Trophic interactions play a vital role in soil functioning and are increasingly considered as important drivers of the soil microbiome and biogeochemical cycles. In the last decade, novel tools to decipher the structure of soil food webs have provided unprecedent advance in describing complex trophic interactions. Yet, the major challenge remains to understand the drivers of the trophic interactions

The fate of soil carbon (C) under climatic warming predominantly depends on temperature sensitivity of soil microbial functioning, but it is poorly understood. Using temporal measurements of soil respiration in an incubation experiment with cross-inoculation of microbial communities to contrasting soils, we constrained a microbial-explicit C model to infer temperature responses of two general microbial

Microbial transformation of crop residue is the key process of soil organic matter (SOM) formation and mineralization, which determines soil fertility and affects global climate change. However, utilization dynamics of residue-derived carbon (residue C) by various microbial communities is still not well understood, especially under different residue quality and soil fertility conditions over a long-term

Rhizosphere microbes play a critical role in plant growth and vitality; however, the combined effect and relative importance of soil and plant traits on the structure of microbial community remain poorly understood. Here, we investigated how soil type and plant species identity affect rhizosphere microbes. Two soil types were assessed, namely that collected from either a rice field or a secondary forest

The functional trait framework provides a powerful corpus of integrated concepts and theories to assess how environmental factors influence ecosystem functioning through community assembly. While common in plant ecology, this approach is under-used in microbial ecology. After an introduction of this framework in the context of microbial ecology and enzymology, we propose an approach 1) to elucidate

Management of the soil microbial community to increase crop productivity is one of the main challenges of modern agriculture, and bacterial inoculants can help to overcome this challenge. In this work, two plant growth-promoting (PGP) bacteria were evaluated under contrasting soil conditions, in order to test a rhizosphere ecology model. This model states that plants select for phosphate (P) solubilizers

Non-target effects of deliberately releasing organisms into a new environment are of great concern due to their potential impact on the biodiversity and functioning of ecosystems. Whereas these studies often focus on invasive species of macro-organisms, the use of microbial inoculants is often expected to have specific effects on particular functions but negligible overall effects on resident microbial

Current mechanistic models for soil organic matter (SOM) that explicitly incorporate ecoenzyme kinetics and thermodynamics have been shown to be superior in predicting SOM dynamics. However, how kinetic parameters (Vmax and Km) and their temperature sensitivity (Q10) are affected by environmental changes (e.g., nitrogen [N] deposition) and substrate chemistry remains a major uncertainty. In this study

Soil organic carbon (SOC) derived from manure increase phosphorus (P) availability by increasing the proportion of organic P (Po) in total P. However, what role SOC plays in the process of converting Po to available P (AP) and who modulates Po mineralization are still poorly understood. In this study, we collected three soil samples under long-term filed treatment with different organic (no carbon

Forest soils represent important terrestrial carbon (C) pools, where C is primarily fixed in plant biomass and then is incorporated in the biomass of fungi and bacteria. Although classical concepts assume that fungi are the main decomposers of the recalcitrant organic matter within plant and microbial biomass, whereas bacteria are considered to mostly utilize simpler compounds, recent studies have

This study aimed to trace the incorporation of 13C-labeled hydrophilic and hydrophobic compounds extracted from maize straw into bacterial and fungal phospholipid fatty acids (PLFAs) in upland and paddy soils. In both soils, the amounts of bacterial 13C-PLFAs recovered from hydrophilic C were 1.2–2.8 times higher than those from hydrophobic C. By contrast, the amounts of fungal 13C-PLFAs recovered

Rather than simple accumulation of individual populations, microorganisms in natural ecosystems form complex ecological networks that are critical to maintain ecosystem functions and services. Although various studies have examined the patterns of microbial community diversity and composition across spatial gradients, whether microbial co-occurrence relationships follow similar patterns remains an

There is insufficient evidence for how cover crop-driven changes to the soil microbial community affect soil organic carbon (SOC) accumulation. One mechanism by which enhanced microbial activity can contribute to SOC accrual is through the conversion of plant inputs to microbial biomass and ultimately necromass that may form organo–mineral associations with soil particles. Here we investigated the

Alpine soils are warming strongly, leading to profound alterations in carbon cycling and greenhouse gas budgets, mediated via the soil microbiome. To explore microbial responses to global warming, we incubated eight alpine soils between 4 and 35 °C and linked the temperature dependency of bacterial growth with alterations in community structures and the identification of temperature sensitive taxa

Plant can accelerate or slow down the soil organic carbon (SOC) decomposition by the rhizosphere priming effects (RPE). In forest ecosystems, the change of light availability due to canopy gap formation strongly influences growth of young trees and rhizosphere microbial activities in soil. However, the responses of RPE of forest young trees to light availability and its driving mechanisms remain elusive

Climate change is expected to affect rainfall dynamics and the global average temperature. Here, we evaluated the effects of those changes, the intense water deficit and warming (+2 °C), on a tropical grassland soil. We tested the correlation between soil extracellular enzyme activities (EEA) and soil respiration (CO2 efflux) and temperature and soil water content (SWC). A climate change simulation

Elevated nitrogen (N) deposition and increased precipitation often occur simultaneously, and have an interactive effect on terrestrial ecosystems, particularly in N-limited temperate forests. However, the effects of interactions between elevated N deposition and increased precipitation on soil communities are unclear. In the present study, we employed a novel approach to simulate N deposition and precipitation

Although increasing number of studies have shown that microorganisms play important roles in plant residue decomposition, an important process for crop productivity and soil fertility in agroecosystems, the underlying ecological processes of microbial community assembly as well as the associated governing factors remain elusive. As such, we conducted three replicate paddy straw decomposition experiments

Application of biochar to soils has been proposed as a novel approach to managing wood residuals, enhancing soil carbon (C) storage and improving soil fertility; however, the majority of biochar studies have been conducted in agricultural systems that rely on tillage and nutrient inputs associated with annual cropping schemes. Few studies have evaluated the influence of biochar on soil processes in

Tree-killing forest disturbances such as storms and bark beetle outbreaks can lead to notable changes in the carbon (C) balance and functioning of forest ecosystems. In this study, the effects of a storm in 2010 followed by an outbreak of European spruce bark beetle (Ips typographus L.) on tree, litter and soil C stocks as well as humus layer C fractions and microbial community composition were examined

The soil microbiome determines crop production and drives nutrient cycling, functions that are altered by fertilization. Yet, we have only begun to understand the effects of fertilization on taxonomic changes on soil microorganisms, while impacts on functional groups across the microbiome and therefore potential soil functioning have never been assessed. Here, using a range of methods including high-throughput

Soil microorganisms require metabolic strategies to cope with the significant variations in oxygen availability that occur in soil over a range of time scales. Characterised ammonia-oxidisers within Thaumarchaeota Groups 1.1a and 1.1b are aerobic, but the oxygen preference and metabolic potential of deeply-rooted Thaumarchaeota remain unknown, with several studies providing evidence for both aerobic

An increasing number of studies demonstrate that tree species biodiversity can affect primary productivity and nutrient cycling in forests due to several factors, such as complementarity, facilitation or selection effects. For instance, resource partitioning in soils has been found to allow a more optimized nutrient uptake in mixed species plots compared with monocultures. However, how these effects

The area known as Farrapos wetlands is a Protected Natural Area of Uruguay and is a RAMSAR site. It is characterized for being one of the most extensive fluvial wetlands of the country, with an important heterogeneity of environments. The aim of this work was to survey native legumes and the nodulating rhizobial symbionts present in this protected area in order to contribute to the conservation of

Anecic earthworms such as Lumbricus terrestris create effective channels for the translocation of organic substances, nutrients (N, P) and water between top- and subsoil. However, studies on localized and linked microbial activities with the biochemical mechanisms within drilosphere are missing. To clarify the enzymatic mechanisms, zymography was combined with 14C imaging by placing 14C-labeled wheat

Urbanisation involves major changes in environmental conditions such as light, temperature, humidity and noise levels, but the effect of urbanisation on soil conditions and soil biodiversity has received less attention. The reported effects on species richness across a rural to urban landscapes are not unequivocal. Positive, negative and neutral effects have been found, but what is causing this ambiguity

Denitrification usually takes place under anoxic conditions and over short periods of time, and depends on readily available nitrate and carbon sources. Variations in CO2 and N2O emissions associated with plant residues have mainly been explained by differences in their decomposability. A factor rarely considered so far is water-extractable organic matter (WEOM) released to the soil during residue

Nitrogen (N) stabilizers, e.g. nitrification inhibitor (NIs), urease inhibitor (UIs), or combined NIs and UIs (NUIs) have been recommended to reduce N losses, and improve fertilizer N use efficiency (NUE) and crop yield. However, the effectiveness of N stabilizers on rice yield and NUE varies greatly and the underlying mechanisms are not well understood. We performed a series of 15N tracing experiments

Despite the importance of plant litter decomposition for ecosystem nutrient cycling and soil fertility, it is still largely unknown how this biogeochemical process is affected by different forms of nitrogen (N). Numerous studies have investigated the effects of exogenous N addition on leaf litter decomposition, while the response of decomposing roots and their microbial communities to externally applied

Climate change and land use intensification are the two most common global change drivers of biodiversity loss. Like other organisms, the soil meso-fauna are expected to modify their functional diversity and composition in response to climate and land use changes. Here, we investigated the functional responses of Collembola, one of the most abundant and ecologically important groups of soil invertebrates

The conversion of rainforests to plantations leads to about 50% loss in the organic carbon (C) content of the soil and strongly influences nitrogen (N) cycling, potentially increasing greenhouse gas emissions. However, the effect of land-use change in forests on the microbial communities responsible for C and N cycling processes remains poorly understood. This study quantified C and N fractions of

Microbial communities influence and are influenced by environmental conditions that, together with the extracellular enzymes produced by soil microorganisms, control the rate of decomposition of organic matter in soil. Here, we aim to characterize the interaction of landscape position and depth on potential enzyme activities in a recently burned forest catchment. To accomplish this, we first characterized

Very small inputs of labile substrates can cause several more times CO2–C to be rapidly evolved from soil than was contained in the added substrates. This effect, termed the triggering response, does not currently have a conclusive mechanistic explanation. In this work 13C-labeled glucose was added (10 μg glucose C g−1 soil) to two Chinese soils, one from a mulberry plantation and another from a grassland

Wetland restoration efforts aim to enhance the structure and function of degraded and damaged wetlands. Unfortunately, restoration techniques often alter a site's soil habitat and plant community structure, which affect the activity and composition of microbial communities. Microbial community structure and activity, as a function of soil texture and plant inputs, were studied in soils collected from

In Mediterranean regions, the accumulation of nitrogenous substrates in soil during summer fallow period has been linked to pulses of N2O emissions upon soil rewetting. Although the mechanisms of N2O emission after soil rewetting have been previously studied, potential mitigation of agronomic practices on N2O pulses is still poorly understood. We studied the N2O emissions after rewetting of degraded

Non-ribosomal peptides (NRPs) and polyketides (PKs) are among the most profuse families of secondary metabolites (SM) produced by bacteria. These compounds are believed to play an important ecological role in microbe-microbe and microbe-plant interactions in soil and roots microbiomes. Over the years, screening of NRPs and PKs in soil bacteria has resulted in high rates of rediscovery, mainly due to

Despite the enormous size of the organic nitrogen (N) pool contained in mineral subsoils, rates of N cycling and soil exoenzyme activities are rarely measured in soils below 10 or 20 cm depth. Furthermore, assumed relationships between N mineralization rates and the activities of various decomposition exoenzymes are poorly characterized. We measured rates of gross and net N mineralization and nitrification

Iron hydroxides serve as an efficient ‘rusty sink’ promoting the stabilization of rhizodeposits into soil organic carbon (SOC). Our work aimed to understand the physicochemical and microbial mechanisms promoting rhizodeposit (rhizo-C) stabilization as influenced by goethite (α-FeOOH) or nitrogen (N), using 13C natural abundance methodologies and DNA sequencing, in the rhizosphere of maize (Zea mays

A high diversity of Apicomplexa was recently found in tropical soils presumably reflecting the diversity of their invertebrate hosts, but such patterns have not been explored in colder regions. We analysed the diversity of Apicomplexa and their potential metazoan hosts in litter and mosses collected in 11 different alpine habitats using an eDNA metabarcoding approach. The abundance and diversity of

Northern peatlands are often dominated by ericaceous shrub species which rely on ericoid mycorrhizal fungi (ERM) for access to organic sources of nutrients, such as nitrogen (N) and phosphorus (P), and host abundant dark septate endophytes (DSE). Relationships between hosts and fungal symbionts may change during deposition of anthropogenic N and P. We studied the long-term effects of N and P addition

Recently, an increasing number of studies use ecoenzymatic stoichiometry for determining nutritional status or nutrient limitations of microbes. According to the ecoenzymatic stoichiometry theory, the ratios of β-1,4-glucosidase (BG) and β-1,4-N-acetylglucosaminidase (NAG) (BG:NAG) or BG and NAG + leucine aminopeptidase (LAP) (BG:(BG + LAP)) reflect microbial carbon (C) vs nitrogen (N) limitation,

Abstract In drylands, soil surfaces in interplant spaces are usually covered by biocrusts, which consist of communities of heterotrophic and chemoautotrophic bacteria, cyanobacteria, mosses, lichens, microalgae, fungi and other organisms. Cyanobacteria are of special interest because of their capacity to promote biocrust succession or increase soil fertility and stability. Therefore, some studies have

Arbuscular mycorrhizal (AM) plants and fungi associate with lower soil organic matter, higher pH, lower phosphorus and higher nitrogen than ectomycorrhizal (EM) ones. However, soil conditions correlate with climatic factors, and we suggest that temperature and humidity have also direct roles in the success of mycorrhiza types. The hypothesis here is that EM perform better at low temperatures than AM

Microbes play critical roles in the cycling of nutrients in forest ecosystems. Many studies have shown that the application of organic fertilizer can alter bacterial diversity; however, the responses of soil microbial functional genes to organic fertilization (particularly biogas slurry fertilization, or in combination with biochar) have not been elucidated as yet. We examined the responses of the

Phosphorus (P) is an essential macronutrient for plant growth, but bioavailable P in soils is often limited due to immobilization resulting from pH and geochemical interactions. Understanding the dynamics of P in soils and elucidating the mechanisms by which plants access P from their environment are critical to evaluating productivity, particularly in nutrient poor environments. Phosphorus from organic