbial genetic markers associated with chemically recalcitrant carbon decomposition remained unchanged despite a decrease in genes associated with chemically labile carbon decomposition. As a consequence, cooling-associated changes correlated with a decrease in soil organic carbon (SOC). Extrapolation of these results suggests that for every 1 °C decrease in annual average air temperature, 0.1 Pg (0.3%) of SOC would be lost from the Tibetan plateau. These results demonstrate that microbial feedbacks to cooling have the potential to differentially impact chemically labile and recalcitrant carbon turnover, which could lead to strong, adverse consequences on soil C storage. Our findings are alarming, considering the frequency of short-term cooling and its scale to disrupt ecosystems and biogeochemical cycling.