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Showing papers in "Soil Biology & Biochemistry in 2013"


Journal ArticleDOI
TL;DR: The collective vision of the future of extracellular enzyme research is offered: one that will depend on imaginative thinking as well as technological advances, and be built upon synergies between diverse disciplines.
Abstract: This review focuses on some important and challenging aspects of soil extracellular enzyme research. We report on recent discoveries, identify key research needs and highlight the many opportunities offered by interactions with other microbial enzymologists. The biggest challenges are to understand how the chemical, physical and biological properties of soil affect enzyme production, diffusion, substrate turnover and the proportion of the product that is made available to the producer cells. Thus, the factors that regulate the synthesis and secretion of extracellular enzymes and their distribution after they are externalized are important topics, not only for soil enzymologists, but also in the broader context of microbial ecology. In addition, there are many uncertainties about the ways in which microbes and their extracellular enzymes overcome the generally destructive, inhibitory and competitive properties of the soil matrix, and the various strategies they adopt for effective substrate detection and utilization. The complexity of extracellular enzyme activities in depolymerising macromolecular organics is exemplified by lignocellulose degradation and how the many enzymes involved respond to structural diversity and changing nutrient availabilities. The impacts of climate change on microbes and their extracellular enzymes, although of profound importance, are not well understood but we suggest how they may be predicted, assessed and managed. We describe recent advances that allow for the manipulation of extracellular enzyme activities to facilitate bioremediation, carbon sequestration and plant growth promotion. We also contribute to the ongoing debate as to how to assay enzyme activities in soil and what the measurements tell us, in the context of both traditional methods and the newer techniques that are being developed and adopted. Finally, we offer our collective vision of the future of extracellular enzyme research: one that will depend on imaginative thinking as well as technological advances, and be built upon synergies between diverse disciplines.

1,475 citations


Journal ArticleDOI
TL;DR: A comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from forest to alpine tundra using a bar-coded pyrosequencing technique suggests that pH is a better predictor of soilacterial elevational distribution and also suggests that vegetation types may indirectly affect soil bacterial Elevational distribution through altering soil C and N status.
Abstract: The elevational patterns of diversity for plants and animals have been well established over the past century. However, it is unclear whether there is a general elevational distribution pattern for microbes. Changbai Mountain is one of few well conserved natural ecosystems, where the vertical distribution of vegetation is known to mirror the vegetation horizontal zonation from temperate to frigid zones on the Eurasian continent. Here, we present a comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from forest to alpine tundra using a bar-coded pyrosequencing technique. The bacterial communities differed dramatically along elevations (vegetation types), and the community composition was significantly correlated with soil pH, carbon/nitrogen ratio (C/N), moisture or total organic carbon (TOC), respectively. Phylogenetic diversity was positively correlated with soil pH ( P = 0.024), while phylotype richness was positively correlated with soil pH ( P = 0.004), total nitrogen (TN) ( P = 0.030), and negatively correlated with C/N ratio ( P = 0.021). Our results emphasize that pH is a better predictor of soil bacterial elevational distribution and also suggest that vegetation types may indirectly affect soil bacterial elevational distribution through altering soil C and N status.

721 citations


Journal ArticleDOI
TL;DR: In this article, the authors provide an overview and new insights into the mechanisms involved in the respiration-moisture relationship, and provide the best estimates of average empirical relationships using published data and comparing the results for contrasting soil types.
Abstract: Soil moisture strongly affects the dynamics of soil organic matter and is an important environmental variable in all models predicting changes in soil carbon stocks from site to global scales. Despite this, the mechanisms determining the response of heterotrophic soil respiration to soil moisture remain poorly quantified, being represented in most current carbon cycle models as simple empirical functions. With the aim of providing an overview and new insights into the mechanisms involved, here we review the observations and theory behind the respiration-moisture relationship. We start by calculating best estimates of average empirical relationships using published data and comparing the results for contrasting soil types. The theoretical linkages between substrate and gas diffusivity in soil pores and heterotrophic respiration are then explored as a function of temperature and textural properties. Based on this theoretical model we interpret the variability of moisture effects observed in previous empirical studies. Transient CO2 efflux–moisture relationships are discussed next, reviewing the theory and models developed in the last years with particular emphasis on the ‘Birch effect’. We continue by giving an overview of recent pore-scale models and consider how these can be used to gain a more mechanistic understanding of carbon storage and stabilization in variably saturated soils. From this review we conclude that current empirical models are useful but limited approximations, with questionable predictive capacity. Significant efforts are still necessary to represent the full range of soil moisture responses in a unifying model with a sound theoretical basis that can help identify common underlying processes. Equations present here, combining diffusion, texture and substrate to model respiration, are a step forward in this direction.

645 citations


Journal ArticleDOI
TL;DR: Because active microorganisms are the solely microbial drivers of main biogeochemical processes, analyses of the active and potentially active fractions are necessary in studies focused on soil functions.
Abstract: Microbial functioning refers to microbial activity because only the active microorganisms drive biogeochemical processes. Despite the importance of active microorganisms, most methods focus on estimating total microbial biomass and fail to evaluate its active fraction. At first, we have described the differences among the active , potentially active , and dormant microbial states in soil and suggested threshold values of parameters for their identification. Secondly, we critically reviewed the ability of a broad range of approaches to estimate and characterize the active and the potentially active microorganisms in soil. Following approaches were evaluated: plate count and microbial cultures; direct microscopy combined with cell staining; ATP, PLFA, DNA and RNA content; microarray analyses; PCR-based approaches; stable isotope probing; soil proteomics, enzymes activity; and various approaches based on respiration and substrate utilization. The “static” approaches, mainly based on the single-stage determination of cell components (ATP, DNA, RNA, and molecular biomarkers), detect well the presence of microorganisms and total biomass, but they fail to evaluate the active part and consequently the functions. In contrast, the dynamic approaches, estimating the changes of these parameters during microbial growth and based on process rates: substrate utilization and product formation, e.g., respiration, help to evaluate active microbial biomass and relate it to specific process rates. Based on a comparison of all approaches for their universality (possibility to analyze active, potentially active and dormant microorganisms), we concluded that 1) direct microscopy with complementary stains, 2) a combination of RNA-based FISH with staining of total microbial biomass, and 3) approaches based on microbial growth were the most advantageous and allowed simultaneous quantitative estimation of active , potentially active, and dormant microorganisms in soil. The active microorganisms compose only about 0.1–2% of the total microbial biomass and very seldom exceed 5% in soils without input of easily available substrates. Nonetheless, the fraction of potentially active microorganisms (ready to start utilization of available substrates within few hours) is much higher, contributing between 10 and 40% (up to 60%) of the total microbial biomass. Therefore, we emphasize the role of potentially active microorganisms with quick response to fluctuating substrate input in soil microhabitats and hotspots. The transition from the potentially active to the active state occurs in minutes to hours, but the shift from dormant to active state takes anywhere from hours to days. Despite very fast activation, the reverse process – fading to the potentially active and dormant stage – requires a much longer period and is very different for individual criteria: ATP, DNA, RNA, enzyme production, respiration rates. This leads to further difficulties in the estimation of the active part of microbial community by methods based on these parameters. Consequently, the standardization, further elaboration, and broad application of approaches focused on the portion of active microorganisms in soil and their functions are urgently needed. We conclude that because active microorganisms are the solely microbial drivers of main biogeochemical processes, analyses of the active and potentially active fractions are necessary in studies focused on soil functions.

625 citations


Journal ArticleDOI
TL;DR: The role of plant-associated bacteria to enhance trace element availability in the rhizosphere is reviewed and the kind of bacteria typically found in association with trace element – tolerating or – accumulating plants are reported and discussed to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction.
Abstract: Phytoextraction makes use of trace element-accumulating plants that concentrate the pollutants in their tissues. Pollutants can be then removed by harvesting plants. The success of phytoextraction depends on trace element availability to the roots and the ability of the plant to intercept, take up, and accumulate trace elements in shoots. Current phytoextraction practises either employ hyperaccumulators or fast-growing high biomass plants; the phytoextraction process may be enhanced by soil amendments that increase trace element availability in the soil. This review will focus on the role of plant-associated bacteria to enhance trace element availability in the rhizosphere. We report on the kind of bacteria typically found in association with trace element – tolerating or – accumulating plants and discuss how they can contribute to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction. This enhanced trace element uptake can be attributed to a microbial modification of the absorptive properties of the roots such as increasing the root length and surface area and numbers of root hairs, or by increasing the plant availability of trace elements in the rhizosphere and the subsequent translocation to shoots via beneficial effects on plant growth, trace element complexation and alleviation of phytotoxicity. An analysis of data from literature shows that effects of bacterial inoculation on phytoextraction efficiency are currently inconsistent. Some key processes in plant–bacteria interactions and colonization by inoculated strains still need to be unravelled more in detail to allow full-scale application of bacteria assisted phytoremediation of trace element contaminated soils.

547 citations


Journal ArticleDOI
TL;DR: In this article, the level of microbial colonisation on the internal and external surfaces of field-aged biochar was examined by scanning electron microscopy, and used 14C-labeled glucose to quantify the rates of microbial activity in different spatial niches of the biochar and the surrounding soil.
Abstract: Biochar application has become a novel and emergent technology for sequestering C, improving soil quality and crop production, and is a potential win–win strategy for ecosystem service delivery. Biochar addition can also stimulate soil microbial activity, and although it is unclear exactly why biochar should benefit soil microorganisms, it is thought that the large surface area and volume of pores provide a significant habitat for microbes. The aim of this study was to determine the level of microbial colonisation of wood-derived biochar that had been buried in an agricultural soil for three years. We have examined the level of colonisation on the internal and external surfaces of field-aged biochar by scanning electron microscopy, and used 14C-labelled glucose to quantify the rates of microbial activity in different spatial niches of the biochar and the surrounding soil. Microbial colonisation of field-aged biochar was very sparse, with no obvious differences between the external and internal surfaces. At the high field application rate of 50 t ha−1, biochar contributed only 6.52 ± 0.11% of the total soil pore space and 7.35 ± 0.81% of the total soil surface area of the topsoil (0–30 cm). Further, 17.46 ± 0.02% of the biochar pores were effectively uninhabitable for most microbes, being

410 citations


Journal ArticleDOI
TL;DR: High stochasticity in individual PCR reactions and distance decay analysis indicated that community similarity decreased slightly with geographical distance, suggesting that sampling of soil fungal communities is more exhaustive, if the authors combine repeated PCR products, and PCR products generated at various annealing temperatures.
Abstract: Next generation metabarcoding is becoming an indispensable tool in fungal community ecology. Here we tested Illumina metabarcoding, a method that generates shorter reads but achieves deeper sequencing than 454 metabarcoding approaches. We found that paired-end Illumina MiSeq data cover the full ITS1 in many fungal lineages and are suitable for environmental fungal community assessment. There was substantial read loss during data cleanup (78.6%), which, however, did not impede the analyses, because of the large number of initial sequences (over 4Mio). We observed a high stochasticity in individual PCR reactions. Comparing three repeated sets of PCRs products showed that 58.5% of the total fungal operational taxonomic units (OTUs) found were not recovered by any single set of PCR reactions. Similarly, comparing three annealing temperatures showed that 63.6% of all fungal OTUs were not recovered using any single annealing temperature. These findings suggest that sampling of soil fungal communities is more exhaustive, if we combine repeated PCR products, and PCR products generated at various annealing temperatures. To analyze the above issues we sampled 16 soil cores along a 270 cm transect in a meadow. In total we recovered 3320 fungal OTUs (based on a 95% similarity threshold). Distance decay analysis indicated that community similarity decreased slightly with geographical distance.

349 citations


Journal ArticleDOI
TL;DR: In this paper, the effect of four different biochar additions on the emission of the greenhouse gases CO2 and N2O, two incubation experiments were established in a temperate sandy loam soil.
Abstract: Biochar produced during pyrolysis of biomass has the potential to reduce greenhouse gas (GHG) emissions from soils. In order to evaluate the effect of four different biochar additions on the emission of the greenhouse gases CO2 and N2O, two incubation experiments were established in a temperate sandy loam soil. Digestate, a waste-product of the wet fermentation of swine manure, and willow wood was slowly pyrolyzed at 350 °C and 700 °C, yielding four biochar types (DS350, DS700, WS350 and WS700). In the first incubation experiment (117 days), C mineralization was monitored in soil amended with biochar at a quantity of 10 Mg ha−1 on an area-basis (biochar to soil ratio of 1:69 on a mass basis) at 50% water filled pore space (WFPS). CO2 emissions from the 350 °C biochar treatments were significantly higher than the control (no biochar) treatment, while we observed no significantly different net C mineralization in the treatments with the 700 °C biochars compared to the control. After fitting a combined zero- plus first-order model to the cumulative C mineralization data, the parameter for the easily mineralizable C pool (CAf) positively correlated with the volatile matter (VM) contents of the biochars. Microbial biomass carbon consistently increased due to all biochar additions, while the dehydrogenase activity increased in the 350 °C biochar treatments but decreased in the 700 °C biochar treatments. Principal component analysis (PCA) of the extracted phospholipid fatty acids (PLFAs) demonstrated that divergent microbial community structures established after the addition of all biochars. The markers for Gram-positive and Gram-negative bacteria were more abundant in the 350 °C biochar treatments compared to the control and to the other biochar treatments. Net N mineralization was higher in the digestate biochar treatments than in the willow biochar treatments and decreased with increasing pyrolysis temperatures and increasing C:N ratio. In a second incubation experiment (15 days) N2O emissions were measured at WFPS of 70% and the same biochars were added in the same quantity as for C mineralization, with the addition of 40 mg KNO3–N kg−1. The cumulative N2O emission after 15 days was positively correlated with the volatile matter content of the biochars and was significantly lower in the 700 °C biochar treatments compared to the control, while no significant differences were found for the 350 °C biochar treatments. This study suggests that volatile matter content could be an important property of biochars in explaining short-term CO2 and N2O emissions from biochar-amended soils.

333 citations


Journal ArticleDOI
TL;DR: In this paper, the effect of N, P and S availability on the net humification efficiency (NHE) following incubation of soil with wheaten straw was investigated, showing that inorganic nutrient availability is critical to sequester C into the more stable FF-SOM pool irrespective of soil type and C input.
Abstract: The more stable fine fraction pool of soil organic matter (FF-SOM; <0.4 mm) has more nitrogen, phosphorus and sulphur (N, P, S) per unit of carbon (C) than the plant material from which it originates and has near constant ratios of C:N:P:S. Consequently, we hypothesised that the sequestration of C-rich crop residue material into the FF-SOM pool could be improved by adding supplementary nutrients to the residues based on these ratios. Here we report on the effect of N, P and S availability on the net humification efficiency (NHE), the change in the size of the FF-SOM pool (as estimated by fine fraction C (FF-C)), following incubation of soil with wheaten straw. Four diverse soils were subjected to seven consecutive incubation cycles, with wheaten straw (10 t ha equivalent) added at the beginning of each cycle, with and without inorganic N, P, S addition (5 kg N, 2 kg P and 1.3 kg S per tonne of straw). This nutrient addition doubled the mean NHE in all soils (from 7% to 15%) and when applied at twice the rate increased NHE further (up to 29%) for the two soils that received this treatment. The FF-N, -P and -S levels increased in concert with FF-C levels in all soils in close agreement with published stoichiometric ratios (C:N:P:S = 10,000:833:200:143). Microbial biomass-C (MB-C) levels were estimated during one incubation cycle and found to increase in parallel with FF-C from 448 μg MB-C g soil (no nutrient addition) to 727 μg MB-C g soil (plus nutrients) and 947 μg MB-C g soil (plus 2× nutrients). There was a significant relationship between MB-C and the change in FF-C during that incubation cycle, providing evidence of a close relationship between the microbial biomass and FF-SOM formation. The two to four-fold increases in NHE achieved with nutrient addition demonstrated that inorganic nutrient availability is critical to sequester C into the more stable FF-SOM pool irrespective of soil type and C input. This has important implications for strategies to build soil fertility or mitigate climate change via increased soil organic C, as the availability and value of these nutrients must be considered.

268 citations


Journal ArticleDOI
TL;DR: In this article, two biochars were prepared at 350 °C and 700 °C (BC700) from Miscanthus giganteus, a C4 plant, naturally enriched with 13C.
Abstract: Biochar has been widely proposed as a soil amendment, with reports of benefits to soil physical, chemical and biological properties. To quantify the changes in soil microbial biomass and to understand the mechanisms involved, two biochars were prepared at 350 °C (BC350) and 700 °C (BC700) from Miscanthus giganteus, a C4 plant, naturally enriched with 13C. The biochars were added to soils of about pH 4 and 8, which were both sampled from a soil pH gradient of the same soil type. Isotopic (13C) techniques were used to investigate biochar C availability to the biomass. Scanning Electron Microscopy (SEM) was used to observe the microbial colonization, and Attenuated Total Reflectance (ATR) to highlight structural changes at the surface of the biochars. After 90 days incubation, BC350 significantly increased the biomass C concentration relative to the controls in both the low (p < 0.05) and high pH soil (p < 0.01). It declined between day 90 and 180. The same trend occurred with soil microbial ATP. Overall, biomass C and ATP concentrations were closely correlated over all treatments (R2 = 0.87). This indicates that neither the biomass C, nor ATP analyses were affected by the biochars, unless, of course, they were both affected in the same way, which is highly unlikely. About 20% of microbial biomass 13C was derived from BC350 after 90 days of incubation in both low and high pH soils. However, less than 2% of biomass 13C was derived from BC700 in the high pH soil, showing very low biological availability of BC700. After 90 days of incubation, microbial colonization in the charsphere (defined here as the interface between soil and biochar) was more pronounced with the BC350 in the low pH soil. This was consistent with the biomass C and ATP results. The microbial colonization following biochar addition in our study was mainly attributed to biochar C availability and its large surface area. There was a close linear relationship between 13CO2 evolved and biomass 13C, suggesting that biochar mineralization is essentially a biological process. The interactions between non-living and living organic C forms, which are vital in terms of soil fertility and the global C cycle, may be favoured in the charsphere, which has unique properties, distinct from both the internal biochar and the bulk soil.

245 citations


Journal ArticleDOI
TL;DR: In this paper, the authors review the drivers structuring fungal, bacterial and archaeal communities in natural peatlands and the response of these microbial communities to natural and anthropogenic disturbances, including fire, drainage, nutrient deposition, peat mining and climate change.
Abstract: Even though large extents of boreal peatlands are still in a pristine condition, especially in North America, extensive areas have been affected by natural or anthropogenic disturbances that change some of the systems from being sinks to sources of carbon dioxide and shift the methane production/consumption patterns through alterations of both above- and below-ground communities and functions. In order to fully assess the role of peatlands on global C balance, now and in the future, it is imperative that we deepen our understanding of the relative contributions of various groups of microorganisms to organic matter transformations. Here, we review the drivers structuring fungal, bacterial and archaeal communities in natural peatlands and the response of these microbial communities to natural and anthropogenic disturbances, including fire, drainage, nutrient deposition, peat mining and climate change. The microbial diversity in peatlands is characterized by organisms that have developed physiological and metabolic adaptations to cope with the constraining conditions found in these ecosystems, such as low oxygen availability, cold temperature, acidity and oligotrophy. Furthermore, these unique organisms sometimes appear to be organized as repeat mosaics responding to vegetation, physico-chemical and hydrological characteristics more than to geographical distance, in other words, similar to the much valued biodiversity aspects of the peatland vegetation itself and associated higher organisms. The response of microbial communities to disturbances is far from fully understood. In particular, whilst many studies have identified changes in microbial community composition or on microbially driven processes following a given disturbance, it remains unclear how the two components, diversity and function, relate with each other. Future challenges involve designing studies that will test whether ecological theories like species sorting, stress physiology, temporal niche or functional redundancy can be used to understand what regulates microbial populations and activity in peatlands, and studies that will allow us to predict more accurately how peatlands respond to global change or anthropogenic disturbances.

Journal ArticleDOI
TL;DR: In this paper, the authors investigated the role of biopores in the nutrient acquisition from arable subsoils and found that subsoil can contribute to more than two-thirds of the plant nutrition of N, P and K, especially when the topsoil is dry or nutrient depleted.
Abstract: In arable farming systems, the term ‘subsoil’ refers to the soil beneath the tilled or formerly tilled soil horizon whereas the latter one is denoted as ‘topsoil’. To date, most agronomic and plant nutrition studies have widely neglected subsoil processes involved in nutrient acquisition by crop roots. Based on our current knowledge it can be assumed that subsoil properties such as comparatively high bulk density, low air permeability, and poverty of organic matter, nutrients and microbial biomass are obviously adverse for nutrient acquisition, and sometimes subsoils provide as little as less than 10% of annual nutrient uptake in fertilised arable fields. Nevertheless, there is also strong evidence indicating that subsoil can contribute to more than two-thirds of the plant nutrition of N, P and K, especially when the topsoil is dry or nutrient-depleted. Based on the existing literature, nutrient acquisition from arable subsoils may be conceptualised into three major process components: (I) mobilisation from the subsoil, (II) translocation to the shoot and long-term accumulation in the Ap horizon and (III) re-allocation to the subsoil. The quantitative estimation of nutrient acquisition from the subsoil requires the linking of field experiments with mathematical modelling approaches on different spatial scales including Process Based Models for the field scale and FunctionaleStructural Plant Models for the plant scale. Possibilities to modify subsoil properties by means of agronomic management are limited, but ‘subsoiling’ e i.e. deep mechanical loosening e as well as the promotion of biopore formation are two potential strategies for increasing access to subsoil resources for crop roots in arable soils. The quantitative role of biopores in the nutrient acquisition from the subsoil is still unclear, and more research is needed to determine the bioaccessibility of nutrients in subsoil horizons.

Journal ArticleDOI
TL;DR: In this article, the authors explored the effects of soil temperature and seasonality on the sizes of extracellular enzyme pools and activities in a temperate hardwood forest soil with dominant Quercus petraea (cambisol, mean annual temperature 9.3°C).
Abstract: The activities of extracellular enzymes that participate in the decomposition of litter and organic matter in forest soils depend on, among other factors, temperature and soil moisture content and also reflect the quality of litter, which changes dramatically after a short litterfall period. Here, we explored the effects of soil temperature and seasonality on the sizes of extracellular enzyme pools and activities in a temperate hardwood forest soil with dominant Quercus petraea (cambisol, mean annual temperature 9.3 °C). We hypothesized that the most significant variation of enzyme activity would occur in the litter, which faces greater variations in temperature, moisture content and chemical quality during the season, which decrease with soil depth. The site exhibited relatively large seasonal temperature differences and moderate changes in soil moisture content. Enzyme activity, microbial biomass, soil moisture content, temperature and pH were monitored for three years in the litter (L), organic horizon (O) and upper mineral horizon (Ah). Enzyme activity in vitro strongly increased with temperature until 20–25 °C, the highest temperatures recorded in situ. While no significant differences in the pools of most extracellular enzymes and in the content of microbial biomass were found among the seasons, enzyme activity typically increased during the warm period of the year, especially in the O and Ah horizons. Approximately 63%, 64%, and 69% of total annual activity was recorded during the warm period of the year in the L, O, and Ah horizons, respectively. Significant positive correlations were observed between soil moisture content and fungal biomass, but not bacterial biomass, indicating a decrease of the fungal/bacterial biomass ratio under dry conditions. The effect of moisture on enzyme activities was not significant except for endoxylanase in the litter. If soil temperature rises as predicted due to global climate change, enzyme activity is predicted to rise substantially in this ecosystem, especially in winter, when decomposition is not limited by drought and fresh litter that can decompose rapidly is present.

Journal ArticleDOI
TL;DR: In this article, a data synthesis was performed to summarize information available in the literature on the temperature sensitivity of soil respiration obtained in laboratory soil incubations and expressed as Q10.
Abstract: The temperature sensitivity of soil respiration is a main factor determining the response of global terrestrial soil carbon to global warming and, consequently, its feedback on atmospheric CO2 concentrations. A data synthesis was performed to summarize information available in the literature on the temperature sensitivity of soil respiration obtained in laboratory soil incubations and expressed as Q10. The influence of common experimental variables and methods, i.e. range of incubation temperatures, length of incubation, calculation methods, and amounts of soil organic carbon, was analyzed. We found a small but significant difference between the Q10 values calculated with different experimental methods as well as time-related trends showing an initial decrease followed by stable values. Q10 values ranged from 0.5 to over 300 and were negatively correlated with temperature, but only at the range of temperatures below 25 °C. A similar dependence of the activation energy (derived from the Arrhenius equation) with temperature was observed. A negative relationship with total organic carbon content of soils was found in forest and grassland ecosystems, with an average decrease in Q10 of 0.02 mgC g−1 soil, explaining their slightly lower mean Q10s compared to cultivated soils. Because most of the observed variability remained unexplained, we emphasize the need for new approaches in future studies to the problem of understanding the temperature sensitivity of soil organic matter decomposition.

Journal ArticleDOI
TL;DR: It was found that zero tillage most affected the bacterial communities, while crop residue management affected the microbial communities more than when conventional tillage was applied, indicating that even though phylotypes changed, the number and diversity of theacterial communities were similar.
Abstract: In this study, the effect of limited tillage versus traditional tillage, residue retention versus removal and crop rotation (maize–wheat) versus monoculture (maize) on the bacterial community structure in soils was investigated by means of 454 pyrosequencing of the 16S rRNA gene. Using taxonomic and phylogenetic information it was found that zero tillage most affected the bacterial communities. The relative abundance of Actinobacteria, Betapreoteobacteria and Gammaproteobacteria was affected by tillage and correlated to the total organic carbon (TOC) and clay content in soil. Residue management had a significant effect on the bacterial community structure when phylogenetic membership and the total enumeration of bacteria were considered. Residue management affected the relative abundance of Bacteroidetes, Betaproteobacteria, Cyanobacteria and Gemmatimonadetes. When no tillage was applied, crop residue management affected the microbial communities more than when conventional tillage was applied. Wheat–maize rotation or crop monoculture did not affect the bacterial community structure. No significant differences in richness, diversity and total abundance of bacteria was found between the treatments. This indicated that even though phylotypes changed, the number and diversity of the bacterial communities were similar.

Journal ArticleDOI
TL;DR: In this paper, the authors show that microbial P mineralization can be a side effect of microbial C acquisition from which plants potentially can benefit, but only a small proportion of the P is incorporated into the microbial biomass.
Abstract: Despite the importance of phosphorus (P) mineralization to maintain soil fertility, little is known about the mechanisms that regulate microbial P mineralization. We tested the hypothesis that microbial P mineralization can be driven by microbial need for carbon (C). For this purpose, net microbial uptake kinetics of 14 C and 33 P from glucose-6-phosphate were studied in a Leptosol depending on availability of C, nitrogen (N), and P. After 60 h of incubation, 16.4% of the 14 C from glucose-6-phosphate was recovered in the microbial biomass, while 33 P incorporation into the microbial biomass was a third less. The higher net uptake of 14 C than of 33 P from the glucose-6-phosphate indicates that soil microorganisms use the organic moiety of phosphorylated organic compounds as a C source, but only use a small proportion of the P. Hence, they mineralize P without incorporating it. Our finding that the net uptake of 14 C and 33 P in the soils amended with inorganic P did not differ from the control treatment indicates that P mineralization was not driven by microbial need for P but rather for C. In a second experiment with three temperate forest soils we found that the activity of 14 C from glucose-6-phosphate in soil solution decreased faster than the activity of 33 P from glucose-6-phosphate. This might suggest that higher net uptake of C than of P from glucose-6-phosphate can also be observed in other temperate forest soils differing in C, N, and P contents from the Leptosol of the main experiment. In conclusion, the experiments show that microbial P mineralization can be a side-effect of microbial C acquisition from which plants potentially can benefit.

Journal ArticleDOI
TL;DR: The need to extend the application of current methods to focus on a greater range of habitats and mycorrhizal types enabling incorporation of mycor rhizal fungal biomass and turnover into biogeochemical cycling models is highlighted.
Abstract: Mycorrhizal fungi constitute a considerable sink for carbon in most ecosystems. This carbon is used for building extensive mycelial networks in the soil as well as for metabolic activity related to nutrient uptake. A number of methods have been developed recently to quantify production, standing biomass and turnover of extramatrical mycorrhizal mycelia (EMM) in the field. These methods include minirhizotrons, in-growth mesh bags and cores, and indirect measurements of EMM based on classification of ectomycorrhizal fungi into exploration types. Here we review the state of the art of this methodology and discuss how it can be developed and applied most effectively in the field. Furthermore, we also discuss different ways to quantify fungal biomass based on biomarkers such as chitin, ergosterol and PLFAs, as well as molecular methods, such as qPCR. The evidence thus far indicates that mycorrhizal fungi are key components of microbial biomass in many ecosystems. We highlight the need to extend the application of current methods to focus on a greater range of habitats and mycorrhizal types enabling incorporation of mycorrhizal fungal biomass and turnover into biogeochemical cycling models.

Journal ArticleDOI
TL;DR: Soil zymography with fluorescent substrates is a very promising approach for studying the distribution of a broad range of extracellular enzymes at microscales and indicates a spatial differentiation of organic P mineralization by various ecophysiological groups that react differently to inorganic P fertilization.
Abstract: Despite its importance for terrestrial nutrient and carbon cycling, the spatial organization of microbial activity in soil and in the rhizosphere is poorly understood. We related carbon allocation by roots to distribution of acid and alkaline phosphatase activity in the rhizosphere of Lupinus albus L. To do so, we further developed soil zymography – an in situ method for the analysis of the two-dimensional distribution of enzyme activity in soil – integrating fluorescent substrates. Soil zymography was combined with 14C imaging, a technique that gives insights into the distribution of photosynthates after labeling plants with 14C. Both acid and alkaline phosphatase activity were up to 5.4-times larger in the rhizosphere than in the bulk soil. While acid phosphatase activity (produced by roots and microorganisms) was closely associated with roots, alkaline phosphatase activity (produced only by microorganisms) was more widely distributed, leading to a 2.5-times larger area of activity of alkaline than of acid phosphatase. These results indicate a spatial differentiation of different ecophysiological groups of organic P mineralizing organisms. The spatial differentiation could be either between microorganisms and L. albus or between microorganisms that produce exclusively alkaline phosphatases on the one hand, and L. albus and root associated microorganisms that produce acid phosphatases on the other hand. The spatial separation of different organic P mineralizing organisms might alleviate a potential competition between them. While alkaline phosphatase activity strongly decreased with P fertilization, acid phosphatase activity was not affected by fertilization, suggesting that alkaline phosphatase-producing microorganisms react more strongly to it than other organic P mineralizing organisms. Alkaline phosphatase activity was high in parts of the rhizosphere where relatively little recent photosynthates were allocated, indicating that rhizodeposition and the activity of alkaline phosphatase-producing microorganisms are not directly related. Our study indicates, first, a spatial differentiation of organic P mineralization by various ecophysiological groups that react differently to inorganic P fertilization and second, that rhizodeposition and alkaline phosphatase-producing microorganisms were not directly related. Finally, we conclude that soil zymography with fluorescent substrates is a very promising approach for studying the distribution of a broad range of extracellular enzymes at microscales.

Journal ArticleDOI
TL;DR: In this article, soil samples from 25-year-old experimental plots continuously cropped with barley (Hordeum vulgare L.) under no-tillage (NT) and chisel tillage (CT) were subjected to a new physical fractionation method to isolate dissolved organic matter (OM), mineral-free particulate OM located outside aggregates (physically and chemically unprotected), OM occluded within both macroaggregates and micro aggregates, respectively, and OM in intimate association with minerals (protected by chemical mechanisms).
Abstract: Conservation tillage practices that entail no or reduced soil disturbance are known to help preserve or accumulate soil organic matter (OM). However, the underlying mechanisms especially at the molecular level are not well understood. In this study soil samples from 25-year-old experimental plots continuously cropped with barley (Hordeum vulgare L.) under no-tillage (NT) and chisel tillage (CT) were subjected to a new physical fractionation method to isolate dissolved OM, mineral-free particulate OM located outside aggregates (physically and chemically unprotected), OM occluded within both macroaggregates and microaggregates (weakly and strongly protected by physical mechanisms, respectively), and OM in intimate association with minerals (protected by chemical mechanisms). The whole soils and OM fractions were analyzed for organic C and N content and by modern nuclear magnetic resonance (NMR) techniques. The soil under NT stored 16% more organic C and 5% more N than the soil under CT. Compared to CT, NT increased free organic C content by 7%, intra-macroaggregate organic C content by 20%, intra-microaggregate organic C content by 63%, and mineral-associated organic C content by 16% and decreased dissolved organic C content by 11%. The mineral-associated OM pool accounted for 65% of the difference in total organic C content between NT and CT, whereas the intra-microaggregate OM only explained 18%, intra-macroaggregate OM 14%, and free OM 11%. The NMR experiments revealed that the free and intra-aggregate OM fractions were dominated by crop-derived materials at different stages of decomposition, whereas the mineral-associated OM pool was predominately of microbial origin. Overall, our results indicate that microbes and microbial by-products associated with mineral surfaces and likely physically protected by entrapment within very small microaggregates constitute the most important pool of OM stabilization and C sequestration in soils under NT. Most probably the slower macroaggregate turnover in NT relative to CT boosts not only the formation of microaggregates and thereby the physical protection of crop-derived particulate OM, but more importantly the interaction between mineral particles and microbial material that results in the formation of very stable organo-mineral complexes.

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TL;DR: It is found that ECM and saprotroph richness did not show spatial structure and did not co-vary with any soil resource, and enzymatic activity on ECM root tips took from the same soil cores used for bulk enzyme analysis did not correlate with the activity of any enzyme measured in the bulk soil, suggesting that ECm contributions to larger-scale soil C and nutrient cycling may occur primarily via extramatrical hyphae outside the rhizosphere.
Abstract: The relative roles of ectomycorrhizal (ECM) and saprotrophic communities in controlling the decomposition of soil organic matter remain unclear. We tested the hypothesis that ECM community structure and activity influences the breakdown of nutrient-rich biopolymers in soils, while saprotrophic communities primarily regulate the breakdown of carbon-rich biopolymers. To test this hypothesis, we used high-throughput techniques to measure ECM and saprotrophic community structure, soil resource availability, and extracellular enzyme activity in whole soils and on ECM root tips in a coastal pine forest. We found that ECM and saprotroph richness did not show spatial structure and did not co-vary with any soil resource. However, species richness of ECM fungi explained variation in the activity of enzymes targeting recalcitrant N sources (protease and peroxidase) in bulk soil. Activity of carbohydrate- and organic P- targeting enzymes (e.g. cellobiohydrolase, β-glucosidase, α-glucosidase, hemicellulases, N-acetyl-glucosaminidase, and acid phosphatase) was correlated with saprotroph community structure and soil resource abundance (total soil C, N, and moisture), both of which varied along the soil profile. These observations suggest independent roles of ECM fungi and saprotrophic fungi in the cycling of N-rich, C-rich, and P-rich molecules through soil organic matter. Enzymatic activity on ECM root tips taken from the same soil cores used for bulk enzyme analysis did not correlate with the activity of any enzyme measured in the bulk soil, suggesting that ECM contributions to larger-scale soil C and nutrient cycling may occur primarily via extramatrical hyphae outside the rhizosphere.

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TL;DR: In this paper, the effects of biochar addition on soil moisture, yield of Phleum pratense (timothy), respiration and N2O emissions in mesocosms with a bare mineral soil or P.pratense stand were investigated.
Abstract: Studies in tropical and temperate regions and in the laboratory have shown that the addition of biochar into agricultural soils has potential to mitigate climate change by increasing crop yield per area, decreasing nitrous oxide (N2O) emissions and increasing soil carbon (C) storage. The impacts of biochar on plant productivity and soil processes are, however, highly variable depending on the properties of the biochar and the soil, plant species and environmental conditions. We studied the effects of biochar addition on soil moisture, yield of Phleum pratense (timothy), respiration and N2O emissions in mesocosms with a bare mineral soil or P. pratense stand. Biochar was made from spruce chips under rather low temperatures (400–450 °C) and was mixed into the whole soil layer of 45 cm during the preparation of the mesocosms. The mesocosms were fertilized with ammonium nitrate (NH4NO3;100 kg N ha−1) at the beginning of the experiment and after each harvest. Air temperature was maintained at 20 °C during the daytime and at 15 °C at night. Soil temperature was kept at a constant 15 °C. Biochar increased soil moisture increasing soil respiration and N2O emissions in the bare soil mesocosms, and yield, nitrogen (N) content and N uptake in P. pratense decreasing N2O efflux in the vegetated mesocosms under dry conditions (surface soil moisture 20–30%). Under wet conditions (surface soil moisture 40–50%), N2O emissions increased in the vegetated mesocosms simultaneously with the decreased N uptake in P. pratense harvest. Biochar could thus benefit agriculture, especially during the dry periods of the growing season, but might also increase N2O emissions. Biochar affected N2O efflux indirectly via soil moisture and plant N uptake.

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TL;DR: It was found that role-shifts prevailed among the network members such as generalists/specialists, significant module memberships and the OTU sets irresponsive to soil variables in one network but responsive in the counterpart network.
Abstract: Most previous studies on soil microbial communities have been focused on species abundance and diversity, but not the interactions among species. In present study, the Molecular Ecological Network Analysis tool was used to study the interactions and network organizations of fungal communities in yield-invigorating (healthy) and -debilitating (diseased) soils induced by prolonged potato monoculture, based on the relative abundances of internal transcribed spacer sequences derived using pyrosequencing. An emphasis was placed on the differences between the healthy and diseased networks. The constructed healthy and diseased networks both showed scale-free, small world and modular properties. The key topological properties and phylogenetic composition of the two networks were similar. However, major differences included: a) the healthy network had more number of functionally interrelated operational taxonomic units (OTUs) than the diseased one; b) healthy network contained 6 (4%) generalist OTUs whereas the diseased contained only 1 (0.6%) marginal generalist OTU; and c) majority (55%) of OTUs in healthy soils were stimulated by a certain set of soil variables but the majorities (63%) in diseased soils were inhibited. Based on these data, a conceptual picture was synthesized: a healthy community was a better organized or a better operated community than the diseased one; a healthy soil was a soil with variables that encouraged majority of fungi whereas a diseased soil discouraged. By comparing the topological roles of different sets of shared OTUs between healthy and diseased networks, it was found that role-shifts prevailed among the network members such as generalists/specialists, significant module memberships and the OTU sets irresponsive to soil variables in one network but responsive in the counterpart network. Soil organic matter was the key variable associated with healthy community, whereas ammonium nitrogen (NH4+–N) and Electrical conductivity (EC) were the key variables associated with diseased community. Major affected phylogenetic groups were Sordariales and Hypocreales.

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TL;DR: In this paper, the authors quantify the effect on emissions of carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) following the addition of two different types of biochar to an Irish tillage soil.
Abstract: The application of biochar produced from wood and crop residues, such as sawdust, straw, sugar bagasse and rice hulls, to highly weathered soils under tropical conditions has been shown to influence soil greenhouse gas (GHG) emissions. However, there is a lack of data concerning GHG emissions from soils amended with biochar derived from manure, and from soils outside tropical and subtropical regions. The objective of this study was to quantify the effect on emissions of carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) following the addition, at a rate of 18 t ha−1, of two different types of biochar to an Irish tillage soil. A soil column experiment was designed to compare three treatments (n = 8): (1) non-amended soil (2) soil mixed with biochar derived from the separated solid fraction of anaerobically digested pig manure and (3) soil mixed with biochar derived from Sitka Spruce (Picea sitchensis). The soil columns were incubated at 10 °C and 75% relative humidity, and leached with 80 mL distilled water, twice per week. Following 10 weeks of incubation, pig manure, equivalent to 170 kg nitrogen ha−1 and 36 kg phosphorus ha−1, was applied to half of the columns in each treatment (n = 4). Gaseous emissions were analysed for 28 days following manure application. Biochar addition to the soil increased N2O emissions in the pig manure-amended column, most likely as a result of increased denitrification caused by higher water filled pore space and organic carbon (C) contents. Biochar addition to soil also increased CO2 emissions. This was caused by increased rates of C mineralisation in these columns, either due to mineralisation of the labile C added with the biochar, or through increased mineralisation of the soil organic matter.

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TL;DR: In this paper, the authors performed a laboratory incubation experiment to address the following questions: 1) Does the temperature sensitivity differ between freshly added organic matter and bulk soil carbon? 2) Do the addition of fresh organic matter stimulate the decomposition of soil organic matter (priming effect) and 3) If so, does this priming effect depend on temperature?
Abstract: The effect of temperature and the influence of fresh substrate addition on soil organic matter decomposition are two key factors we need to understand to forecast soil carbon dynamics under climate change and rising CO 2 levels. Here we perform a laboratory incubation experiment to address the following questions: 1) Does the temperature sensitivity differ between freshly added organic matter and bulk soil carbon? 2) Does the addition of fresh organic matter stimulate the decomposition of soil organic matter (“priming effect”)? 3) If so, does this priming effect depend on temperature? In our study, we incubated sieved soil samples without and with two labelled plant litters with different 13 C signals for 199 days. The incubations were performed with two diurnal temperature treatments (5–15 °C, 15–25 °C) in a flow-through soil incubation system. Soil CO 2 production was continuously monitored with an infrared gas analyser, while the 13 C signal was determined from gas samples. Phospholipid fatty acids (PLFA) were used to quantify microbial biomass. We observed that the instantaneous temperature sensitivity initially did not differ between the original and the amended soil. However in the amended treatment the temperature sensitivity slightly but significantly increased during the incubation time, as did the PLFA amount from microbial biomass. Further, we found that addition of fresh plant material increased the rate of decomposition of the original soil organic matter. On a relative basis, this stimulation was similar in the warm and cold treatments (46% and 52%, respectively). Overall our study contrasts the view of a simple physico-chemically derived substrate–temperature sensitivity relationship of decomposition. Our results rather request an explicit consideration of microbial processes such as growth and priming effects.

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Shixiu Zhang1, Qi Li1, Ying Lü1, Xiaoping Zhang1, Wenju Liang1 
TL;DR: In this paper, the contribution of soil biota induced by tillage systems to carbon sequestration among different aggregate size fractions was evaluated and it was found that the increase in microbial biomass and nematode abundance and the alteration in their community composition at the micro-niche within aggregates could contribute to the higher C sequestration.
Abstract: It is increasingly believed that substantial soil organic carbon (SOC) can be sequestered in conservation tillage system by manipulating the functional groups of soil biota. Soil aggregates of different size provide diverse microhabitats for soil biota and consequently influence C sequestration. Our objective was to evaluate the contributions of soil biota induced by tillage systems to C sequestration among different aggregate size fractions. Soil microbial and nematode communities were examined within four aggregate fractions: large macroaggregates (>2 mm), macroaggregates (2e1 mm), small macroaggregates (1e0.25 mm) and microaggregates ( 1 mm aggregate fractions were different from those in 1m m aggregates, while more gram-positive bacteria and plant-parasitic nematodes might increase C accumulation within <1 mm aggregates. Our findings suggested that the increase in microbial biomass and nematode abundance and the alteration in their community composition at the micro-niche within aggregates could contribute to the higher C sequestration in conservation tillage systems (NT and RT). 2013 Elsevier Ltd. All rights reserved.

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TL;DR: In this paper, solid state 13C NMR spectroscopy and proximate chemical analysis have been used to characterize litter organic C in a litterbag experiment with 64 different litter types decomposing under controlled conditions of temperature and water content.
Abstract: Predictions of litter decomposition rates are critical for modelling biogeochemical cycling in terrestrial ecosystems and forecasting organic carbon and nutrient stock balances. Litter quality, besides climatic conditions, is recognized as a main factor affecting decay rates and it has been traditionally assessed by the C/N and lignin/N ratios of undecomposed materials. Here, solid state 13C NMR spectroscopy and proximate chemical analysis have been used to characterize litter organic C in a litterbag experiment with 64 different litter types decomposing under controlled conditions of temperature and water content. A statistical comparative analysis provided evidence that C/N and lignin/N ratios, showing different trends of correlation with decay rates at different decomposition stages, can be used to describe the quality of undecomposed litter, but are unable to predict mass loss of already decomposed materials. A principal component regression (PCR) model based on 13C NMR spectra, fitted and cross-validated by using either two randomly selected sets of litter types, showed highly fitting predictions of observed decay rates throughout the decomposition process. The simple ratio 70–75/52–57 corresponding to O-alkyl C of carbohydrates and methoxyl C of lignin, respectively, showed the highest correlation with decay rate among different tested parameters. These findings enhance our understanding of litter quality, and improve our ability to predict decomposition dynamics. The 13C NMR-based 70–75/52–57 ratio is proposed as an alternative to C/N and lignin/N ratios for application in experimental and modelling work.

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TL;DR: This work compared three substrates commonly used to assay phenol oxidase and peroxidase in soil and compared activities, finding that activities on the substrates followed the trend PYGL > L-DOPA > ABTS and were inversely related to substrate redox potential.
Abstract: Microbial phenol oxidases and peroxidases mediate biogeochemical processes in soils, including microbial acquisition of carbon and nitrogen, lignin degradation, carbon mineralization and sequestration, and dissolved organic carbon export. Measuring oxidative enzyme activities in soils is more problematic than assaying hydrolytic enzyme activities because of the non-specific, free radical nature of the reactions and complex interactions between enzymes, assay substrates, and the soil matrix. We compared three substrates commonly used to assay phenol oxidase and peroxidase in soil: pyrogallol (PYGL, 1,2,3-trihydroxybenzene), L-DOPA (L-3,4-dihydroxyphenylalanine), and ABTS (2,2 0 -azino-bis(3ethylbenzthiazoline-6-sulfonic acid). We measured substrate oxidation in three soils across a pH gradient from 3.0 to 10.0 to determine the pH optimum for each substrate. In addition, we compared activities across 17 soils using the three substrates. In general, activities on the substrates followed the trend PYGL > L-DOPA > ABTS and were inversely related to substrate redox potential. PYGL and ABTS were not suitable substrates at pH > 5, and ABTS oxidation often declined with addition of peroxide to the assay. Absolute and relative oxidation rates varied widely among substrates in relation to soil type and assay pH. We also tested whether autoclaved or combusted soils could be used as negative controls for the influence of abiotic factors (e.g., soil mineralogy) on oxidative activity. However, neither autoclaving nor combustion produced reliable negative controls because substrate oxidation still occurred; in some cases, these treatments enhanced substrate oxidation rates. For broad scale studies, we recommend that investigators use all three substrates to assess soil oxidation potentials. For focused studies, we recommend evaluating substrates before choosing a single option, and we recommend assays at both the soil pH and a reference pH (e.g., pH 5.0) to determine the effect of assay pH on oxidase activity. These recommendations should contribute to greater comparability of oxidase potential activities across studies.

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TL;DR: In this paper, two soils from adjacent forest and grassland sites in central Alberta were subjected to different pH treatments to evaluate the short-term effects of pH on soil gross N transformations using the 15 N tracing technique.
Abstract: Soil pH can be affected by land use change and acid deposition and is one of the primary regulators of nutrient cycling in the soil. In this study, two soils from adjacent forest and grassland sites in central Alberta were subjected to different pH treatments to evaluate the short-term effects of pH on soil gross N transformations using the 15 N tracing technique and calculated by the numerical model FLUAZ. For the forest soil, gross N H 4 + immobilization increased faster than gross N mineralization rates with increasing soil pH, leading to a declining pattern in net N mineralization rates; however, none of those rates changed with pH in the grassland soil. In contrast, the increase in pH significantly stimulated gross and net nitrification rates while soil acidification decreased gross and net nitrification rates for both the forest and grassland soils. The ratio of gross nitrification to gross N H 4 + immobilization rates (N/IA) was significantly increased by KOH addition but declined to nearly zero by HCl addition for each soil. The low and high KCl addition treatments partially or completely inhibited gross nitrification rates, respectively, but gross mineralization was less sensitive to salt additions than the nitrification process. We conclude that based on the short-term laboratory incubation experiments both pH and salt (osmotic effect) affected gross N transformations and pH had contrasting effects on gross and net nitrogen mineralization but not on nitrification in the adjacent forest and grassland soils.

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TL;DR: Analysis of the microbial community that developed after 4 years of testing different soil-crop management systems in the savannah–forest transition zone of Eastern Ghana indicated that members of the Acidobacteria GP4 and GP6 were more abundant in soils with relatively high SOC whereas Acidob bacteria GP1, GP7, and Actinobacteria were more prevalent in soil with lower SOC.
Abstract: We analyzed the microbial community that developed after 4 years of testing different soil-crop management systems in the savannah–forest transition zone of Eastern Ghana where management systems can rapidly alter stored soil carbon as well as soil fertility. The agricultural managements were: (i) the local practice of fallow regrowth of native elephant grass ( Pennisetum purpureum ) followed by biomass burning before planting maize in the spring, (ii) the same practice but without burning and the maize receiving mineral nitrogen fertilizer, (iii) a winter crop of a legume, pigeon pea ( Cajanus cajan ), followed by maize, (iv) vegetation free winter period (bare fallow) followed by maize, and (v) unmanaged elephant grass-shrub vegetation. The mean soil organic carbon (SOC) contents of the soils after 4 years were: 1.29, 1.67, 1.54, 0.80 and 1.34%, respectively, differences that should affect resources for the microbial community. From about 290,000 sequences obtained by pyrosequencing the SSU rRNA gene, canonical correspondence analysis showed that SOC was the most important factor that explained differences in microbial community structure among treatments. This analysis as well as phylogenetic ecological network construction indicated that members of the Acidobacteria GP4 and GP6 were more abundant in soils with relatively high SOC whereas Acidobacteria GP1, GP7, and Actinobacteria were more prevalent in soil with lower SOC. Burning of winter fallow vegetation led to an increase in Bacillales, especially those belonging to spore-forming genera. Of the managements, pigeon-pea cultivation during the winter period promoted a higher microbial diversity and also sequestered more SOC, presumably improving soil structure, fertility, and resiliency.

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TL;DR: In this article, a laboratory incubation study was conducted to quantify CO2 and N2O production during sequential dry/wet cycles and under constant soil moisture conditions along a gradient of SOM contents in two soil types representing different texture classes.
Abstract: Soil organic matter (SOM) content and texture are important factors affecting carbon (C) and nitrogen (N) mineralisation under constant soil moisture but their effects on organic matter mineralisation and associated biogenic gas (carbon dioxide (CO2) and nitrous oxide (N2O)) production during dry/wet cycles is poorly understood. A laboratory incubation study was conducted to quantify CO2 and N2O production during sequential dry/wet cycles and under constant soil moisture conditions along a gradient of SOM contents in two soil types representing different texture classes (silt loam vs. clay loam). Three soil moisture treatments were established: wet (WW; field capacity), moderately dry (MD; 120% of soil moisture content (SMC) at wilting point (WP)) and very dry (VD; 80% of SMC at WP). To each of the two ‘dry’ treatments two different dry/wet treatments were applied where the soils were either maintained continuously dry (MD & VD) or subjected to three sequential 20-day long dry/wet cycles (MDW & VDW) during the treatment phase of the experiment. At field capacity soil moisture content, the rate of C mineralisation increased with increases in SOC content and the increase per unit of C was twice as high in silt loam (0.30 mg CO2-C g−1 SOC d−1) as in clay loam (0.13 mg CO2-C g−1 SOC d−1) soils. N2O-N emissions also increased with increasing in SOC content. However, in contrast to C mineralisation, the effect was four-fold greater for clay loam (1.38 μg N2O-N g−1 SOC d−1) than silt loam (0.32 μg N2O-N g−1 SOC d−1) soils. Following rewetting, the VDW and MDW soils produced a short-term C mineralisation flush that was, on average, 30% and 15% greater, respectively, than in WW soils. However, the flush of C mineralisation was not sufficient to compensate for the reduction in mineralisation during the drying phase of each cycle, resulting in a lower total C mineralisation from MDW and VDW soils, on average, compared with WW soils over the three sequential dry/wet cycles. The C mineralisation flush also remained a relatively constant proportion of the total C mineralised from both silt loam (23%) and clay loam soils (22%), irrespective of their SOC content. In contrast, the short-term flush of N2O that followed rewetting of dry soil accounted for 62% and 68% of the total N2O emissions from silt loam and clay loam soils, respectively. On average, the total N2O emissions from dry/wet treatments imposed on silt loam and clay loam soils were 33% and 270% greater, respectively, than from the WW treatments, though the effect varied greatly and depended on SOC content. Overall, N2O emissions were highest where we had a combination of fine texture, an adequate supply of available C (i.e. high SOM content), and a water-filled pore space (WFPS) > 0.60 cm cm−3 at field capacity. Prediction of C mineralisation over dry/wet cycles using mineralisation data from soils at constant moisture content is possible, but knowledge of the stress history for the soil would be required to improve accuracy. The prediction of N2O-N emissions during dry/wet cycles using emission data from soils at constant moisture was very inaccurate, due to the inherent spatial variability of N2O emissions.