The feeding ecology of soil animals is seldom investigated in the winter when the soil is covered with a layer of snow. Collembola (springtails) are winter-active arthropods that appear on the snow surface, especially on sunny days, and remain active in microhabitats under the snow. Since winter-active Collembola must be consuming food, we assessed the food resources for these Collembola with stable isotope and bacterial 16S rRNA gene amplicon sequencing methods. We collected two Desoria species from the snow surface and Tomocerus cf. jilinensis from subnivean microhabitats. The stable isotope signatures of winter-active Collembola species differed significantly from the soil litter layer. The isotopic signature of Desoria sp.1 was similar to the snow. Furthermore, the putative food resource (bacteria) ingested by Desoria sp.3 and Tomocerus cf. jilinensis had a similar isotopic signature as snow, but not litter. All three Collembola species ingested a large proportion of Cyanobacteria. Moreover, a large proportion of bacteria associated with Collembola were putative symbionts. Bacterial communities and their associated metabolic functions were more similar in the two congeneric Desoria species than with Tomocerus cf. jilinensis. Our findings suggest that winter-active Collembola mainly feed on resources present in the snow layer. Stable isotope and amplicon sequencing methods are promising techniques to evaluate the diets of soil animals that remain active in snow-covered soils.

Clay-sized soil minerals are known to protect organic carbon (OC) from mineralisation by formation of organo-mineral associations limiting its availability to microorganisms. The impact of soil fauna on these processes is poorly known. The aim of this study was to investigate the effect of earthworms on organic matter (OM) decomposition and association with minerals during a laboratory experiment. We used a model system consisting of fresh OM incubated with and without epigeic earthworms (Eisenia andrei and foetida) in presence of different types and amounts of phyllosilicates (kaolinite, montmorillonite) and an iron oxide (goethite) and combinations of these minerals. Our experimental setup included a high OM:mineral ratio to represent the soil-litter interphase. We monitored OC mineralization during 196 days. Additionally, we investigated physicochemical parameters and chemical OM characteristics of decomposition products by determination of water-soluble OC (WSOC) and acquisition of solid-state 13C NMR spectra. We also analysed microscale organisation of the organo-mineral associations produced with and without earthworms by transmission electron microscopy (TEM). Earthworms enhanced OC mineralisation in all treatments. They also led to greater reductions of OC emissions in the presence of minerals as compared to the mineral-free control, depending on the type and amount of minerals added. The presence of earthworms affected microbial biomass, the concentration of WSOC and increased the contribution of aromatic compounds to OM decomposition products. Microscale analyses by TEM showed that earthworms favoured association of minerals with partly degraded OM along with completely degraded material, while in absence of earthworms only completely degraded OM was associated with minerals. We conclude that earthworms impact OM decomposition through (1) their effect on microbial biomass and the physicochemical parameters of microbial habitat and (2) the formation of OM associations by changing the OM types associated to minerals and possibly by creating closer association of partly degraded OM and iron oxides. The stability of these associations remains to be investigated.

Aerobic methane oxidation is driven by both abiotic and biotic factors which are often confounded in the soil environment. Using a laboratory-scale reciprocal inoculation experiment with two native soils (paddy and upland agricultural soils) and the gamma-irradiated fraction of these soils, we aim to disentangle and determine the relative contribution of abiotic (i.e., soil edaphic properties) and biotic (i.e., initial methanotrophic community composition) controls of methane oxidation during re-colonization. Methane uptake was appreciably higher in incubations containing gamma-irradiated paddy than upland soil after inoculation with both native soils despite of different initial methanotrophic community composition, suggesting an overriding effect of the soil edaphic properties in positively regulating methane oxidation. Community composition was similar in incubations with the same starting inoculum as determined by quantitative and qualitative pmoA gene analyses. Thus, results suggested that the initial community composition affects the trajectory of community succession to an extent, but not at the expense of the methanotrophic activity under high methane availability; edaphic properties override initial community composition in regulating methane oxidation.

Phytate is considered a poorly available plant P source but proved to be useful for particular soil bacteria strains. In soil-free conditions, it has been shown that bacteria locked up the mineralized phosphorus from phytate whereas bacterial grazers like nematodes were able to deliver P to plants. Here, we aimed to determine if the interactions between phytate-mineralizing bacteria, bacterial grazer nematodes, and mycorrhizal fungi could increase plant P acquisition from phytate in high P-adsorbing soils. Pinus pinaster was grown in a Cambisol supplemented with phytate. Plants, whether associated or not associated with the ectomycorrhizal fungus Hebeloma cylindrosporum, were either inoculated or not inoculated with the phytase-releasing bacteria Bacillus subtilis and the bacterial-feeding nematode Rhabditis sp. After 100 days, the dual inoculation of bacteria and nematodes significantly increased net plant P accumulation. We observed that, on average, mycorrhizal plants accumulated more P in their shoots than non-mycorrhizal plants. However, the highest plant P acquisition efficiency was found when the three soil organisms were present in the P. pinaster rhizosphere. We conclude that, in a highly inorganic P-fixing soil, plant P acquisition from phytate strongly depends on the grazing of phytate-mineralizing bacteria. Our results confirm the importance of the soil microbial loop to improve plant P nutrition from phytate, which should be considered a route to improve the utilization of this source of poorly available P by plants.

Nitrite (NO2−) accumulation and associated production of nitric oxide (NO) and nitrous oxide (N2O) gases in soils amended with nitrogen (N) fertilizers are well documented, but there remains a poor understanding of their regulation and variation among soil types. We examined responses to urea inputs in two soils at five temperatures from 5 to 30 °C and developed a process-driven model to describe the dynamics. A microcosm system was used to measure ammonia gas (NH3), ammonium (NH4+), NO2−, nitrate (NO3−), NO, N2O and pH over 12 weeks. Unexpectedly, NO2−, NO and N2O production tended to increase as soil temperature declined in both soils. The maximum NO2− concentration, or compensation point (CP), differed by soil type but the time required to reach CP decreased exponentially with increasing temperature in both soils. A two-step nitrification model (’2SN’) accounted for interactions of ammonia-oxidation (AmO), nitrite oxidation (NiO), urea hydrolysis, NH4+ sorption, N gas production and pH dynamics. Both steps of nitrification (AmO and NiO) were modeled using NH3 inhibition kinetics. The model adequately simulated the observed dynamics and temperature responses and showed that increased uncoupling of AmO and NiO at colder temperatures resulted from their differential temperature responses. The dynamics observed here may be important following high-rate and banded N fertilizer applications and in ruminant urine patches. The results may help explain elevated N2O emissions observed under cold temperatures. The 2SN model can account for interactions among multiple processes and may be useful for studying the effects of management practices and climate factors, including climate change scenarios, on soil N cycling.

Organic forms of phosphorus (P) tend to accumulate in soils with long-term fertilization, however they are generally not easily available to crops. Many crop plants are obligately arbuscular mycorrhizal (AM) and AM fungi are known for not being able to produce phosphatases, the enzyme involved in the mineralization of organic P. AM fungi are able to recruit bacteria in the hyphosphere which can produce phosphatases and access organic P. It is thought that fructose produced by AM fungi acts as a signal to select these bacteria. We designed a system to test whether fructose could stimulate phosphatase activity in the maize hyphosphere. The concentration of fructose produced by AM fungi and the large concentration of fructose equivalent to the entire concentration of hyphal exudate carbon, were added. Small concentrations of fructose did not stimulate phosphatase activity in soil, cause shifts in bacterial community structure or select phosphatase producing species. However, at large concentrations of fructose, phosphatase activity was increased and this was associated with a larger bacterial population and a shift in bacterial community structure towards species which specialized in using fructose and glucose for energy metabolism, such as Saccharibacteria. Nevertheless, there was no specific shift towards species which harbored alkaline phosphatase genes and it is suggested that the change in phosphatase activity was due to subtle shifts in the properties of the phosphatases being produced. These results suggest that fructose was unable to act as a signal to select phosphatase producing bacteria in soil, but could act as an energy source to stimulate phosphatase activity by shifting soil bacterial community structure.

This research investigated the effect of long-term phosphorus (P) addition relative to carbon (C) availability on nitrous oxide (N2O) emissions from an ungrazed grassland soil via two incubation experiments. No significant effect of soil P on N2O was found under C-limited conditions, while under added-C, cumulative N2O was significantly higher from low-P (p<0.05) rather than high-P soils. CO2 was not significantly different between P-levels. This highlights the influence of soil P on N2O emissions under non C-limiting conditions. This is one of the first studies demonstrating available-C moderating the effect of P on N2O emissions from temperate grassland soils.

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were <24 h, whilst several days for nitrate. In clay soils, bacterial, archaeal, AOA, and AOB communities were clearly distinct from those in Chalk and Greensand soils. Spatially and temporally, AOA were more abundant than AOB. Notably, Nitrososphaera were predominant, comprising 37.4% of archaeal communities, with the vast majority of AOA found in Chalk and Greensand soils. AOA abundance positively correlated with nitrate concentration, whereas AOB abundance correlated with ammonium and nitrite concentrations, suggesting that these N compounds may be potential drivers for AOA/AOB niche differentiation in these grassland soils.

The interaction between root exudates and soil microbes has been hypothesised as the primary mechanism for the biodegradation of organic pollutants in the rhizosphere. However, the mechanisms governing this loss process are not completely understood. This study aimed to investigate the effect of two important compounds within root exudates (citric and malic acid) on 14C-phenanthrene desorption and bioaccessibility in soil. Overall results showed that the presence of both citric and malic acid (>100 mmol l−1) enhanced the desorption of 14C-phenanthrene; this appeared to be concentration dependant. Increases in extractability were not reflected in a higher bioaccessibility. Despite enhancing the desorption of 14C-phenanthrene in soil, there is no direct evidence indicating that citric or malic acid have the ability to promote the biodegradation of 14C-phenanthrene from soil. Results from this study provide a novel understanding of the role that substrates, typically found within the rhizosphere due to root exudation, play in the bioaccessibility and biodegradation of hydrocarbons in contaminated soil.

Biocrusts are a functional unit in arid and semiarid areas, their development has significant recruitment and screening effects on soil microbial communities. Microbial composition of biocrusts exhibits significant geographical patterns, but the regulation of biocrust development on the geographical patterns in unclear. In this study, we examined bacterial communities from cyanobacterial-lichen and moss crust soils in five desert habitats in northern China, and evaluated the relative importance of environmental factors and biocrust development versus geographic distance to the distance–decay relationship. To explore the effects of the sampling scale on geographical patterns, we also examined soil bacterial communities along the slope of sand dunes. Across the five desert habitats, bacterial α-diversity, phylogenetic diversity, and the dominant bacterial phyla in cyanobacterial-lichen crusts did not increase consistently with precipitation increase, instead bacterial community composition was mainly impacted by soil nutrients (SOC, TP) and biocrust development (thickness, cover and Chl a). Bacterial β-diversity in both cyanobacterial-lichen and moss crusts showed strong distance-decay relationships across the landscape scale; bacterial community composition in cyanobacterial-lichen crusts differed significantly among five desert habitats. Environmental and biocrust development variables explained bacterial community variation better than geographic distance, suggesting a weaker influence of dispersal limitation on the bacterial communities in biocrusts. In addition, the distance-decay rate was higher at the slope than that at the landscape scale, suggesting a fast turnover rate of bacterial community communities induced by topography. Our study implies that soil attributes and biocrust development have more profound impacts on soil bacterial communities than precipitation, which provides novel insights into the geographical distribution and assemblage of soil bacterial communities in deserts. Moreover, our study is significant with respect to understanding the potential responses of soil microbial communities to climate change in desert areas under the scenario of increasing precipitation variation.

A process-based understanding of soil carbon (C) sequestration and stabilization has not been precisely characterized due to the lacking of linkage between microbial proliferation and mortality. In this study, stable isotope probing of phospholipid fatty acids and amino sugars were used to determine the microbial responses and microbial residue retention in two soils (Mollisol and Ultisol) with 13C-labeled glucose addition. The microbial responses stimulated by glucose were greater in C-poor Ultisol than in C-rich Mollisol. However, the transformation of labile C to microbial residues in Mollisol was more rapid. Therefore, the starvation effect may control microbial growth and microbial residue production, and thus resulting in distinct sequestration and stabilization process of labile C in different soils.

The impact of increasing amounts of labile C input on priming effects (PE) on soil organic matter (SOM) mineralization remains unclear, particularly under anoxic conditions and under high C input common in microbial hotspots. PE and their mechanisms were investigated by a 60-day incubation of three flooded paddy soils amended with13C-labeled glucose equivalent to 50–500% of microbial biomass C (MBC). PE (14–55% of unamended soil) peaked at moderate glucose addition rates (i.e., 50–300% of MBC). Glucose addition above 300% of MBC suppressed SOM mineralization but intensified microbial N acquisition, which contradicted the common PE mechanism of accelerating SOM decomposition for N-supply (frequently termed as “N mining”). Particularly at glucose input rate higher than 3 g kg−1 (i.e., 300–500% of MBC), mineral N content dropped on day 2 close to zero (1.1–2.5 mg N kg−1) because of microbial N immobilization. To cope with the N limitation, microorganisms greatly increased N-acetyl glucosaminidase and leucine aminopeptidase activities, while SOM decomposition decreased. Several discrete peaks of glucose-derived CO2 (contributing >80% to total CO2) were observed between days 13–30 under high glucose input (300–500% of MBC), concurrently with CH4 peaks. Such CO2 dynamics was distinct from the common exponential decay pattern, implicating the recycling and mineralization of 13C-enriched microbial necromass driven by glucose addition. Therefore, N recycling from necromass was hypothesized as a major mechanism to alleviate microbial N deficiency without SOM priming under excess labile C input. Compound-specific 13C-PLFA confirmed the redistribution of glucose-derived C among microbial groups, i.e., necromass recycling. Following glucose input, more than 4/5 of total 13C-PLFA was in the gram-negative and some non-specific bacteria, suggesting these microorganisms as r-strategists capable of rapidly utilizing the most labile C. However, their 13C-PLFA content decreased by 70% after 60 days, probably as a result of death of these r-strategists. On the contrary, the 13C-PLFA in gram-positive bacteria, actinomycetes and fungi (K-strategists) was initially minimal but increased by 0.5–5 folds between days 2 and 60. Consequently, the necromass of dead r-strategists provided a high-quality C–N source to the K-strategists. We conclude that under severe C excess, N recycling from necromass is a much more efficient microbial strategy to cover the acute N demand than N acquisition from the recalcitrant SOM.

It is not clear how soil organic carbon (SOC) and its related microbial processes respond to climate warming in subtropical forest, which limits our ability to predict the response and feedback of such forests to future warming. Here, we translocated a forest microcosm from a high-elevation site to a low-elevation site (600 m–30 m a.s.l.) in a subtropical forest, to study the responses of SOC fractions, microbial communities and enzyme activities to increases in soil temperature (ca. 1.69 °C). Results showed that translocation to a warmer region significantly decreased the total SOC content by an average of 21.1% after three years of soil warming. Warming non-significantly decreased the particulate organic C (POC) and microbial C (MBC) content by 15.7% and 15.2%, respectively, and increased the light fraction organic C (LFOC) and dissolved organic C (DOC) content by 15.5% and 2.3%, respectively. By contrast, warming significantly decreased the <53 μm fraction organic C (N-POC, −15.3%) and heavy fraction organic C (HFOC, −14.8%) content. Warming significantly decreased the relative abundance of total bacteria (−2.7%), G+ bacteria (−6.1%), G− bacteria (−6.6%) and actinomycetes (−10.8%), but increased the relative abundance of fungi (+22%). The oxidase and mass-specific oxidase activities were significantly increased by 32–70% in the warming soils. The decline in the N-POC was highly correlated to the increases in the relative abundance of fungi, the ratio of fungal to bacterial biomass (F:B), oxidase and mass-specific oxidase activities. Our results suggest that climate warming may increase the potential for fungal decomposition of mineral-associated organic C by increasing oxidase activities, leading to greater C losses in the subtropical forest than previously estimated.

Increasing atmospheric nitrogen (N) deposition has substantially affected carbon (C) and nutrient cycling in forest ecosystems. However, the responses of different soil organic carbon (SOC) fractions with different turnover rates to N addition are highly divergent, and the underlying mechanisms remain elusive. In this study, we explored the responses of surface soil (0–10 cm) characteristics and microbial communities to six years of experimental N addition (0, 50, 100 and 150 kg N ha−1 yr−1) in a subtropical evergreen broadleaf forest in southern China. Our results showed that N addition led to significant soil acidification (pH from 5.3 to 4.9). Microbial biomass carbon and total microbial, bacterial and fungal abundance (phospholipid fatty acid, PLFA) were reduced by N addition, but extracellular enzymes involved in C, N and phosphorus (P) cycling were not responsive to N addition. Soil extractable Ca2+ concentration was depleted by N addition, while other extractable cations (Fe3+, Al3+, Mg2+, K+, Na+) were not affected. Moreover, N addition did not significantly change the C and N concentration of bulk soil. We further separated the bulk soil into particulate organic matter (>53 μm, POM) and mineral-associated organic matter (<53 μm, MAOM) fractions by wet sieving. Interestingly, C in the POM fraction was significantly increased by N addition, while C in the MAOM fraction was depleted by N addition. Correlation analysis and structural equation modeling results suggested that N addition may suppress microbial decomposition of plant inputs and thus lead to accumulation of C in the POM fraction, while it may reduce the mineral sorption of microbial necromass and products and thus cause depletion of C in the MAOM fraction. Taken together, our results highlighted the vulnerability of soil C in the stable MAOM fraction to N addition, and emphasized the role of soil metals (particularly extractable Ca2+) and pH in controlling soil C storage under N addition.

Shifting from conventional tillage to a no-till system can contribute to improving soil carbon sequestration and sustaining crop productivity. However, our understanding of the soil nitrogen (N) process through insights into the no-till effect on soil denitrification remains elusive. Here, we compiled data from 323 observations in 57 studies and quantified the responses of soil denitrification and the size and activity of the denitrifying community to no-till vs. conventional tillage. Across all studies, no-till significantly increased soil denitrification (85%) compared to conventional tillage. The no-till effect on soil denitrification was significantly dependent upon N fertilizer management, with a greater increase with N fertilization than without (101 vs. 46%). The increased soil denitrification under no-till was attributed to increases in the size and activity of the denitrifying community. On average, the potential denitrification activity, the total number of denitrifiers, and the abundance of denitrifying genes were increased by 66, 116, and 14–70%, respectively, in response to no-till. Our results demonstrate that soil denitrification under no-till leads to increased soil nitrous oxide (N2O) emission. This is supported by a larger response of soil N2O emission compared to the total denitrification, together with a significant increase (33%) in the (nirK + nirS)/nosZ ratio under no-till conditions. Therefore, the increased soil denitrification under no-till conditions may have negative impacts on soil N cycling and mitigation of N2O emission.

The role of phosphorus (P) mediating nitrogen (N) transformation processes is poorly understood which raises an important question: Does P, like soil pH, have a strong control in altering the cycling of soil N? From 2010 to 2018, pH and/or P availability was elevated with lime and P fertilizer in three mixed mesophytic deciduous forests on the unglaciated portion of the Allegheny Plateau, southeast Ohio, USA. We hypothesized that in addition to soil pH, P addition can influence the cycling of soil N because both can change N dynamics, which can alter nitrification rates. Increasing soil pH increased nitrification and nitrate pools by 30 and 4 times, respectively during the growing season. Furthermore, elevating P also stimulated nitrification and increased soil nitrate pools by 10 and 2 times, respectively. However, the influence of raising soil pH on nitrification was diminished when combined with P addition. Results suggest that N biogeochemical processes are sensitive to P availability, but the mechanistic nature of this relationship appears complex with unclear feedback systems regulating nitrification rates from these deciduous forests.

Future climate change scenarios predict increases in surface temperature as well as atmospheric CO2 concentration. In this study we simultaneously addressed individual and combined effects of these factors on the soil microbial community structure and function. We tested linear as well as non-linear responses in a multifactorial climate manipulation experiment. After two years of climate change manipulations on a pre-Alpine managed grassland, topsoil samples were taken for analysis of functional enzyme activities, as well as microbial community structure. Besides, soil and vegetation parameters were measured to allow evaluation of direct and indirect effects. Pronounced and statistically significant spatial effects were observed on our field site for some variables. It is assumed that the history of site preparation could provide an explanation for the observed differences. Elevation of temperature or atmospheric CO2 did not induce strong shifts of soil fungal or bacterial communities. Only the inclusion of the spatial effects in the response surface model allowed the detection of subtle microbial responses to climate change scenarios. Mucor globulifera responded to temperature and CO2 in a pattern similar to soil water content. An increase in the relative abundance of coprophilous white rot fungi was observed upon warming, and this might be attributed to preferences of macrofauna for warmer plots. Specific extracellular enzyme activities were positively correlated with each other, especially within two groups of enzymes, which were involved in C-acquisition and in N-mining. The latter group responded positively to elevated CO2 concentrations. Chitinolytic activity increased with the relative abundance of the nematophagous and entomopathogenic ascomycete Purpureocillium lilacinum. We conclude that the indirect effects of future climate change scenarios prevail over direct effects on soil microbial community composition and function. Soil water content, nutrient pools, atmospheric CO2 and plant root identity were identified as drivers of the observed changes after removal of unintended spatial effects. Application of advanced statistical tools, which take spatial variability into account, was necessary to detect these effects. Minor changes in the fungal community occurred already after a short period of climate manipulation. More pronounced effects of elevated atmospheric CO2 concentration and surface warming on soil microbial community structure and function are expected on the longer-term, but indirect effects will most likely remain the dominant drivers.

Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. Because cover cropping can form an agroecosystem distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Despite the growing number of primary literature sources investigating the relationship between cover cropping and the soil microbiome, there has not been a quantitative research synthesis that is sufficiently comprehensive and specific to this relationship. We conducted a meta-analysis by compiling the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome.

Metaldehyde, a xenobiotic cyclic ether, is used as molluscicide of choice in agriculture and horticulture, but recently its detection in drinking water sources has become a major cause of concern. We isolated eight new metaldehyde-degrading bacterial strains from allotment and agricultural soils and identified a highly-conserved gene cluster shared amongst one gamma and five beta-proteobacteria, and absent from closely-related, non-degrading type strains. Chemical mutagenesis, and heterologous expression in E. coli, confirmed that this gene cluster is responsible for metaldehyde degradation. Other metaldehyde-degrading isolates that lack this pathway indicate that multiple degradation mechanisms have evolved. We demonstrated accelerated biodegradation of metaldehyde in multiple soils, highlighting the importance of the biological component in metaldehyde degradation in nature. We confirmed that the metaldehyde-degrading population in soil is proliferating in response to metaldehyde, but no bulk changes in the composition of the community as a whole were detected, indicating the process is governed by a few rare taxa. Here, we identified the first genetic determinants for the biological degradation of metaldehyde in soil paving the way for targeted bioremediation strategies.

In agroecosystems, efficient fertilizer use is key to optimizing productivity and reducing nutrient losses that can be detrimental for the environment, such as nitrous oxide (N2O) emissions. Because microbial communities regulate nitrogen (N) fate in soils, some agrochemicals inhibit specific transformations to reduce N losses. Our study aimed to describe short-term dynamics of N-cycling genes and transcripts and N2O emissions after fertilization with urea-ammonium nitrate (UAN) with or without the addition of nitrification plus urease inhibitors (NUI). The experiment consisted of 4-ha corn plots located in SE Ontario, Canada, where field-scale N2O emissions were monitored continuously using micro-meteorological techniques. Soil samples (0–10 cm) were taken 10 days before (baseline) and 2, 6, 9, 13 and 16 days after fertilization, and immediately flash-frozen. We co-extracted DNA and RNA and, using real-time PCR, quantified genes/transcripts targeting total bacteria (16S rRNA) and key N-cycling groups: ureolytic (ureC), ammonia-oxidizers (bacterial/archaeal amoA), nitrite-reducers (nirK/nirS) and N2O-reducers (clade I/II nosZ). The addition of NUI did not prevent an N2O flux event but reduced its duration and magnitude by more than 50%, and net cumulative N2O emissions for the sampling period by ∼68%. NUI effects on N-cycling microorganisms were evident on day 9, as a transient reduction (40–56%) of ammonia-oxidizers and denitrifiers. Changes in transcripts were minor and only detectable on ureC (day 2), nirS and clade II nosZ (day 9). NUI did not interfere with temporal fluctuations in nirK and nirS, but it differentially affected nosZ response to a later rainfall event. Unexpectedly, N2O emissions were negatively associated with the ratio between nitrite-reducers and N2O-reducers. NUI effects on N-cycling microorganisms were minor and transient but resulted in a field-scale reduction in N2O emissions, possibly due to a combination of environmental factors and legacy effects from previous years of treatment.

It is critical to identify the community assembly patterns (i.e., deterministic or stochastic processes) of soil microbes and the potential driving factors to better predict the belowground biodiversity and functioning in forest ecosystems. Here, a combined approach of neutral model and multivariate analysis was employed to examine the soil bacterial communities in 12 undisturbed forests in China, spanning a wide latitudinal range from 21.6°N to 50.8°N. A clear divergent pattern was found for community composition, indicating that deterministic processes dominated the community assembly of soil bacteria. The α-diversity (richness) nonlinearly changed from tropical to cold temperate zones, with the lowest and highest values detected in subtropical and temperate zones, respectively. Although no latitudinal pattern was observed for β-diversity (community variation), there were clear climate zone patterns. Unlike the minor effects of mean annual precipitation (MAP) and temperature (MAT) on bacterial α-diversity, MAP and MAT were important factors affecting soil bacterial β-diversity. Soil pH was a strong driver of α- and β-diversity, but plant factors had only minor effects. Altogether, this study highlights the unexpected importance of climatic factors in shaping bacterial β-diversity in forest soils. Our findings have implications for future investigations of bacterial community dynamics in forest ecosystems, particularly the responses of community composition to global climate change scenarios across large geographical scales.

Current soil phosphorus (P) management is neither environmentally nor economically sustainable. Soil biodiversity has been offered as a solution to unsustainable land management and to promote ecosystem service provision. We know soil biology is instrumental in plant access to soil P, but specific effects of biological complexity, (used here to describe the number of links between different organisms), under different P levels on plant productivity are not well understood. We conducted a meta-analysis on relevant literature, which reported the response of terrestrial plants of economic and anthropogenic importance to P conditions, and controlled for biological treatments across different land-uses (arable, grassland and woodland). We hypothesised that: 1) in arable systems increased biological complexity will enhance plant productivity; 2) in perennial systems such as grassland and woodlands, increasing biological complexity will have no effect; 3) increasing the fertility of the system by addition of P fertiliser will reduce any benefits of biological complexity. We found that soil organisms are not always beneficial to plant shoot biomass, but that the effects of - and interaction among - bacteria, protozoa, nematodes, mycorrhizae, collembola and earthworms differ in their impact on plant biomass (positive or negative) dependent on the presence of other community members, P-level status and time. These findings bring into question existing frameworks that link below-ground biodiversity with above-ground plant productivity. We recommend further experimental work be conducted which controls for land-use, P status, and soil biological composition and complexity. Such work should be followed by future systematic reviews, which could pragmatically inform more tailored biological management for plant P requirements, land-use and ecosystem service provision. To enable further meta-analyses of this type we recommend habitual inclusion of sufficient experimental detail and data, as a prerequisite for publication and a useful way to utilise increased online publication space.

Atmospheric nitrogen (N) deposition has rapidly increased in subtropical ecosystems and may have altered the input of aboveground litter to soil, which substantially impacts soil carbon (C) and nutrient cycling. But how the soil processes and properties respond to N deposition under uncertain fresh litter input is poorly understood. In order to examine the responses of soil respiration and biochemical properties to N addition and aboveground litter manipulation, a field N addition and litterfall manipulation interaction experiment was performed in an evergreen broadleaf forest on the western edge of the Sichuan Basin in China. Three levels of N addition, including an N control (CN, ambient N input) and low N (LN, + 50 kg N ha−1 year−1) and high N (HN, + 150 kg N ha−1 year−1), and three levels of litterfall manipulation, including intact litter input (L0, no litter alteration), litter reduction (L−, reduced by 50%) and litter addition (L+, increased by 50%), were conducted monthly starting in January 2014 and August 2015, respectively. Soil respiration was measured monthly from January 2016 to December 2017. Soil samples were collected four times, in October 2016 and January, April and July 2017, to measure soil biochemical properties. The results showed that: (1) short-term N addition did not significantly alter the aboveground litter input in this forest; (2) soil respiration decreased with elevating N input and was associated with amount of litterfall input; (3) N addition increased the total organic C (TOC) concentration in topsoil in subplots without litterfall alteration but did not affect TOC in subplots with increased or decreased litter-input; (4) N addition decreased soil pH and did not affect soil microbial biomass regardless of whether litterfall was altered or not; (5) short-term litter manipulation did not affect any soil properties in the N control plots, but both litterfall reduction and addition tended to reduce surface soil TOC concentration in the N-added plots; and (6) both N addition and litterfall manipulation showed stronger effects on organic soil than on mineral soil. These findings indicated that elevated N input increased the surface soil C content by reducing soil respiration mainly via enhancing stabilization of soil organic matter rather than by reducing soil microbial biomass, and that altered litterfall may mitigate the N-induced increase in soil C. Because of temporal lag, long-term experimentation is needed to investigate the response of soil to altered litter input under different N addition conditions.

Microbial activity in drylands is mediated by the magnitude and frequency of growing season rain events that will shift as climate change progresses. Nitrogen is often co-limiting with water availability to dryland plants. This study investigated how microbes important to the nitrogen (N) cycle and soil N availability varied temporally and spatially in the context of a long-term rainfall variability experiment in the northern Chihuahuan Desert. Specifically, biological soil crust (biocrust) chlorophyll content, fungal abundance, and inorganic N were measured in soils adjacent to individuals of the grassland foundation species, Bouteloua eriopoda, and in the unvegetated interspace at multiple time points associated with experimental monsoon rainfall treatments. Treatments included 12 small weekly (5 mm) or 3 large monthly (20 mm) rain events, which had been applied during the summer monsoon for nine years prior to this study. Additionally, target plant C:N ratios were measured, and 15N-glutamate was added to biocrusts to determine potential for nutrient transport to B. eriopoda. Biocrust chlorophyll was up to 67% higher in the small weekly and large monthly rainfall treatments compared to ambient controls. Fungal biomass was 57% lower in soil interspaces than adjacent to plants but did not respond to rainfall treatments. Ammonium and nitrate concentrations near plants declined through the sampling period but varied little in soil interspaces. There was limited movement of 15N from interspace biocrusts to leaves but high 15N retention occurred in the soils even after additional ambient and experimental rain events. Plant C:N ratio was unaffected by rainfall treatments. The long-term alteration in rainfall regime in this experiment did not change how short-term microbial abundance or N availability responded to the magnitude or frequency of rain events at the end of the growing season, suggesting a limited response of N availability to future climate change.

Earthworms enhance soil structure, the decomposition of organic matter and the dissemination of beneficial soil organisms such as the entomopathogenic nematodes (EPNs). Nevertheless, the effects of earthworm feeding behavior or cutaneous excreta (CEx) on the performance of EPNs as biological control agents is poorly understood. We hypothesised that the presence of earthworms or their excreta reduces EPN fitness, measured in terms of pathogenicity and reproductive success. In laboratory experiments we first evaluated the killing ability of EPNs against Galleria mellonella (Lepidoptera: Pyralidae) larvae when inoculated in autoclaved soil alone or in combination with the earthworm Eisenia fetida (Haplotaxida: Lumbricidae) or their excreta. We also evaluated EPN efficacy and reproduction when exposed to CEx derived from E. fetida at two concentrations (1.5 and 10 IJs/cm2). For both experiments, we tested four steinernematids (Steinernema carpocapsae, S. feltiae, S. glaseri, and S. khuongi) and two heterorhabditids (Heterorhabditis bacteriophora and H. zealandica). The presence of earthworms or their excreta resulted in significant reduction of the larval mortality caused by some of the steinernematids at certain timings depending of the species (P < 0.015), while heterorhabditids were mainly not affected. Both S. feltiae and H. zealandica progeny production was significantly reduced (P < 0.01) when exposed to CEx. Hence, we showed that the presence of CEx might alter the biocontrol performance of certain EPN species, especially steinernematids bigger than 600 μm in size (S. feltiae, S. glaseri, and S. khoungi), by affecting their pathogenicity and reproductive success.

Lignocellulose is the main component of forest litter. Due to the recalcitrance of coniferous litter, nutrient turnover is usually slower in coniferous plantations. Lignocellulose decomposition is reportedly rapid in mixed-species litter, but the underlying microbial metabolic pathways that may explain this rapid rate are not well-studied. We collected litter at 60, 150, 270, and 360 days after leaf fall at three plantation types: larch, sassafras, and larch/sassafras mixed plantations. We investigated the contents of lignocellulose components, enzyme activities, microbial communities, and potential genetic functional pathways related to lignocellulose degradation. Most rates of lignocellulose component degradation and enzyme activities in mixed litter during decomposition were significantly higher than in larch litter. The relative abundances of Betaproteobacteria and Dothideomycetes, which are involved in lignocellulose degradation, were significantly higher in mixed-species litter than in larch litter. Bacterial cellulose and hemicellulose, and fungal lignin degradation genes were significantly influenced by plantation forest type. Mantel tests showed that (i) the content of lignocellulose significantly correlated with bacterial and fungal community composition and enzyme activities, and (ii) fungal decomposers might be the main drivers of lignocellulose degradation in different litter types. Mixing larch and sassafras litter changed the composition of the microbial community and the lignocellulose-degradation gene complement, accelerated the decomposition of lignocelluloses, and restored soil quality.

Extracellular enzymes catalyze plant litter decomposition, including enzymes that degrade holocellulose (E2) and lignin (E3). To estimate relative enzyme activities associated with observed patterns of hollocellulose (C2) and lignin (C3) decay, we set observed decay rates equal to reverse Michaelis-Menten equations. Results were consistent with empirical studies, showing a negative relationship of E2/(E2+E3) to litter lignin content, C3/(C2+C3), above a minimum threshold at which lignin begins to decay. This threshold was previously reported to be 40% lignin content, but our results demonstrated substantial variability with litter type and environment. To our knowledge, this is the first mechanistic explanation of microbial allocation of cellulolytic and ligninolytic enzymes as a function of the lignin concentration of the lignocellulose complex but raises further questions about factors controlling the threshold for lignin decay, such as nitrogen availability.

The projected increase of extreme precipitation and freeze-thawing events may lead to frequent occurrence of anaerobiosis in upland soils, which has significant impacts on biogeochemical processes affecting soil carbon loss. However, compared to mineralization, the impacts of anaerobiosis (potentially accompanied by fermentation) on soil organic carbon (SOC) leaching is limited. Here we conducted microcosm and intact soil column incubation experiments to examine processes influencing SOC leaching from four typical Chinese grassland soils under simulated anaerobiosis. Compared to aerobiosis, non-fermenting anaerobiosis increased the pH, dissolved phenol concentrations and aromaticity of soil leachates. In contrast, fermenting anaerobiosis induced acetate accumulation, lowered pH, stimulated phenol oxidative activity and generally decreased aromaticity in soil leachates in both microcosm and soil column experiments relative to aerobiosis. Both anaerobiosis potentially induced a strong release of dissolved organic carbon (DOC) accompanied by iron and nitrate reduction, especially with fermentation. However, DOC in soil leachates decreased in alpine subsoils under fermentation relative to aerobiosis. This interesting phenomenon was mainly attributed to (i) minimal iron reduction and dissolution in the alpine subsoils and (ii) enhanced DOC oxidation by elevated phenol oxidative activity in the fermentation relative to aerobiosis treatments. These results collectively indicate that anaerobiosis may increase SOC leaching and its magnitude is dependent on the extent of iron reduction and pH variations. Fermentation-enhanced release of ferrous iron and acetate may have an even stronger influence on the downstream biogeochemistry. Hence, temporary anaerobiosis warrants better recognition and investigation in the Mongolian (relative to Qinghai-Tibetan) grasslands that show high soil iron reduction potentials and are predicted to experience increased extreme precipitation in the future.

Microbially-derived nitrogen (N) has been considered as one of important contributors to soil organic N, but few studies have quantified the rate of necromass N decomposition. Here, via an in situ incubation of 15N-labeled necromass, we found that 33.1–39.5% of the initial 15N stabilized in the soil as non-living organic N after 803 days of incubation. Bacterial, fungal, and actinobacterial necromass N showed similar decomposition pattern and mean residence time. The decomposition of microbial necromass N was best simulated by a two-pool model where a labile pool decomposed rapidly (0.4 years), and a more recalcitrant pool decomposed at a much slower rate. This finding contrasted with the decomposition of plant litter N, which was better simulated by a single-pool model. The stabilization of necromass N in soils after more than two years suggests the important contribution of microbial residues to soil organic N, which is most likely due to mineral protection from decomposition.

Root litter decomposition is the dominant source of soil organic carbon (C) and nitrogen (N) in grasslands. Few studies, however, have explored the effect of root litter diversity on soil C and N cycling. This study investigated the effects of species diversity and functional traits of root litter on soil CO2 and N2O release, net ammonification, net nitrification, and net N mineralization based on a 56-day incubation of grassland soils with root litter mixtures containing one, two, or four native plant species. The increasing species richness of root litter decreased the cumulative CO2 and N2O release in the soil, but enhanced the net ammonification, nitrate immobilization, and N mineralization. Root litter diversity has a predominant non-additive antagonistic effect on the release of soil CO2 and N2O, and a synergistic effect on the net ammonification, nitrate immobilization, and N mineralization in the soil. The functional identity rather than functional diversity of root traits explains most of the variation in soil C and N cycling. A high C: N ratio and low concentrations of N, P, K, and Di-O-alkyl-C (characteristic of celluloses) were found to be key to the antagonistic effects associated with cumulative release of CO2 from the soil. For net N ammonification and mineralization, the synergistic effect was principally induced by the high levels of carbohydrate-C and N and the low C: N ratios in root litter mixtures. Our study highlights the role and mechanisms of increased root litter diversity in decreasing soil CO2 and N2O release and in increasing the net N mineralization via non-additive antagonistic and synergistic effects of dominant root traits.

In principle, greenhouse gas emissions can be offset by increasing soil carbon stocks. Full utilisation of that potential, however, requires a good understanding of the controls on carbon stocks to identify factors that can be modified through management changes and distinguish those from factors that are inherent soil properties that cannot be modified. Here, we present a conceptual model of protected (or stabilised) carbon stocks in soils based on observations from two farms in New Zealand, and from a combined soils data set from observations from throughout New Zealand. These data showed that These observations improve our understanding of the important carbon-protection mechanisms in the soil, with significant implications for the optimal manipulation of carbon input rates into different soils to maximise overall soil carbon storage. They imply that overall carbon storage of soils could be enhanced by physically transferring any available carbon from soils with low to soils with high specific surface areas.

Pyrogenic organic matter (PyOM) is produced by the incomplete combustion of organic matter, and can represent a large portion of total soil organic carbon in both fire-affected systems and managed systems where PyOM is added intentionally as a soil amendment. The effects of PyOM on the structure of soil microbial communities remain a topic of fundamental interest, and a number of studies have begun to identify and characterize the PyOM-associated microbial community. However, it is unclear to what extent the effects of PyOM on soil bacteria are consistent. Our goals were to synthesize current related studies to (1) determine if there is a detectable and consistent “charosphere” community that characterizes PyOM-amended soils, (2) distinguish consistent responders at the phylum level to PyOM amendments, and (3) identify individual PyOM-responsive taxa that increase in relative abundance consistently across different soil types. We re-analyzed publicly available raw 16S Illumina sequencing data from studies that investigated the bacterial communities of PyOM-amended soils. We determined that soil source is more important than PyOM for shaping the trajectory of the community composition. Although we were able to identify a few genera that respond positively and somewhat consistently to PyOM amendments, including Nocardioides, Micromonospora, Ramlibacter, Noviherbaspirillum, and Mesorhizobium, in general, neither phylum-level nor genus-level responses to PyOM were consistent across soils and PyOM types. We offer suggestions for our future efforts to synthesize the effects PyOM may have on soil microbial communities in an array of different systems. Due to the dual challenges of high functional diversity at fine taxonomic scales in bacteria, and diverse ranges of soil and PyOM properties, researchers conducting future studies should be wary of reaching a premature consensus on PyOM effects on soil bacterial community composition. In addition, we emphasize the importance of focusing on effect sizes, their real-world meanings, and on cross-study effect consistency, as well as making data publicly available to enable syntheses such as this one.

We report a space-for-time substitution study predicting the impacts of climate change on vegetated maritime Antarctic soils. Analyses of soils from under Deschampsia antarctica sampled from three islands along a 2,200 km climatic gradient indicated that those from sub-Antarctica had higher moisture, organic matter and carbon (C) concentrations, more depleted δ13C values, lower concentrations of the fungal biomarker ergosterol and higher concentrations of bacterial PLFA biomarkers and plant wax n-alkane biomarkers than those from maritime Antarctica. Shallow soils (2 cm depth) were wetter, and had higher concentrations of organic matter, ergosterol and bacterial PLFAs, than deeper soils (4 cm and 8 cm depths). Correlative analyses indicated that factors associated with climate change (increased soil moisture, C and organic matter concentrations, and depleted δ13C contents) are likely to give rise to increases in Gram negative bacteria, and decreases in Gram positive bacteria and fungi, in maritime Antarctic soils. Bomb-14C analyses indicated that sub-Antarctic soils at all depths contained significant amounts of modern 14C (C fixed from the atmosphere post c. 1955), whereas modern 14C was restricted to depths of 2 cm and 4 cm in maritime Antarctica. The oldest C (c. 1,745 years BP) was present in the southernmost soil. The higher nitrogen (N) concentrations and δ15N values recorded in the southernmost soil were attributed to N inputs from bird guano. Based on these analyses, we conclude that 5–8 °C rises in air temperature, together with associated increases in precipitation, are likely to have substantial impacts on maritime Antarctic soils, but that, at the rates of climate warming predicted under moderate greenhouse gas emission scenarios, these impacts are likely to take at least a century to manifest themselves.

Multiple and rapid environmental changes in the Arctic have major consequences for the entire ecosystem. Soil water chemistry is one component with important implications for understanding climate feedbacks, plant growth, microbial turnover and net greenhouse gas emissions. Here we assess the contrasting growing season soil water chemistry in a Low arctic Greenlandic mesic tundra heath and a fen, which have been subjected to factorial treatments of summer warming using open top chambers (OTCs), snow addition using snow fences, which increase soil temperature in late winter, and shrub removal mimicking herbivory attack. Dissolved Organic Carbon (DOC) and plant nutrients, including NO3−, NH4+, PO42+ and total dissolved N were measured during multiple growing seasons (2013–2016) to quantify the treatment effects on nutrient availability at two dominating, but contrasting, vegetation types. Ambient nutrient concentrations at the mesic tundra heath decreased throughout the growing season and increased during senescence, while concentrations were highest during peak growing season in the fen. The content of NH4+ and DOC were highest in the fen, whereas NO3− was highest in the mesic tundra heath. The fen had no seasonal pattern. Summer warming in the mesic tundra heath did not change the availability of nutrients, but in combination with shrub removal, both NO3− and DOC concentrations increased, likely due to reduced plant uptake. Shrub removal alone increased NO3− in one growing season, and, combined with snow addition, increased DOC. Significant effects of shrub removal were mostly found in 2016. Snow addition combined with summer warming increased DOC and total N concentrations and highlights the potential loss of dissolved C from the ecosystem. In the fen, shrub removal alone and combined with summer warming decreased DOC. Snow addition alone and in combination with summer warming similarly decreased DOC. In the mesic tundra heath, shrub removal caused higher soil water contents in all years. In the dry and warm 2016, it meant <10% soil water content in controls and 15–20% in shrub removal plots during the peak growing season, which may have relieved soil moisture limitation on mineralization rates in the latter. We conclude that soil water chemistry is vegetation-specific, and that treatment effects are surprisingly limited when comparing multiple years with contrasting precipitation patterns. Herbivory may have larger impact in very dry, warm summers and, together with extreme weather events, exert similar or larger effects than four years of temperature manipulations. The effects of summer warming or increased winter snow depend on ecosystem type and moisture status of the soil. The combination of multi-year and multi-site studies therefore seem important for understanding future biogeochemical dynamics in Arctic landscapes.

There is a current lack of mechanistic understanding on the relationships between a soil microbial community, crop production, and nutrient fertilization. Here, we combined ecological network theory with ecological resistance index to evaluate the responses of microbial community to additions of multiple inorganic and organic fertilizers, and their associations with wheat production in a 35-year field experiment. We found that microbial phylotypes were grouped into four major ecological clusters, which contained a certain proportions of fast-growers, copiotrophic groups, and potential plant pathogens. The application of combined inorganic fertilizers and cow manure led to the most resistant (less responsive) microbial community, which was associated with the highest levels of plant production, nutrient availability, and the lowest relative abundance of potential fungal plant pathogens after 35 years of nutrient fertilization. In contrast, microbial community was highly responsive (low resistance) to inorganic fertilization alone or plus wheat straw, which was associated with lower crop production, nutrient availability, and higher abundance of potential fungal plant pathogens. Our work demonstrates that the response of microbial community to long-term nutrient fertilizations largely regulates plant production in agricultural ecosystems, and suggests that manipulating these microbial phylotypes may offer a sustainable solution to the maintenance of field productivity under long-term nutrient fertilization scenarios.

Dissimilatory nitrate reduction to ammonia (DNRA) is one of the three processes of soil nitrate reduction. However, relationships between DNRA microbes and nutrient fertilization are poorly known. We studied the DNRA microbial community in a Ferralic Cambisol containing plots including control without fertilization, swine manure fertilization (M), chemical fertilization (NPK), and chemical/manure combined fertilization (MNPK) treatments. The abundance of DNRA microbes, represented by the nrfA gene abundance, ranged from 2 × 107 to 5.8 × 107 g−1 dry soil and was positively correlated with soil moisture and total phosphorus (TP) and negatively correlated with NH4+ and total potassium (TK). The potential DNRA rate ranged from 0.5 to 1.5 μg N g−1 dry soil h−1. The α-diversity of the DNRA bacteria increased in the M-treated plots, and the dominant DNRA bacterial OTUs were assigned to the phyla Proteobacteria, Verrucomicrobia and Acidobacteria. PCoA and redundancy analysis indicated that the composition of the DNRA bacteria was strongly impacted by the long-term fertilization regimes and was associated with pH, TN, TP and TC followed by moisture, NH4+ and C/NO3−. Interestingly, the composition of the DNRA bacterial community, the properties of the soil (TP, AK and C/N) and the interactions of these factors (soil properties × DNRA composition) explained the DNRA rate. Collectively, these data suggested that the DNRA potential in the Ferralic Cambisol is possibly controlled by the stoichiometry of macronutrient and the composition of DNRA microbes but not their total abundance.

This study presents the relationship between inputs of elements (especially biominerals), their recycling mechanisms and the average residence time of the major elements in mull humus. In forest ecosystems with generally low element inputs, decomposing leaf litter is an important source of soil nutrients. While the processes and the release speeds of elements, such as C, N and P, are well determined during litter degradation, less is known about elements like Fe, Al, Mg, Mn, Si, Ca, K, or Na, some of which are essential for tree nutrition. The objective of this study was to determine the average residence time of these elements in mull-type humus for 3 different soils: a Dystric Cambisol (S1), Eutric Cambisol (S2) and Rendzic Leptosol (S3), in the same beech grove of the northeast of France and to identify the main mechanisms controlling them. To achieve this goal, the approach used: 1) scanning electron microscope observation of the evolution and recycling of elements during litter degradation; 2) quantification of total inputs and their form (soluble/insoluble) in the litterfall and the contribution of exploitation residues; 3) quantification and evolution of litter stocks; and 4) calculation and comparison of the residence time of the elements according to their form. Calculation of inputs and stocks of elements in humus made it possible to assess the residence time of each elements. The average residence times were between 58.4 and 13.1 y for Fe and Al; 3.3 and 1.6 y for Si, N, S and Ca; 2.2 and 1.2 y for Mn, Mg, Na, P and C; and 0.6 and 0.8 y for K. The results were similar for the three soils except for the Mn stock and inputs, which were lower in S3, and for the Si input, which decreased from S1 to S3. The results of the study indicate that the residence times of K, P, Na, Mg and S decreased with the percentage of soluble forms. Conversely, they increased when elements were principally in the form of biominerals (Si, Ca), such as in plant tissues, organic molecules (N) and more resistant tissues, or intervened in sorption mechanisms (Al, Fe) and biotic recycling mechanisms, such as testate amoebae (Si, Ca, P, Mn) and fungal hyphae (Ca, Mn, P) and abiotic precipitation (Si).

The desire to understand and distinguish the relative growth and activity of ammonia oxidising archaea (AOA) and ammonia oxidising bacteria (AOB) in soil nitrification has increased the search for selective inhibitors of these two groups. This study aimed to investigate the potency and specificity of simvastatin as a specific AOA inhibitor in pure cultures and in soil and to determine the effect of AOA inhibition on both ammonia oxidation activity and growth of AOB, under the hypothesis that AOB growth is higher when competition for NH4+ from AOA is removed. Simvastatin selectively inhibited pure cultures of all tested AOA at concentrations of 8–100 μM. In soil microcosms incubated for 21 days with low and high NH4+ concentrations, AOA but not AOB were selectively inhibited by simvastatin in both acidic (pH 4.5) and near-neutral (pH 6.5) soils. Additionally, growth of AOB significantly increased at both NH4+ concentrations following inhibition of AOA by simvastatin, suggesting that competition for substrate between AOA and AOB is a key factor restraining AOB growth in NH4+-limited soils. Simvastatin can therefore be used as a selective AOA inhibitor to investigate kinetic characteristics of AOB in soils and to study competition between AOA and AOB in complex environments.

The ameliorating effect of deep banding of nutrient-rich organic amendments, termed subsoil manuring, on improving physical structure of sodic high-clay subsoils, has been often attributed to organic amendments per se. However, this cannot explain the transformation of soil physical properties between the rip-lines, away from the amendments. This study assessed the effect of deep-banding nutrient-rich amendments on aggregation and dispersion of a clay subsoil in the presence and absence of wheat (Triticum aestivum) roots under controlled environment conditions. A specially-designed dual-column was set up to simulate a soil profile where a well-structured topsoil overlaid a sodic clay subsoil with an exchangeable sodium percentage (ESP) of 21%. The five amendments include a control (zero amendments), fertilizer nutrients (NPKS), wheat straw + fertilizer nutrients (straw/NPKS), poultry litter (PL) and poultry litter + controlled-release fertilizer (PL/mac). All amendments were added to the centre of the subsoil, 6 cm below the base of the topsoil. Our results showed that the presence of deep-placed nutrient-rich amendments, such as straw/NPKS and PL/mac, greatly enhanced deep root proliferation in this sodic clay subsoil, and resulted in the rapid build-up of large (>2000 μm) water-stable macroaggregates. There was a significant (P < 0.05) positive linear relationship between the root length density and the formation of large macroaggregates in the subsoil adjacent to and below the amendment. The stimulation of microbial growth by root exudates or by mucilage, as indicated by a significantly higher bacterial and fungal abundance (P < 0.05) in the planted than unplanted soils, is likely to have contributed to the formation of these macroaggregates. The effectiveness of wheat straw/NPKS in promoting the formation of macroaggregates in the unplanted soil could be attributed to the ‘straw effect’ which induced a marked increase in fungal growth (P < 0.05). Soil electrical conductivity (EC) and aggregate size were the key determinants of clay dispersion in the aggregated subsoil. Plant roots showed a contrasting effect on clay dispersion: increasing clay dispersion by reducing soil EC while suppressing clay dispersion via root-induced increases in large macroaggregates. We argue that the degree of slaking or disaggregation is likely to determine the net effect of roots on clay dispersion, and that root effect on increasing dispersion of macroaggregates in wet subsoil is limited. The major finding of the study is that increased aggregation in a dispersive clay subsoil can occur when wheat roots grow actively in these layers, in response to deep-placed nutrient-rich amendments.

Most soil N transformations studies are carried out using soil incubations without plants, despite the fact that plant-soil interactions potentially influence soil N dynamics. In this study, gross N transformation rates were quantified using a subtropical acidic forest with and without plants (and under different soil storage conditions). The results showed that the gross rates of N mineralization in air-dried and rewetted soil significantly increased, while the gross rates of nitrification and immobilization decreased, compared with fresh soil. Soil storage for more than one month at 4 °C (typical refrigerated conditions) and room temperature (25 °C) did not affect the gross rates of soil N mineralization and immobilization but significantly inhibited heterotrophic nitrification rates. Moreover, plants grown in the soil significantly stimulated gross rates of N mineralization, autotrophic and heterotrophic nitrification, and NO3− immobilization. Plant NH4+ uptake rates (3.74 mg N kg−1 d−1) were 374 times greater than the NH4+ immobilization rate (0.01 mg N kg−1 d−1). The competition for NH4+ between plants and soil microorganisms led to strong feedback effects on soil N transformations. Based on our results we recommend to carry out 15N tracing studies with plants to more realistically mimic field conditions. 15N tracing techniques in combination with 15N-tracing models, such as NtracePlant, provide a robust method to quantify soil N transformations and plant N uptake rates in plant-soil systems.

The regeneration of induced biological soil crusts (IBSCs) is regarded as an effective strategy for combating desertification. Three types of BSCs, namely, cyanobacterial, lichen and moss, are well-accepted as the main succession phases and are hypothesized to represent a continuous process. Herein, natural BSCs (NBSCs) and IBSCs with accurate ages from a 59-year-long field study were investigated to understand the entire BSC succession process. Shifts in nutrient levels, microbial composition and ecological functions suggested that cyanobacterial inoculation successfully accelerated BSC succession from decades to years by promoting the microbial multifunctions related to carbon and nitrogen fixation. The four state transitions of the BSC community accompanied by the turn-over of carbon and nitrogen fixators provide clues to the factors restricting the recovery process and to the highest hierarchy level of arid ecosystems. This study provides the first description of the continuous BSC succession, comprehensively discusses the mechanisms of BSC formation and succession and provides important guides for selection of strategies for the engineering reversals of desertification.

The improvement of aeration conditions in the rhizosphere is beneficial for crop growth and productivity. However, its effects on the soil microbial community are less known. Due to microbial sentivity to environmental changes, transporting micro-nano bubble water (MNBW) to the crop rhizosphere is expected to shift soil microbial community. A two-year MNBW irrigation field experiment consisting of two mixing ratios of MNBW and groundwater (high level of MNBW, HO: 1:0 and low level of MNBW, LO: 1:4), and a control treatment (CK, groundwater without MNBs), was conducted in a sugarcane plantation station at Guangxi, China. The results indicated that MNBW irrigation, particularly with the high level (HO), changed the composition and potential functionality of the soil bacterial community, reduced its diversity and altered microbial co-occurrence patterns. Structural equation modeling (SEM) demonstrated that MNBW irrigation directly affected soil microbial community and soil fertility, and indirectly promoted sugarcane yield. Overall, this study highlighted that the application of MNBW improved plant yield, and this response was strongly associated with a better nutritional content of MNBW irrigated soils and changes in the bacterial community.

The input of labile organics by plant roots stimulates microbial activity and therefore facilitates biochemical process rates in the rhizosphere compared to bulk soil, forming microbial hotspots. However, the extent to which the functional properties of soil microorganisms are different in the hotspots formed in soils with contrasting fertility remains unclear. We identified the hotspots related to different levels of Zea mays L. root architecture by zymography of leucine aminopeptidase in two soils with contrasting fertility. The hotspots localized by tiny wet-needle approach around first- and second-order roots were compared for parameters of microbial growth and enzyme kinetics. The pattern of hotspot distribution was more dispersed and the hotspot area was one order of magnitude smaller around first- versus second-order roots. The specific microbial growth rate (μm) and biomass of active microorganisms were soil-specific, with no difference between the hotspots and bulk soil in the fertile soil. In contrast, in the soil poor in organic matter and nutrients, 1.2-fold higher μm and greater growing biomass were found in the hotspots versus bulk soil. Lower enzyme affinity (1.3-2.2 times higher Km value) of β-glucosidase and leucine aminopeptidase to the substrate was detected in the hotspots versus bulk soil, whereas only β-glucosidase showed higher potential enzyme activity (Vmax) in the hotspots, being 1.7-2.1 times greater than that in bulk soil. Notably, the activity of C-acquiring enzyme, β-glucosidase positively correlated with the biomass of actively growing microorganisms. The fertile soil, on the whole, showed greater Vmax and catalytic efficiency (Vmax/Km) and an approximately 2.5 times shorter substrate turnover time as compared to the poor soil. Therefore, we conclude that i) the differences in microbial growth strategy between rhizosphere hotspots and bulk soil were dependent on soil fertility; ii) affinity of hydrolytic enzyme systems to substrate was mainly modulated by plant, whereas potential enzymatic activity was driven by both plant and soil quality.

Phospholipid fatty acids (PLFAs) have been used to trace bacterial life in extremely carbon-poor soils of the hyperarid Atacama Desert. However, the low abundances of bacteria and, thus, PLFAs increases the risk of contamination by exogenous PLFAs. Here, we assess whether field sampling strategies (super-clean, clean, and regular sampling protocols) have an effect on PLFA diversity and abundance in hyperarid Atacama soils or whether laboratory processing or true environmental heterogeneity control PLFA inventories. Our results show no exogenous PLFA contribution during sample processing in the lab and statistical analyses (ANOVA, Kruskal-Wallis) reveal that PLFA abundances do not differ significantly between replicate samples (n = 3) taken with the three different sampling strategies. Rather than sampling strategy, our results show that PLFA abundances in the investigated soil replicates rather reflect true environmental heterogeneity of primarily bacterial biomass (in the absence of indigenous fungi), potentially related to small-scale physicochemical differences.

Soil organic matter (SOM) is the dominant reservoir of terrestrial organic carbon and nitrogen, and microbial necromass represents a primary input to it. However, knowledge of stabilization mechanisms and direct measurements of the decomposition of microbial-derived SOM are lacking. Here we report a novel 15N isotope pool dilution approach using labeled amino sugars and muropeptides as tracers to quantify the decomposition of proteins and microbial cell walls, which allows to estimate in situ decomposition rates of microbial-derived SOM. Our results demonstrate that microbial cell walls are as recalcitrant as soil protein, exhibiting comparable turnover times across various ecosystems. The bacterial peptidoglycan in soils was primarily decomposed to muropeptides which can be directly utilized by microbes without being further depolymerized to free amino compounds. Moreover, bacterial peptidoglycan decomposition was correlated with soil microbial biomass while fungal chitin and soil protein decomposition were correlated with high soil pH and fine soil texture. This approach thereby provides new insights into the decomposition pathways and stabilization mechanisms of microbial-derived SOM constituents pertaining to SOM persistence.

The kinetics of soil microbial extracellular enzymes are important in regulating soil organic matter decomposition and ecosystem function. However, it is still unclear how the kinetic parameters (Vmax and Km) of hydrolytic and polyphenol oxidative enzymes respond to increased nitrogen (N) deposition and to what extent they regulate microbial respiration under N enrichment. We measured the Vmax and Km of seven soil hydrolytic enzymes and polyphenol oxidase (PPO) in a temperate steppe after 15 years of multi-level N addition treatments. Soil microbial respiration and physicochemical properties in the steppe were also monitored. The results showed that soil microbial respiration decreased exponentially with increasing N addition. The Vmax of carbon (C)-degrading and N-degrading hydrolytic enzymes decreased and the Vmax of acid phosphatase (AP) increased with increasing N addition. The reduction in the Vmax of C- and N-degrading hydrolytic enzymes was primarily caused by the decrease in soil pH under N enrichment. The Km of most hydrolytic enzymes decreased, expect for the Km of AP and β-xylosidase (BX), which increased with increasing N addition. As N addition increased, Vmax and Km of PPO first increased, maximized at 8 g N m−2 y−1, and then decreased. We conducted model averaging to assess the influence of the kinetic parameters on soil microbial respiration across candidate models. The results indicated that the Vmax and Km of BG were the best predictors for soil microbial respiration. The structural equation modeling result further indicated that the response of microbial respiration to N deposition was directly mediated by the response of BG kinetics: N-induced acidification had a negative impact on Vmax and Km for BG, which led to a decrease in microbial respiration. Our empirical data on enzyme Vmax, Km and their relationship to microbial respiration should be useful for modelling how microbes and substrates interact to regulate soil carbon cycling under N enrichment.

Soil enzymes are indicative of soil microbial carbon (C) and nutrient limitations. They are playing an important role in global C and nutrient cycles. However, we know little about whether soil microbial C and nutrient limitations are pervasive across broad spatial scales, and how soil enzymes respond to the addition of nitrogen (N) and phosphorus (P). Here we used a nutrient addition network across eight forest ecosystems ranging from temperate forests to tropical forests in eastern China and conducted a vector analysis using soil enzymatic stoichiometry to examine the spatial distributions of soil microbial C and nutrient limitations. We also examined the effect of nutrient addition on the extent of soil microbial resource use limitation. Our results showed that soil microbial C limitation was greater in the temperate forests than in the tropical forests, but did not vary with soil depth. Soil microbial P vs. N limitation decreased with latitude, while increased with soil depth. We found a negative relationship between soil microbial C limitation and the relative P vs. N limitation, and the strength of the negative relationship decreased with soil depth. Furthermore, we found that climate (mean annual precipitation and temperature), soil pH and soil nutrients were significantly correlated with soil microbial C and nutrient limitation. Climate and soil properties accounted for ∼23% and ∼87% variations in soil microbial C and nutrient limitations, respectively. However, nutrient addition accounted for only ∼1% variations in soil microbial C and nutrient limitations and thus did not alleviate soil microbial C limitation or the relative P vs. N limitation. We conclude that soil microbial C and nutrient limitations are more likely driven by climate and soil physicochemical properties, but not by nutrient addition in the eight forest ecosystems. Our findings suggest that soil microbial C and nutrient limitations may reflect the long-term evolutionary adaptation of soil microbial communities to focal soil nutrient environments and climate. Short-term changes in nutrient availability by fertilization may have a weaker effect on the functioning of soil microbial communities than climate and soil physicochemical properties.

Theory states that tree growth in lowland tropical forests on old, weathered soils is limited by low phosphorous (P) availability. However, evidence for P limitation from nutrient manipulation experiments remains unclear, which raises the question whether trees are taking up added P. In French Guianese lowland rainforest, we measured changes in nitrogen (N) and P availability before and up to two months after N and P addition. We measured in soils with intact root systems and soils excluding roots and mycorrhizal fungi with root exclusion cylinders. When the root system was excluded, P addition increased P availability to a much greater extent and for a longer time than where the roots remained undisturbed. N dynamics were unaffected by root presence/absence. These results indicate rapid root uptake of P, but not of N, suggesting very effective P acquisition in these lowland rainforests.