Abstract: Pyrogenic carbon (biochar) amendment is increasingly discussed as a method to increase soil fertility while sequestering atmospheric carbon (C). However, both increased and decreased C mineralization has been observed following biochar additions to soils. In an effort to better understand the interaction of pyrogenic C and soil organic matter (OM), a range of Florida soils were incubated with a range of laboratory-produced biochars and CO 2 evolution was measured over more than one year. More C was released from biochar-amended than from non-amended soils and cumulative mineralized C generally increased with decreasing biomass combustion temperature and from hardwood to grass biochars, similar to the pattern of biochar lability previously determined from separate incubations of biochar alone. The interactive effects of biochar addition to soil on CO 2 evolution (priming) were evaluated by comparing the additive CO 2 release expected from separate incubations of soil and biochar with that actually measured from corresponding biochar and soil mixtures. Priming direction (positive or negative for C mineralization stimulation or suppression, respectively) and magnitude varied with soil and biochar type, ranging from −52 to 89% at the end of 1 year. In general, C mineralization was greater than expected (positive priming) for soils combined with biochars produced at low temperatures (250 and 400 °C) and from grasses, particularly during the early incubation stage (first 90 d) and in soils of lower organic C content. It contrast, C mineralization was generally less than expected (negative priming) for soils combined with biochars produced at high temperatures (525 and 650 °C) and from hard woods, particularly during the later incubation stage (250–500 d). Measurements of the stable isotopic signature of respired CO 2 indicated that, for grass biochars at least, it was predominantly pyrogenic C mineralization that was stimulated during early incubation and soil C mineralization that was suppressed during later incubation stages. It is hypothesized that the presence of soil OM stimulated the co-mineralization of the more labile components of biochar over the short term. The data strongly suggests, however, that over the long term, biochar–soil interaction will enhance soil C storage via the processes of OM sorption to biochar and physical protection.

Abstract: The determination of the phospholipid fatty acid (PLFA) pattern of soil organisms has become one of the most commonly used methods to study microbial community structure. Here we recapitulate the background of our work applying the PLFA method to soil in the early 1990s. We also stress that although the PLFA method was, and still is, a rapid and sensitive method to detect changes in the microbial community in soil, as with all popular methods it can be misused. We discuss problems in PLFA interpretation, the extent of turn-over of PLFAs in soil, and the flawed use of diversity indices to evaluate PLFA patterns.

Abstract: Microbial digestive enzymes in soil and litter have been studied for over a half century, yet the under- standing of microbial enzymes as drivers of ecosystem processes remains hindered by methodological differences among researchers and laboratories. Modern techniques enable the comparison of enzyme activities from different sites and experiments, but most researchers do not optimize enzyme assay methods for their study sites, and thus may not properly assay potential enzyme activity. In this review, we characterize important procedural details of enzyme assays, and define the steps necessary to properly assay potential enzyme activities in environmental samples. We make the following recom- mendations to investigators measuring soil enzyme activities: 1) run enzyme assays at the environ- mental pH and temperature; 2) run proper standards, and if using fluorescent substrates with NaOH addition, use a standard time of 1 min between the addition of NaOH and reading in a fluorometer; 3) run enzyme assays under saturating substrate concentrations to ensure V max is being measured; 4) confirm that product is produced linearly over the duration of the assay; 5) examine whether mixing during the reaction is necessary to properly measure enzyme activity; 6) find the balance between dilution of soil homogenate and assay variation; and 7) ensure that enzyme activity values are properly calculated. These steps should help develop a unified understanding of enzyme activities in ecosystem ecology.

Abstract: It is increasingly recognized that soil microbes have the ability to decompose old recalcitrant soil organic matter (SOM) by using fresh carbon as a source of energy, a phenomena called priming effect (PE). However, efforts to determine the consequences of this PE for soil carbon and nitrogen dynamics are in their early stage. Moreover, little is known about the microbial populations involved. Here we explore the consequences of PE for SOM dynamics and mineral nitrogen availability in a soil incubation experiment (161 days), combining the supply of dual-labeled (13C and 14C) cellulose and mineral nutrients. The microbial groups involved in PE were investigated using molecular fingerprinting techniques (FAMEs and B- and F-ARISA). We show that mean residence time of SOM pool controlled by the PE decreased from 3130 years in the subsoil, where the availability of fresh carbon is very low, to 17–39 years in the surface layer. This result suggests that the decomposition of this recalcitrant soil C pool is strictly dependent on the presence of fresh C and is not an energetically viable mean of accessing C for soil microbes. We also suggest that fungi are the predominant actors of cellulose decomposition and induced PE and they adjust their degradation activity to nutrient availability. The predominant role of fungi can be explained by their ability to grow as mycelium which allows them to explore soil space and mine large reserve of SOM. Finally, our results support the existence of a bank mechanism that regulates nutrient and carbon sequestration in soil: PE is low when nutrient availability is high, allowing sequestration of nutrients and carbon; in contrast, microbes release nutrients from SOM when nutrient availability is low. This bank mechanism may help to synchronize the availability of soluble nutrients to plant requirement and contribute to long-term SOM accumulation in ecosystems.

Abstract: Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.

Abstract: The aim of this work was to determine the magnitude of the priming effect, i.e. short-term changes in the rate (negative or positive) of mineralisation of native soil organic carbon (C), following addition of biochars. The biochars were made from Miscanthus giganteus , a C4 plant, naturally enriched with 13 C. The biochars were produced at 350 °C (biochar350) and 700 °C (biochar700) and applied with and without ryegrass as a substrate to a clay-loam soil at pH 3.7 and 7.6. A secondary aim was to determine the effect of ryegrass addition on the mineralisation of the two biochars. After 87 days, biochar350 addition caused priming effects equivalent to 250 and 319 μg CO 2 –C g −1 soil, in the low and high pH soil, respectively. The largest priming effects occurred at the start of the incubations. The size of the priming effect was decreased at higher biochar pyrolysis temperatures, which may be a way of controlling priming effects following biochar incorporation to soil, if desired. The priming effect was probably induced by the water soluble components of the biochar. At 87 days of incubation, 0.14% and 0.18% of biochar700 and 0.61% and 0.84% of biochar350 were mineralized in the low and high pH soil, respectively. Ryegrass addition gave an increased biochar350 mineralisation of 33% and 40%, and increased biochar700 at 137% and 70%, in the low and high pH soils, respectively. Certainly, on the basis of our results, if biochar is used to sequester carbon a priming effect may occur, increasing CO 2 –C evolved from soil and decreasing soil organic C. However, this will be more than compensated for by the increased soil C caused by biochar incorporation. A similar conclusion holds for accelerated mineralisation of biochar due to incorporation of fresh labile substrates. We consider that our results are the first to unequivocally demonstrate the initiation, progress and termination of a true positive priming effect by biochar on native soil organic C.

Abstract: The application of biochar to soil has been shown to cause an apparent increase in soil respiration. In this study we investigated the mechanistic basis of this response. We hypothesized that increased CO2 efflux could occur by: (1) Biochar-induced changes in soil physical properties (bulk density, porosity, moisture content); (2) The biological breakdown of organic carbon (C) released from the biochar; (3) The abiotic release of inorganic C contained in the biochar; (4) A biochar-induced stimulation of decomposition of native soil organic matter (SOM) which could occur both biotically or abiotically; (5) The intrinsic biological activity of the biochar results in the liberation of CO2. Our results show that most of the extra CO2 produced after biochar addition to soil came from the equal breakdown of organic C and the release of inorganic C contained in the biochar. Using long-term 14C-labelled SOM, we show that biochar repressed native SOM breakdown, counteracting the release of CO2 from the biochar. A range of mechanisms to describe this negative priming response is presented. Although biochar-induced significant changes in the physical characteristics of the soil, overall this made no contribution to changes in soil respiration. Similarly, the evidence from our study suggests that changes in soluble polyphenols do not help explain the respiration response. In summary, biochar induced a net release of CO2 from the soil; however, this C loss was very small relative to the amount of C stored within the biochar itself (ca. 0.1%). This short-term C release should therefore not compromise its ability to contribute to long-term C sequestration in soil environments.

Abstract: Recognition of biochar as a potential tool for long-term carbon sequestration with additional agronomic benefits is growing However, the functionality of biochar in soil and the response of soils to biochar inputs are poorly understood It has been suggested, for example, that biochar additions to soils could prime for the loss of native organic carbon, undermining its sequestration potential This work examines the priming potential of biochar in the context of its own labile fraction and procedures for their assessment A systematic set of biochar samples produced from C4 plant biomass under a range of pyrolysis process conditions were incubated in a C3 soil at three discrete levels of organic matter status (a result of contrasting long-term land management on a single site) The biochar samples were characterised for labile carbon content ex-situ and then added to each soil Priming potential was determined by a comparison of CO2 flux rates and its isotopic analysis for attribution of source The results conclusively showed that while carbon mineralisation was often higher in biochar amended soil, this was due to rapid utilisation of a small labile component of biochar and that biochar did not prime for the loss of native organic soil organic matter Furthermore, in some cases negative priming occurred, with lower carbon mineralisation in biochar amended soil, probably as a result of the stabilisation of labile soil carbon

Abstract: Soils are the major source of the greenhouse gas nitrous oxide (N2O) to our atmosphere. A thorough understanding of terrestrial N2O production is therefore essential. N2O can be produced by nitrifiers, denitrifiers, and by nitrifiers paradoxically denitrifying. The latter pathway, though well-known in pure culture, has only recently been demonstrated in soils. Moreover, nitrifier denitrification appeared to be much less important than classical nitrate-driven denitrification. Here we studied a poor sandy soil, and show that when moisture conditions are sub-optimal for denitrification, nitrifier denitrification can be a major contributor to N2O emission from this soil. We conclude that the relative importance of classical and nitrifier denitrification in N2O emitted from soil is a function of the soil moisture content, and likely of other environmental conditions as well. Accordingly, we suggest that nitrifier denitrification should be routinely considered as a major source of N2O from soil.

Abstract: The response of soil microbial communities following changes in land-use is governed by multiple factors. The objectives of this study were to investigate (i) whether soil microbial communities track the changes in aboveground vegetation during succession; and (ii) whether microbial communities return to their native state over time. Two successional gradients with different vegetation were studied at the W. K. Kellogg Biological Station, Michigan. The first gradient comprised a conventionally tilled cropland (CT), mid-succession forest (SF) abandoned from cultivation prior to 1951, and native deciduous forest (DF). The second gradient comprised the CT cropland, early-succession grassland (ES) restored in 1989, and long-term mowed grassland (MG). With succession, the total microbial PLFAs and soil microbial biomass C consistently increased in both gradients. While bacterial rRNA gene diversity remained unchanged, the abundance and composition of many bacterial phyla changed significantly. Moreover, microbial communities in the relatively pristine DF and MG soils were very similar despite major differences in soil properties and vegetation. After >50 years of succession, and despite different vegetation, microbial communities in SF were more similar to those in mature DF than in CT. In contrast, even after 17 years of succession, microbial communities in ES were more similar to CT than endpoint MG despite very different vegetation between CT and ES. This result suggested a lasting impact of cultivation history on the soil microbial community. With conversion of deciduous to conifer forest (CF), there was a significant change in multiple soil properties that correlated with changes in microbial biomass, rRNA gene diversity and community composition. In conclusion, history of land-use was a stronger determinant of the composition of microbial communities than vegetation and soil properties. Further, microbial communities in disturbed soils apparently return to their native state with time.

Abstract: This paper is an extensive review of the research that has been undertaken on near-infrared (NIR) and mid-infrared (MIR) spectroscopy applied to soil particularly for determining carbon (C) content. The objective is to determine which acquisition method (NIR, MIR, in the field or in the laboratory) might be recommended for the purpose of C stock measurement with a particular interest in carbon credit trading. For this purpose, an optimal method has to satisfy the dual constraints of low-cost and high throughput analysis. The various methods proposed in the literature are compared. In order to make comparisons as reliable as possible, special attention has been paid to the conditions of data acquisition (sample preparation), and to calibration and validation procedures. In particular, whether the validation has been carried out on fully independent samples or on samples similar to the ones of the calibration set greatly influences the results. Also, for C stock measurement, it is absolutely necessary to measure the bias of the prediction in order to be conclusive about the feasibility of the method. However, only few researchers provide this parameter and we recommend including it as a matter of course in future reports. Finally, although MIR on dried and ground samples is the most accurate method, on-the-go and in-field sensors provide predictions accurate enough to show promise in being a valuable component of technologies that would be used for C-credit purposes. But in order to meet the cost/accuracy trade-off, the main issue using such field sensors is to be able to simultaneously measure the bulk density or, better, to directly measure the volumetric concentration of C in soil. This circumvents the costs of field extraction and laboratory analysis. This is the next great challenge to be met by soil scientists.

Abstract: Arbuscular mycorrhizal (AM) fungi form associations with most land plants and can control carbon, nitrogen, and phosphorus cycling between above- and belowground components of ecosystems. Current estimates of AM fungal distributions are mainly inferred from the individual distributions of plant biomes, and climatic factors. However, dispersal limitation, local environmental conditions,and interactions among AM fungal taxa may also determine local diversity and global distributions. We assessed the relative importance of these potential controls by collecting 14,961 DNA sequences from 111 published studies and testing for relationships between AM fungal community composition and geography, environment, and plant biomes. Our results indicated that the global species richness of AM fungi was up to six times higher than previously estimated, largely owing to high beta diversity among sampling sites. Geographic distance, soil temperature and moisture, and plant community type were each significantly related to AM fungal community structure, but explained only a small amount of the observed variance. AM fungal species also tended to be phylogenetically clustered within sites, further suggesting that habitat filtering or dispersal limitation is a driver of AM fungal community assembly. Therefore, predicted shifts in climate and plant species distributions under global change may alter AM fungal communities.

Abstract: The effects of pyrogenic carbon on the microbial diversity of forest soils were examined by comparing two soil types, fire-impacted and non-impacted, that were incubated with laboratory-generated biochars. Molecular and culture-dependent analyses of the biochar-treated forest soils revealed shifts in the relative abundance and diversity of key taxa upon the addition of biochars, which were dependent on biochar and soil type. Specifically, there was an overall loss of microbial diversity in all soils treated with oak and grass-derived biochar as detected by automated ribosomal intergenic spacer analysis. Although the overall diversity decreased upon biochar amendments, there were increases in specific taxa during biochar-amended incubation. DNA sequencing of these taxa revealed an increase in the relative abundance of bacteria within the phyla Actinobacteria and Gemmatimonadetes in biochar-treated soils. Together, these results reveal a pronounced impact of pyrogenic carbon on soil microbial community composition and an enrichment of key taxa within the parent soil microbial community.

Abstract: Iron and phosphorus availability is low in many soils; hence, microorganisms and plants have evolved mechanisms to acquire these nutrients by altering the chemical conditions that affect their solubility. In plants, this includes exudation of organic acid anions and acidification of the rhizosphere by release of protons in response to iron and phosphorus deficiency. Grasses (family Poaceae) and microorganisms further respond to Fe deficiency by production and release of specific chelators (phytosiderophores and siderophores, respectively) that complex Fe to enhance its diffusion to the cell surface. In the rhizosphere, the mutual demand for Fe and P results in competition between plants and microorganisms with the latter being more competitive due to their ability to decompose plant-derived chelators and their proximity to the root surface; however microbial competitiveness is strongly affected by carbon availability. On the other hand, plants are able to avoid direct competition with microorganisms due to the spatial and temporal variability in the amount and composition of exudates they release into the rhizosphere. In this review, we present a model of the interactions that occur between microorganisms and roots along the root axis, and discuss advantages and limitations of methods that can be used to study these interactions at nanometre to centimetre scales. Our analysis suggests mechanisms such as increasing turnover of microbial biomass or enhanced nutrient uptake capacity of mature root zones that may enhance plant competitiveness could be used to develop plant genotypes with enhanced efficiency in nutrient acquisition. Our model of interactions between plants and microorganisms in the rhizosphere will be useful for understanding the biogeochemistry of P and Fe and for enhancing the effectiveness of fertilization.

Abstract: Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO2 (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.

Abstract: Biochar application to soil has been proposed as a mechanism for improving soil quality and the long term sequestration of carbon. The implications of biochar on pesticide behavior, particularly in the longer term, however, remains poorly understood. Here we evaluated the influence of biochar type, time after incorporation into soil, dose rate and particle size on the sorption, biodegradation and leaching of the herbicide simazine. We show that typical agronomic application rates of biochar (10–100 t ha−1) led to alterations in soil water herbicide concentrations, availability, transport and spatial heterogeneity. Overall, biochar suppressed simazine biodegradation and reduced simazine leaching. These responses were induced by a rapid and strong sorption of simazine to the biochar which limits its availability to microbial communities. Spatial imaging of 14C-labeled simazine revealed concentrated hotpsots of herbicide co-localized with biochar in the soil profile. The rate of simazine mineralization, amount of sorption and leaching was inversely correlated with biochar particle size. Biochar aged in the field for 2 years had the same effect as fresh biochar on the sorption and mineralization of simazine, suggesting that the effects of biochar on herbicide behavior may be long lasting. We conclude that biochar application to soil will reduce the dissipation of foliar applied pesticides decreasing the risk of environmental contamination and human exposure via transfer in the food chain, but may affect the efficacy of soil-applied herbicides.

Abstract: The availability of Soil Organic Nitrogen (SON) determines soil fertility and biomass production to a great extent. SON also affects the amounts and turnover rates of the soil organic carbon (SOC) pools. Although there is increasing awareness of the impact of the nitrogen (N) cycle on the carbon (C) cycle, the extent of this interaction and the implications for soil organic matter (SOM) dynamics are still under debate. Therefore, present knowledge about the inter-relationships of the soil cycles of C and N as well as current ideas about SON stabilization are summarized in this paper in order to develop an advanced concept of the role of N on C sequestration. Modeling global C-cycling, it was already recognized that SON and SOC are closely coupled via biomass production and degradation. However, the narrow C/N ratio of mature soil organic matter (SOM) shows further that the impact of SON on the refractory SOM is beyond that of determining the size of the active cycling entities. It affects the quantity of the slow cycling pool and as a major contributor it also determines its chemical composition. Although the chemical nature of SON is still not very well understood, both improved classical wet chemical analyses and modern spectroscopic techniques provide increasing evidence that almost the entire organic N in fire-unaffected soils is bound in peptide-like compounds and to a lesser extent in amino sugars. This clearly points to the conclusion, that such compounds have greater importance for SOM formation than previously assumed. Based on published papers, I suggest that peptides even have a key function in the C-sequestration process. Although the mechanisms involved in their medium and long-term stabilization are far from understood, the immobilization of these biomolecules seems to determine the chemistry and functionality of the slow cycling SOM fraction and even the potential of a soil to act as a C sink. Pyrogenic organic N, which derives mostly from incomplete combustion of plant and litter peptides is another under-rated player in soil organic matter preservation. In fire-prone regions, its formation represents a major N stabilization mechanism, leading to the accumulation of heterocyclic aromatic N, the stability of which is still not elaborated. The concept of peptide-like compounds as a key in SOM-sequestration implies that for an improved evaluation of the potential of soils as C-sinks our research focus as to be directed to a better understanding of their chemistry and of the mechanisms which are responsible for their resistance against biochemical degradation in soils.

Abstract: The scarcity of non-renewable resources such as soils and fertilizers and the consequences of climate change can dramatically influence the food security of future generations. Mutualistic root microorganisms such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) can improve plant fitness. We tested the growth response of wheat (Triticum aestivum [L.]), rice (Oriza sativa [L.]) and black gram (Vigna mungo [L.], Hepper) to an inoculation of AMF and PGPR alone or in combination over two years at seven locations in a region extending from the Himalayan foothills to the Indo-Gangetic plain. The AMF applied consisted of a consortium of different strains, the PGPR of two fluorescent Pseudomonas strains (Pseudomonas jessenii, R62; Pseudomonas synxantha, R81), derived from wheat rhizosphere from one test region. We found that dual inoculation of wheat with PGPR and AMF increased grain yield by 41% as compared to un-inoculated controls. Yield responses to the inoculants were highest at locations with previously low yields. AMF or PGPR alone augmented wheat grain yield by 29% and 31%, respectively. The bio-inoculants were effective both at Zero and at farmers’ practice fertilization level (70 kg N ha−1, 11 kg P ha−1 in mineral form to wheat crop). Also raw protein (nitrogen × 5.7) and mineral nutrient concentration of wheat grains (phosphorus, potassium, copper, iron, zinc, manganese) were higher after inoculation (+6% to +53%). Phosphorus use efficiency of wheat grains [kg P grain kg−1 P fertilizer] was increased by 95%. AMF and PGPR application also improved soil quality as indicated by increased soil enzyme activities of alkaline and acid phosphatase, urease and dehydrogenase. Effects on rice and black gram yields were far less pronounced over two cropping seasons, suggesting that AMF and PGPR isolated from the target crop were more efficient. We conclude that mutualistic root microorganisms have a high potential for contributing to food security and for improving nutrition status in southern countries, while safeguarding natural resources such as P stocks. (c) Elsevier

Abstract: This review focuses on literature pertaining to the interactions of soil yeasts with biotic and abiotic factors in their environment. Soil yeasts not only affect microbial and plant growth, but may also play a role in soil aggregate formation and maintenance of soil structure. Serving as a nutrient source for bacterial, faunal and protistan predators, soil yeasts contribute to essential ecological processes such as the mineralization of organic material and dissipation of carbon and energy through the soil ecosystem. Some soil yeasts may also play a role in both the nitrogen and sulphur cycles and have the ability to solubilize insoluble phosphates making it more readily available for plants. Recently, the potential of soil yeasts as plant growth promoters and soil conditioners has been studied with the goal of using them in the field of sustainable agriculture.

Abstract: The objective of this review was to identify, address and rank knowledge gaps in our understanding of five major soil C and N interactions across a range of scales – from molecular to global. The studied five soil C and N interactions are: i) N controls on the soil emissions of greenhouse gases, ii) plant utilisation of organic N, iii) impact of rhizosphere priming on C and N cycling, iv) impact of black N on the stabilisation of soil organic matter (SOM) and v) representation of fractions of SOM in simulation models. We ranked the identified knowledge gaps according to the importance we attached to them for functional descriptions of soil–climate interactions at the global scale, for instance in general circulation models (GCMs). Both the direct and indirect influences on soil–climate interactions were included. We found that the level of understanding declined as the scale increased from molecular to global for four of the five topics. By contrast, the knowledge level for SOM simulation models appeared to be highest when considered at the ecosystem scale. The largest discrepancy between knowledge level and importance was found at the global modelling scale. We concluded that a reliable quantification of greenhouse gas emissions at the ecosystem scale is of utmost importance for improving soil–climate representation in GCMs. We see as key questions the identification of the role of different N species for the temperature sensitivity of SOM decomposition rates and its consequences for plant available N.

Abstract: Plants often impact the rate of native soil organic matter turnover through root interactions with soil organisms; however the role of root-microbial interactions in mediation of the “priming effect” is not well understood. We examined the effects of living plant roots and N fertilization on belowground C dynamics in a California annual grassland soil (Haploxeralf) during a two-year greenhouse study. The fate of 13 C-labeled belowground C (roots and organic matter) was followed under planted ( Avena barbata ) and unplanted conditions, and with and without supplemental N (20 kg N ha −1 season −1 ) over two periods of plant growth, each followed by a dry, fallow period of 120 d. Turnover of belowground 13 C SOM was followed using 13 C-phospholipid fatty acid (PLFA) biomarkers. Living roots increased the turnover and loss of belowground 13 C compared with unplanted soils. Planted soils had 20% less belowground 13 C present than in unplanted soils after 2 cycles of planting and fallow. After 2 treatment cycles, unlabeled soil C was 4.8% higher in planted soils than unplanted. The addition of N to soils decreased the turnover of enriched belowground 13 C during the first treatment season in both planted and unplanted soils, however no effect of N was observed thereafter. Our findings suggest that A. barbata may increase soil C levels over time because root and exudate C inputs are significant, but that increase will be moderated by an overall faster C mineralization rate of belowground C. N addition may slow soil C losses; however, the effect was minor and transient in this system. The labeled root-derived 13 C was initially recovered in gram negative (highest enrichment), gram positive, and fungal biomarkers. With successive growing seasons, the labeled C in the gram negative and fungal markers declined, while gram positive markers continued to accumulate labeled belowground C. The rhizosphere of A. barbata shifted the microbial community composition, resulting in greater abundances of gram negative markers and lower abundances of gram positive, actinobacteria and cyclopropyl PLFA markers compared to unplanted soil. However, the longer-term utilization of labeled belowground C by gram positive bacteria was enhanced in the rhizosphere microbial community compared with unplanted soils. We suggest that the activities of gram positive bacteria may be major controllers of multi-year rhizosphere-related priming of SOM decomposition.

Abstract: Rice paddy soils are characterized by anoxic conditions, anaerobic carbon turnover, and significant emissions of the greenhouse gas methane. A main source for soil organic matter in paddy fields is the rice crop residue that is returned to fields if not burned. We investigated as an alternative treatment the amendment of rice paddies with rice residues that have been charred to black carbon. This treatment might avoid various negative side effects of traditional rice residue treatments. Although charred biomass is seen as almost recalcitrant, its impact on trace gas (CO 2 , CH 4 ) production and emissions in paddy fields has not been studied. We quantified the degradation of black carbon produced from rice husks in four wetland soils in laboratory incubations. In two of the studied soils the addition of carbonised rice husks resulted in a transient increase in carbon mineralisation rates in comparison to control soils without organic matter addition. After almost three years, between 4.4% and 8.5% of the black carbon added was mineralised to CO 2 under aerobic and anaerobic conditions, respectively. The addition of untreated rice husks resulted in a strong increase in carbon mineralisation rates and in the same time period 77%–100% of the added rice husks were mineralised aerobically and 31%–54% anaerobically. The 13 C-signatures of respired CO 2 gave a direct indication of black carbon mineralisation to CO 2. In field trials we quantified the impact of rice husk black carbon or untreated rice husks on soil respiration and methane emissions. The application of black carbon had no significant effect on soil respiration but significantly enhanced methane emissions in the first rice crop season. The additional methane released accounted for only 0.14% of black carbon added. If the same amount of organic carbon was added as untreated rice husks, 34% of the applied carbon was released as CO 2 and methane in the first season. Furthermore, the addition of fresh harvest residues to paddy fields resulted in a disproportionally high increase in methane emissions. Estimating the carbon budget of the different rice crop residue treatments indicated that charring of rice residues and adding the obtained black carbon to paddy fields instead of incorporating untreated harvest residues may reduce field methane emissions by as much as 80%. Hence, the production of black carbon from rice harvest residues could be a powerful strategy for mitigating greenhouse gas emissions from rice fields.

Abstract: The various ecosystem functions of soil organic matter (SOM) depend on both its quantity and stability. Numerous fractionation techniques have been developed to characterize SOM stability, and thermal analysis techniques have shown promising results to describe the complete continuum of SOM in whole soil samples. However, the potential link between SOM thermal stability and biological or chemical stability has not yet been adequately explored. The objective of this study was to compare conventional chemical and biological methods used to characterize SOM stability with results obtained by thermal analysis techniques. Surface soil samples were collected from four North American grassland sites along a continental mean annual temperature gradient, each with a native and cultivated land use. Soil organic C concentrations ranged from 6.8 to 33 g C kg −1 soil. Soils were incubated for 588 days at 35 °C, and C mineralization rates were determined periodically throughout the incubation by measuring CO 2 concentration using an infrared gas analyzer (IRGA) to calculate biological indices of SOM stability. Hot-water extractable organic C (HWEOC) contents were determined before and after incubation as chemical indices. Finally, samples from before and after incubation were analyzed by simultaneous thermal analysis (i.e., thermogravimetry (TG) and differential scanning calorimetry (DSC)) to determine thermal indices of SOM stability. Long-term incubation resulted in the mineralization of up to 33% of initial soil C. The number of days required to respire 5% of initial soil organic carbon (SOC), ranged from 27 to 115 days, and is proposed as a standardized biological index of SOM stability. The number of days was greater for cultivated soils compared to soils under native vegetation, and generally decreased with increasing site mean annual temperature. HWEOC (as % of initial SOC) did not show consistent responses to land use, but was significantly lower after long-term incubation. Energy density (J mg −1 OM) was greater for soils under native vegetation compared to cultivated soils, and long-term incubation also decreased energy density. The temperatures at which half of the mass loss or energy release occurred typically showed larger responses to land use change than to incubation. Strong correlations demonstrated a link between the thermal and biogeochemical stability of SOM, but the interpretation of the thermal behavior of SOM in bulk soil samples remains equivocal because of the role the mineral component and organo-mineral interactions.

Abstract: Soil fungi are highly diverse and act as the primary agents of nutrient cycling in forests. These fungal communities are often dominated by mycorrhizal fungi that form mutually beneficial relationships with plant roots and some mycorrhizal fungi produce extracellular and cell-bound enzymes that catalyze the hydrolysis of nitrogen (N)- and phosphorus (P)- containing compounds in soil organic matter. Here we investigated whether the community structure of different types of mycorrhizal fungi (arbuscular and ectomycorrhizal fungi) is correlated with soil chemistry and enzyme activity in a northern hardwood forest and whether these correlations change over the growing season. We quantified these relationships in an experimental paired plot study where white-tailed deer (access or excluded 4.5 yrs) treatment was crossed with garlic mustard (presence or removal 1 yr). We collected soil samples early and late in the growing season and analyzed them for soil chemistry, extracellular enzyme activity and molecular analysis of both arbuscular mycorrhizal (AM) and ectomycorrhizal/saprotrophic fungal communities using terminal restriction fragment length polymorphism (TRFLP). AM fungal communities did not change seasonally but were positively correlated with the activities of urease and leucine aminopeptidase (LAP), enzymes involved in N cycling. The density of garlic mustard was correlated with the presence of specific AM fungal species, while deer exclusion or access had no effect on either fungal community after 4.5 yrs. Ectomycorrhizal/saprotrophic fungal communities changed seasonally and were positively correlated with most soil enzymes, including enzymes involved in carbon (C), N and P cycling, but only during late summer sampling. Our results suggest that fine scale temporal and spatial changes in soil fungal communities may affect soil nutrient and carbon cycling. Although AM fungi are not generally considered capable of producing extracellular enzymes, the correlation between some AM taxa and the activity of N acquisition enzymes suggests that these fungi may play a role in forest understory N cycling.

Abstract: We used metabolic tracers and modeling to analyze the response of soil metabolism to a sudden change in temperature from 4 to 20 °C. We hypothesized that intact soil microbial communities would exhibit shifts in pentose phosphate pathway and glycolysis activity in the same way as is regularly observed for individual microorganisms in pure culture. We also hypothesized that increased maintenance respiration at higher temperature would result in greater energy production and reduced carbon use efficiency (CUE). Two hours after temperature increase, respiration increased almost 10-fold. Although all metabolic processes were increased, the relative activity of metabolic processes, biosynthesis, and energy production changed. Pentose phosphate pathway was reduced (17–20%), while activities of specific steps in glycolysis (51%) and Krebs cycle (7–13%) were increased. In contrast, only small but significant changes in biosynthesis (+2%), ATP production (−3%) and CUE (+2%) were observed. In a second experiment, we compared the metabolic responses to temperature increases in soils from high and low elevation. The shift in activity from pentose phosphate pathway to glycolysis with higher temperature was confirmed in both soils, but the responses of Krebs cycle, biosynthesis, ATP production, and CUE were site dependent. Our results indicate that 1) in response to temperature, communities behave biochemically similarly to single species and, 2) our understanding of temperature effects on CUE, energy production and use for maintenance and growth processes is still incomplete.

Abstract: Two processes contribute to changes of the δ13C signature in soil pools: 13C fractionation per se and preferential microbial utilization of various substrates with different δ13C signature. These two processes were disentangled by simultaneously tracking δ13C in three pools – soil organic matter (SOM), microbial biomass, dissolved organic carbon (DOC) – and in CO2 efflux during incubation of 1) soil after C3–C4 vegetation change, and 2) the reference C3 soil. The study was done on the Ap horizon of a loamy Gleyic Cambisol developed under C3 vegetation. Miscanthus giganteus – a perennial C4 plant – was grown for 12 years, and the δ13C signature was used to distinguish between ‘old’ SOM (>12 years) and ‘recent’ Miscanthus-derived C ( Based on the δ13C changes in SOM, we showed that the estimated turnover time of old SOM increased by two years per year in 9 years after the vegetation change. The relative increase in the turnover rate of recent microbial C was 3 times faster than that of old C indicating preferential utilization of available recent C versus the old C. Combining long-term field observations with soil incubation reveals that the turnover time of C in microbial biomass was 200 times faster than in total SOM. Our study clearly showed that estimating the residence time of easily degradable microbial compounds and biomarkers should be done at time scales reflecting microbial turnover times (days) and not those of bulk SOM turnover (years and decades). This is necessary because the absence of C reutilization is a prerequisite for correct estimation of SOM turnover. We conclude that comparing the δ13C signature of linked pools helps calculate the relative turnover of old and recent pools.

Abstract: In salt-affected soils, soil organic carbon (SOC) levels are usually low as a result of poor plant growth; additionally, decomposition of soil organic matter (SOM) may be negatively affected. Soil organic carbon models, such as the Rothamsted Carbon Model (RothC), that are used to estimate carbon dioxide (CO2) emission and SOC stocks at various spatial scales, do not consider the effect of salinity on CO2 emissions and may therefore over-estimate CO2 release from saline soils. Two laboratory incubation experiments were conducted to assess the effect of soil texture on the response of CO2 release to salinity, and to calculate a rate modifier for salinity to be introduced into the RothC model. The soils used were a sandy loam (18.7% clay) and a sandy clay loam (22.5% clay) in one experiment and a loamy sand (6.3% clay) and a clay (42% clay) in another experiment. The water content was adjusted to 75%, 55%, 50% and 45% water holding capacity (WHC) for the loamy sand, sandy loam, sandy clay loam and the clay, respectively to ensure optimal soil moisture for decomposition. Sodium chloride (NaCl) was used to develop a range of salinities: electrical conductivity of the 1:5 soil: water extract (EC1:5) 1, 2, 3, 4 and 5 dS m−1. The soils were amended with 2% (w/w) wheat residues and CO2 emission was measured over 4 months. Carbon dioxide release was also measured from five salt-affected soils from the field for model evaluation. In all soils, cumulative CO2–C g−1 soil significantly decreased with increasing EC1:5 developed by addition of NaCl, but the relative decrease differed among the soils. In the salt-amended soils, the reduction in normalised cumulative respiration (in percentage for the control) at EC1:5 > 1.0 dS m−1 was most pronounced in the loamy sand. This is due to the differential water content of the soils, at the same EC1:5; the salt concentration in the soil solution is higher in the coarser textured soils than in fine textured soils because in the former soils, the water content for optimal decomposition is lower. When salinity was expressed as osmotic potential, the decrease in normalised cumulative respiration with increasing salinity was less than with EC1:5. The osmotic potential of the soil solution is a more appropriate parameter for estimating the salinity effect on microbial activity than the electrical conductivity (EC) because osmotic potential, unlike EC, takes account into salt concentration in the soil solution as a function of the water content. The decrease in particulate organic carbon (POC) was smaller in soils with low osmotic potential whereas total organic carbon, humus-C and charcoal-C did not change over time, and were not significantly affected by salinity. The modelling of cumulative respiration data using a two compartment model showed that the decomposition of labile carbon (C) pool is more sensitive to salinity than that of the slow C pool. The evaluation of RothC, modified to include the decomposition rate modifier for salinity developed from the salt-amended soils, against saline soils from the field, suggested that salinity had a greater effect on cumulative respiration in the salt-amended soils. The results of this study show (i) salinity needs to be taken into account when modelling CO2 release and SOC turnover in salt-affected soils, and (ii) a decomposition rate modifier developed from salt-amended soils may overestimate the effect of salinity on CO2 release.

Abstract: It is generally accepted that during the early stages of residue decomposition, easily available compounds are decomposed, leading to a relative increase in more recalcitrant compounds in the later stages of decomposition and that these changes in substrate availability are associated with changes in microbial community composition. However most studies on residue decomposition are conducted over several weeks or months; little is known about the changes in microbial community composition in the first weeks of decomposition. To address this knowledge gap, we incubated wheat residues inoculated with a microbial suspension in mesh bags buried in sand for 30 days, with sampling on days 0, 2, 4, 6, 8, 10, 15, 20, 25 and 30. Of the C added with the residues, 10, 18 and 25% had been respired on days 10, 20 and 30, respectively. The sum of PLFAs (phospholipid fatty acids), as an indicator of microbial biomass, increased strongly in the first 4 days and then decreased. The concentration of bacterial fatty acids was maximal on days 2 and 4, whereas the concentration of fungal fatty acids peaked on day 15. Microbial community composition (based on PLFA patterns) changed rapidly, with significant changes in the first 8 days and from day 8 to day 20. There were no significant changes in microbial community composition after day 20. The concentration of water-soluble C decreased strongly in the first 8 days, suggesting that the rapid changes in microbial community in this period are related to the changes in water-soluble C. Residue C chemistry, assessed by 13C NMR spectroscopy, changed little during the incubation period. This study showed that microbial community composition in decomposing residues changes rapidly in the first 1–2 weeks, which is, at least partly, the result of competition for the easily available compounds in the water-soluble fraction. After depletion of the water-soluble compounds, the microbial community composition changes more slowly.

Abstract: At the end of the 19th century an experimental study had already reported N gas production during microbial nitrate reduction, which significantly exceeded the amount of nitrate N supplied to the microorganism. The observed excess gas production was suggested to be caused by a reaction of nitrous acid (produced during microbial nitrate reduction) with amino acids contained in the nutrient solution. Since the 1980’s a number of 15N tracer experiments revealed that this biotic excess gas production was based on the formation of hybrid N2O and/or hybrid N2. It was shown that the N–N linkage forms due to a microbially mediated N-nitrosation reaction by which one N atom of nitrite or nitric oxide combines via a nitrosyl intermediate with one N atom of another N species (e.g., amino compound). Because of its cooccurrence with conventional denitrification this process was later on termed “codenitrification”. Although the phenomenon of N2O and N2 formation by codenitrification was recognised over a century ago its impact on global N cycling is still unclear today. Nonetheless, the present literature review reveals codenitrification as a potentially important process of biospheric N cycling since (i) most codenitrifying species are already known as typical denitrifiers (e.g., Pseudomonas sp., Fusarium sp. etc.) and (ii) codenitrification was already reported to occur within the three domains archaea, bacteria, and eukarya (kingdom fungi). Furthermore, the present literature suggests that codenitrification acts not only as an additional source of N gas formation due to a mobilisation of organic N by N-nitrosation, but also acts as an N immobilising process due to a bonding of inorganic N (e.g., from NO3− or NO2−) onto organic compounds due to e.g., N- or even C-nitrosation reactions. From this it can be concluded that N gas formation by codenitrification represents a sub-phenomenon of a variety of possible biotic nitrosation reactions. Moreover, the review reveals that biotic nitrosation also occurs among nitrifying species, even under aerobic conditions. Furthermore, recent studies support the assumption that even anaerobic ammonium oxidation (anammox) appears to be based on biotically mediated N-nitrosation. Therefore, we propose to introduce the term BioNitrosation, which includes all biotically mediated nitrosation reactions resulting either in N gas release or in N immobilisation, independently from the acting microbial species or the environmental conditions.