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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.

Background: In 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., Results: The 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., Conclusions: Our 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 increasing prevalence of antibiotic-resistant microorganisms imposes a global threat to public health. The over reliant use of antibiotics in the food industry has contributed considerably to the dissemination of antibiotics into various environments, yet the mechanisms by which antibiotic dissemination influences the assembly of the microbial community continues to remain obscure. Here, we examine bacterial and fungal community assemblies in swine manure, compost, compost amended, and unamended agricultural soil in five suburban areas of Beijing, China. Total antibiotic concentration decreased by factors of 10-1000 from manure and compost to soils. The bacterial α-diversity was found to be low in manure and compost samples, while the fungal α-diversity was similar across all samples. We detected significantly (p < 0.05) higher relative abundances of well recognized pathogenic microbial taxa, virulence associated genes, and antibiotic resistance genes (ARGs) in manure and compost than those in agricultural soils, revealing the higher microbial capacity of pathogenicity, virulence and antibiotic resistance. Unexpectedly, the relative abundances of both bacterial and fungal taxa did not predict the antibiotic concentration. A possible explanation was that bacterial and fungal communities were mainly shaped by random assemblies. Rather, antibiotic concentration could be well predicted by relative abundances of antibiotic resistance, stress and virulence associated genes. Despite the weak interconnection between ARGs and the microbiome, we demonstrate that microbial genes should be the focal point in tracking the ecological effects of antibiotic dissemination by revealing microbial community patterns along the dissemination chain of antibiotics., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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.

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.)

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 < 0.05) shifted. The relative abundances of both taxonomic markers and functional genes related to nitrifying bacteria were also changed. The observation highlighted herein, showing a high level of sensitivity with respect to functional traits (functionally categorized taxa or genes) in differentiating mild environmental disturbance, suggests that the key level at which to address microbial responses may not be "species" (by means of rRNA taxonomy), but rather at the functional gene level.

Determining the temporal scaling of biodiversity, typically described as species-time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (-50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39-0.64) than those of plants and animals (w = 0.21-0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world.

Both fungi and bacteria play essential roles in regulating soil carbon cycling. To predict future carbon stability, it is imperative to understand their responses to environmental changes, which is subject to large uncertainty. As current global warming is causing range shifts toward higher latitudes, we conducted three reciprocal soil transplantation experiments over large transects in 2005 to simulate abrupt climate changes. Six years after soil transplantation, fungal biomass of transplanted soils showed a general pattern of changes from donor sites to destination, which were more obvious in bare fallow soils than in maize cropped soils. Strikingly, fungal community compositions were clustered by sites, demonstrating that fungi of transplanted soils acclimatized to the destination environment. Several fungal taxa displayed sharp changes in relative abundance, including Podospora, Chaetomium, Mortierella and Phialemonium. In contrast, bacterial communities remained largely unchanged. Consistent with the important role of fungi in affecting soil carbon cycling, 8.1%-10.0% of fungal genes encoding carbon-decomposing enzymes were significantly (p < 0.01) increased as compared with those from bacteria (5.7%-8.4%). To explain these observations, we found that fungal occupancy across samples was mainly determined by annual average air temperature and rainfall, whereas bacterial occupancy was more closely related to soil conditions, which remained stable 6 years after soil transplantation. Together, these results demonstrate dissimilar response patterns and resource partitioning between fungi and bacteria, which may have considerable consequences for ecosystem-scale carbon cycling., (© 2019 John Wiley & Sons Ltd.)

Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems., (© 2017 John Wiley & Sons Ltd.)

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.)

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.

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.)

Studies on the molecular ecology of microbial communities in soils amended with biochar are potentially biased by changes in soil DNA extraction efficiency caused by DNA adsorption to biochar. To examine the extent to which this might occur, we evaluated a kit-free method for soil DNA extraction as well as MoBio's PowerSoil® commercial kit with and without phenol/chloroform/isoamyl (PCI) modification. DNA extraction efficiencies were quantified for soils amended with four biochar types that were added to either clay or sand soils at a rate of 3 % ( w/ w). Prior to extraction, all soil treatments were spiked with bacteria transformed with plasmids carrying a green fluorescent protein ( gfp) gene, as a molecular marker. DNA purity and yield were assessed spectrophotometrically and fluorometrically. Quantitative PCR (qPCR) was utilized to enumerate gfp copy numbers extracted per gram soil. Results showed that qPCR-quality DNA could be efficiently extracted from biochar-amended soils using the PowerSoil® kit with or without PCI modification. However, the modified protocol resulted in an average of approximately 3 times greater yield than the provided protocol. Of the tested methods, none demonstrated reduced DNA extraction efficiency or purity when amended with the varying biochars. [ABSTRACT FROM AUTHOR]

Currently, there are substantial knowledge gaps on the impacts of cover crops on soil resources in tree cropping systems, wherein they are typically planted in interrow alleys and maintained for multiple years. While cover crops uptake soil nutrients and water, they can also prevent soil water evaporative losses and return nutrients to soils via decomposition of plant residues and stimulation of microbial nutrient cycling. This field sampling study examined variances in soil conditions across 5- and 7-year-old, cover cropped pecan orchards. We collected soil beneath cover crops and beneath adjacent trees, where soil was kept bare, to evaluate impacts of cover on the soil biota, nutrients, carbon, and their dynamics across a production season. We employed routine soil chemical analyses, phospholipid fatty acid (PLFA) analysis, and high throughput sequencing of 16 S rRNA genes and ITS regions for soils collected at four time points. We revealed that the cover cropped alley soils contained higher relative abundances of microbes that use labile soil substrates in resource rich conditions than did the tree row soils. Soil chemical analyses provided additional evidence that the cover crops did not deplete soil nutrients and reduce soil moisture, but rather, enhanced soil nutrient and moisture contents during many of the sampling time points. Notably, cover crop plant species correlated with soil nutrients and plant beneficial microbes, which may warrant consideration when selecting cover crop species. The tree row and cover cropped alley soils had different proportions of plant-beneficial mycorrhizal fungi. The tree rows supported higher numbers of ectomycorrhizal (ECM) fungi and alleys had higher relative abundances of arbuscular mycorrhizal (AM) fungi, suggesting potential benefits for tree species like pecan, which support dual colonization by AM and ECM Fungi. Altogether, the cover crops enhanced soil carbon, nutrients, and microbial populations in a pecan orchard and these impacts were frequently larger in a 7-year-old versus 5-year-old orchard. [Display omitted] • Alley cover crops in pecan orchards promote distinct soil conditions. • Cover crop soils had higher carbon, nitrogen, and moisture than soil under trees. • Soil microbial biomass and copiotroph oligotroph ratios were enhanced under cover crops. • AM and ECM fungi were differentially abundant under cover or trees. • Some cover crop plant species correlated with soil health indicators. [ABSTRACT FROM AUTHOR]