Showing papers in "Soil Biology & Biochemistry in 2015"

Microbial hotspots and hot moments in soil: Concept & review

Abstract: Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time – the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the average rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates. For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2–20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output – by decomposition rates of litter – and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. We estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil. By this review, we raised the importance of concepts and ecological theory of distribution and functioning of microorganisms in soil.

Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw

Abstract: Addition of organic matter such as livestock manures and plant residues is a feasible practice to mitigate soil degradation caused by long-term application of chemical fertilizers, and the mitigation is largely mediated though activities of the soil-dwelling microorganisms. However, the roles of different kinds of organic matter in maintaining bacterial community structure have not been assessed in a comparative manner. In this study, 454 pyrosequencing of 16S rRNA gene was employed to compare the bacterial community structure among soils that had been subjected to 30 years of NPK fertilization under six treatment regimes: non-fertilization control, fertilization only, and fertilization combined with the use of pig manure, cow manure or low- and high-level of wheat straws. Consistent with expectation, long-term application of NPK chemical fertilizers caused a significant decrease of bacterial diversity in terms of species richness (i.e. number of unique operational taxonomic units (OTU)), Faith's index of phylogenetic diversity and Chao 1 index. Incorporation of wheat straw into soil produced little effects on bacterial community, whereas addition of either pig manure or cow manure restored bacterial diversity to levels that are comparable to that of the non-fertilization control. Moreover, bacterial abundance determined by quantitative PCR was positively correlated with the nutritional status of the soil (e.g., nitrate, total nitrogen, total carbon, available phosphorus); however, bacterial diversity was predominantly determined by soil pH. Together, our data implicate the role of livestock manures in preventing the loss of bacterial diversity during long-term chemical fertilization, and highlight pH as the major deterministic factor for soil bacterial community structure.

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees

Abstract: In forest ecosystems, trees represent the major primary producers and affect the chemical composition and microbial processes in the ecosystem via specific litter chemistry and rhizodeposition. Effects of trees on the abundance of soil microorganisms have been previously observed but the extent to which trees affect the composition of microbial communities remains unknown. Here we analyse the factors affecting the composition of bacterial and fungal communities in forest litter and soil under seven tree species studied at twenty-eight spatially independent sites of similar age developed on the same initial substrate. Microbial communities differed between litter and soil. Bacterial communities were more diverse than fungal communities, especially in litter, and exhibited higher evenness. Eighty percent of the bacterial sequences belonged to the 200–250 most dominant operational taxonomic units (OTUs), and 80% of the fungal sequences were composed of only 23–28 OTUs. The effect of tree species on the microbial-community composition was significant in both litter and soil for fungi as well as bacteria. In bacteria, the tree effect was likely partly mediated by litter and soil pH. Fungal taxa showed a greater tendency to be tree-specific: 35–37% of the dominant fungal OTUs but only 0–3% of the bacterial OTUs were restricted to 1 or 2 trees, and 15–45% of the fungi and 80% of the bacteria were common under 6 or 7 trees. Microbial taxa were demonstrated to associate with less trees than would be expected based on the patterns of their abundance in samples and the tree identity thus affects their occurrence. The numbers of observed dominant fungal OTUs in the study area increased faster with an increasing numbers of trees, indicating high β-diversity. Although the proportion of the arbuscular mycorrhizal and ectomycorrhizal fungi differed among trees, the tree-specific fungal taxa were both root-symbiotic and saprotrophic. The effect of trees on the composition of microbial community was demonstrated to be stronger than other soil properties and to explain a large proportion of variation in community composition, especially in fungi.

Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: Implications for soil quality

Abstract: Conservation agriculture practices, such as reduced tillage, cover crops and fertilization, are often associated with greater microbial biomass and activity that are linked to improvements in soil quality. This study characterized the impact of long term (31 years) tillage (till and no-till), cover crops (Hairy vetch - Vicia villosa and winter wheat- Triticum aestivum , and a no cover control), and N-rates (0, 34, 67 and 101 kg N ha −1 ) on soil microbial community structure, activity and resultant soil quality calculated using the soil management assessment framework (SMAF) scoring index under continuous cotton ( Gossypium hirsutum) production on a Lexington silt loam in West Tennessee. No-till treatments were characterized by a significantly greater (P Consequently, the total organic carbon (TOC) and β-glucosidase SMAF quality scores were significantly greater under no-till compared to till and under the vetch compared to wheat and no cover treatments, resulting in a significantly greater overall soil quality index (SQI). Our results demonstrate that long-term no-till and use of cover crops under a low biomass monoculture crop production system like cotton results in significant shifts in the microbial community structure, activity, and conditions that favor C, N and P cycling compared to those under conventional tillage practices. These practices also led to increased yields and improved soil quality with no-till having 13% greater yields than till and treatments under vetch having 5% increase in soil quality compared to no cover and wheat.

Salt effects on the soil microbial decomposer community and their role in organic carbon cycling: A review

Abstract: Salinization of soil is recognised as one of the most pressing environmental challenges to resolve for the next century. We here conduct a synoptic review of the available research on how salt affects decomposer microbial communities and carbon (C) cycling in soil. After summarizing known physiological responses of microorganisms to salinity, we provide a brief overview and qualification of a selection of widely applied methods to assess microorganisms in soil to date. The dominant approaches to characterise microbial responses to salt exposure have so far been microbial biomass and respiration measurements. We compile datasets from a selection of studies and find that (1) microbial biomass-carbon (C) per C held in soil organic matter shows no consistent pattern with long-term (field gradients) or short-term (laboratory additions) soil salinity level, and (2) respiration per soil organic C is substantially inhibited by higher salt concentrations in soil, and consistently so for both short-term and long-term salinity levels. Patterns that emerge from extra-cellular enzyme assessments are more difficult to generalize, and appear to vary with the enzyme studied, and its context. Growth based assessments of microbial responses to salinization are largely lacking. Relating the established responses of microbial respiration to that of growth could provide an estimate for how the microbial C-use efficiency would be affected by salt exposure. This would be a valuable predictor for changes in soil C sequestration. A few studies have investigated the connection between microbial tolerance to salt and the soil salinity levels, but so far results have not been conclusive. We predict that more systematic inquiries including comprehensive ranges of soil salinities will substantiate a connection between soil salinity and microbial tolerance to salt. This would confirm that salinity has a direct effect on the composition of microbial communities. While salt has been identified as one of the most powerful environmental factors to structure microbial communities in aquatic environments, no up-to-date sequence based assessments currently exist from soil. Filling this gap should be a research priority. Moreover, linking sequencing based assessments of microbial communities to their tolerance to salt would have the potential to yield biomarker sets of microbial sequences. This could provide predictive power for, e.g., the sensitivity of agricultural soils to salt exposure, and, as such, a useful tool for soil resource management. We conclude that salt exposure has a powerful influence on soil microbial communities and processes. In addition to being one of the most pressing agricultural problems to solve, this influence could also be used as an experimental probe to better understand how microorganisms control the biogeochemistry in soil. (C) 2014 Elsevier Ltd. All rights reserved. (Less)

Sugars in soil and sweets for microorganisms: Review of origin, content, composition and fate

Abstract: Sugars are the most abundant organic compounds in the biosphere because they are monomers of all polysaccharides. We summarize the results of the last 40 years on the sources, content, composition and fate of sugars in soil and discuss their main functions. We especially focus on sugar uptake, utilization and recycling by microorganisms as this is by far the dominating process of sugar transformation in soil compared to sorption, leaching or plant uptake. Moreover, sugars are the most important carbon (C) and energy source for soil microorganisms. Two databases have been created. The 1st database focused on the contents of cellulose, non-cellulose, hot-water and cold-water extractable sugars in soils (348 data, 32 studies). This enabled determining the primary (plant-derived) and secondary (microbially and soil organic matter (SOM) derived) sources of carbohydrates in soil based on the galactose + mannose/arabinose + xylose (GM/AX) ratio. The 2nd database focused on the fate of sugar C in soils (734 data pairs, 32 studies using 13 C or 14 C labeled sugars). 13 C and 14 C dynamics enabled calculating the: 1) initial rate of sugar mineralization, 2) mean residence time (MRT) of C of the applied sugars, and 3) MRT of sugar C incorporated into 3a) microbial biomass and 3b) SOM. The content of hexoses was 3–4 times higher than pentoses, because hexoses originate from plants and microorganisms. The GM/AX ratio of non-cellulose sugars revealed a lower contribution of hexoses in cropland and grassland (ratio 0.7–1) compare to forest (ratio 1.5) soils. 13 C and 14 C studies showed very high initial rate of glucose mineralization (1.1% min −1 ) and much higher rate of sugars uptake by microorganisms from the soil solution. Considering this rate along with the glucose input from plants and its content in soil solution, we estimate that only about 20% of all sugars in soil originate from the primary source – decomposition of plant litter and rhizodeposits. The remaining 80% originates from the secondary source – microorganisms and their residues. The estimated MRT of sugar C in microbial biomass was about 230 days, showing intense and efficient internal recycling within microorganisms. The assessed MRT of sugar C in SOM was about 360 days, reflecting the considerable accumulation of sugar C in microbial residues and its comparatively slow external recycling. The very rapid uptake of sugars by microorganisms and intensive recycling clearly demonstrate the importance of sugars for microbes in soil. We speculate that the most important functions of sugars in soil are to maintain and stimulate microbial activities in the rhizosphere and detritusphere leading to mobilization of nutrients by accelerated SOM decomposition – priming effects. We conclude that the actual contribution of sugar C (not only whole sugar molecules, which are usually determined) to SOM is much higher than the 10 ± 5% commonly measured based on their content.

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China

Abstract: Although the effects of chemical fertilization management on microbial communities in soils have been well studied, few studies have examined such impacts of long-term chemical fertilizations on the microbial community in black soils common to northeast China. We applied high-throughput pyrosequencing and quantitative PCR of the 16S rRNA gene to investigate bacterial communities in a long-term fertilizer experiment started in 1980. The following fertilizer treatments were compared with control plots (no fertilizer): N1 (low nitrogen fertilizer), N2 (high nitrogen fertilizer), N1P1 (low nitrogen plus low phosphorus fertilizers) and N2P2 (high nitrogen plus high phosphorus fertilizers). All fertilization treatments resulted in decreases in soil pH and increases in wheat yield and concentrations of total nitrogen, organic matter and KCl-extractable NO3− and NH4+. Fertilization also led to a significant decrease in total 16S rRNA gene abundance and bacterial diversity. The phyla Proteobacteria, Acidobacteria and Actinobacteria dominated in all fertilized treatments. There was an increase in relative abundance of Actinobacteria, Proteobacteria, TM7 and Verrucomicrobia across all fertilized treatments compared to unfertilized controls, whereas phyla Acidobacteria and Nitrospirae decreased. The bacterial communities in unfertilized controls and lower-mineral fertilizers (i.e. N1 and N1P1) were predominantly composed of Acidobacteria, Actinobacteria and Proteobacteria, and separated from the communities where more concentrated fertilizer regimes were used (i.e. N2 and N2P2) based on principal coordinates analysis. Soil pH and NO3− concentration appeared to be the most important factors in shaping bacterial communities. Our findings suggested that long-term inorganic fertilizer regimes reduced the biodiversity and abundance of bacteria. The influence of more concentrated fertilizer treatments was greater than that of lower concentrations.

Soil microbial biomass C:N:P stoichiometry and microbial use of organic phosphorus

Abstract: Microbial mineralization and immobilization of nutrients strongly influence soil fertility. We studied microbial biomass stoichiometry, microbial community composition, and microbial use of carbon (C) and phosphorus (P) derived from glucose-6-phosphate in the A and B horizons of two temperate Cambisols with contrasting P availability. In a first incubation experiment, C, nitrogen (N) and P were added to the soils in a full factorial design. Microbial biomass C, N and P concentrations were analyzed by the fumigation-extraction method and microbial community composition was analyzed by a community fingerprinting method (automated ribosomal intergenic spacer analysis, ARISA). In a second experiment, we compared microbial use of C and P from glucose-6-phosphate by adding 14 C or 33 P labeled glucose-6-phosphate to soil. In the first incubation experiment, the microbial biomass increased up to 30-fold due to addition of C, indicating that microbial growth was mainly C limited. Microbial biomass C:N:P stoichiometry changed more strongly due to element addition in the P-poor soils, than in the P-rich soils. The microbial community composition analysis showed that element additions led to stronger changes in the microbial community in the P-poor than in the P-rich soils. Therefore, the changed microbial biomass stoichiometry in the P-poor soils was likely caused by a shift in the microbial community composition. The total recovery of 14 C derived from glucose-6-phosphate in the soil microbial biomass and in the respired CO 2 ranged between 28.2 and 37.1% 66 h after addition of the tracer, while the recovery of 33 P in the soil microbial biomass was 1.4–6.1%. This indicates that even in the P-poor soils microorganisms mineralized organic P and took up more C than P from the organic compound. Thus, microbial mineralization of organic P was driven by microbial need for C rather than for P. In conclusion, our experiments showed that (i) the microbial biomass stoichiometry in the P-poor soils was more susceptible to additions of C, N and P than in the P-rich soils and that (ii) even in the P-poor soils, microorganisms were C-limited and the mineralization of organic P was mainly driven by microbial C demand.

Manure-based biogas fermentation residues – Friend or foe of soil fertility?

Abstract: Anaerobic digestion of organic residues has the potential to significantly contribute to a shift from fossil to renewable energy. The by-product, anaerobic slurry, does have properties that are different from the undigested material. There are concerns of soil organic matter depletion in soils, enhanced greenhouse gas and odour emissions, and pathogen spread upon production and use of biogas slurries as fertilizer. However, considering the pros and cons, anaerobic digestion of residues does have positive effects for the climate, the environment and for the farmer, compared to the use of undigested matter.

Effects of long-term manure applications on the occurrence of antibiotics and antibiotic resistance genes (ARGs) in paddy soils: Evidence from four field experiments in south of China

Abstract: Most studies of the effects of manure amendment on the occurrence of antibiotics and antibiotic resistance genes (ARGs) in soil employ the investigation of grab samples or short-term laboratory studies. However, the effects of long-term manure applications on antibiotics, ARGs and their vertical distribution in paddy soil in field experiments are lacking. We assessed the concentrations of antibiotics, ARGs and their vertical distribution in paddy soil receiving long-term manure applications in four field experiments. High concentrations of tetracyclines were detected in most manured soils, while sulfonamides were not detectable. Long-term manure amendments generally increased the antibiotic concentrations and ARGs abundances in the paddy soil over decades. However, in some sites such significant trends of ARGs could not be observed. The abundance of ARGs was statistically correlated with antibiotics and soil properties including pH and soil organic matter (SOM), indicating their importance in the selection of resistance genes. Tetracyclines could be detected in soil at different depths and the concentrations of tetracyclines and abundance of ARGs generally decreased with increasing soil depths.

Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China

Abstract: Black soils (Mollisols) are one of the most important soil resources for maintaining food security in China, and they are mainly distributed in northeast China. A previous comprehensive study revealed the biogeographical distribution patterns of bacterial communities in the black soil zone. In this study, we used the same soil samples and analyzed the 454 pyrosequencing data for the nuclear ribosomal internal transcribed spacer (ITS) region to examine the fungal communities in these black soils. A total of 220,812 fungal ITS sequences were obtained from 26 soil samples that were collected across the black soil zone. These sequences were classified into at least 5 phyla, 20 classes, greater than 70 orders and over 350 genera, suggesting a high fungal diversity across the black soils. The diversity of fungal communities and distribution of several abundant fungal taxa were significantly related to the soil carbon content. Non-metric multidimensional scaling and canonical correspondence analysis plots indicated that the fungal community composition was most strongly affected by the soil carbon content followed by soil pH. This finding differs from the bacterial community results, which indicated that soil pH was the most important edaphic factor in determining the bacterial community composition of these black soils. A variance partitioning analysis indicated that the geographic distance contributed 20% of the fungal community variation and soil environmental factors that were characterized explained approximately 35%. A pairwise analysis revealed that the diversity of the fungal community was relatively higher at lower latitudes, which is similar to the findings for the bacterial communities in the same region and suggests that a latitudinal gradient of microbial community diversity might occur in the black soil zone. By incorporating our previous findings on the bacterial communities, we can conclude that contemporary factors of soil characteristics are more important than historical factor of geographic distance in shaping the microbial community in the black soil zone of northeast China.

Microbial physiology and necromass regulate agricultural soil carbon accumulation

Abstract: Strategies for mitigating soil organic carbon (SOC) losses in intensively managed agricultural systems typically draw from traditional concepts of soil organic matter formation, and thus emphasize increasing C inputs, especially from slowly decomposing crop residues, and reducing soil disturbance. However these approaches are often ineffective and do not adequately reflect current views of SOC cycling, which stress the important contributions of microbial biomass (MB) inputs to SOC. We examined microbial physiology as an alternate mechanism of SOC accumulation under organic (ORG) compared to conventional (CT) agricultural management practices, where ORG is accumulating C despite fewer total C inputs and greater soil tillage. We hypothesized that microbial communities in ORG have higher growth rates (MGR) and C use efficiencies (CUE) and that this relates to greater MB production and ultimately higher retention of new C inputs. We show that ORG had 50% higher CUE (±8 se) and 56% higher MGR (±22 se) relative to CT (p

Soil aggregation: Influence on microbial biomass and implications for biological processes

Abstract: Our 1988 paper, describing the effects of cultivation on microbial biomass and activity in different aggregate size classes, brought together the ‘aggregate hierarchy theory’ and the ‘microbial biomass concept’. This enabled us to identify the relationships between microbial and microhabitat (aggregate) properties and organic matter distribution and explain some of their responses to disturbance. By combining biochemical and direct microscopy based quantification of microbial abundance with enzyme activities and process measurements, this study provided evidence for the role of microbial biomass (especially fungi) in macroaggregate dynamics and carbon and nutrient flush following cultivation. In the last ten years environmental genomic techniques have provided much new knowledge on bacterial composition in aggregate size fractions yet detailed information about other microbial groups (e.g. fungi, archaea and protozoa) is lacking. We now know that soil aggregates are dynamic entities – constantly changing with regard to their biological, chemical and physical properties and, in particular, their influences on plant nutrition and health. As a consequence, elucidation of the many mechanisms regulating soil C and nutrient dynamics demands a better understanding of the role of specific members of microbial communities and their metabolic capabilities as well as their location within the soil matrix (e.g. aggregates, pore spaces) and their reciprocal relationship with plant roots. In addition, the impacts of environment and soil type needs to be quantified at the microscale using, wherever possible, non-destructive ‘ in situ ’ techniques to predict and quantify the impacts of anthropogenic activities on soil microbial diversity and ecosystem level functions.

Contribution of exudates, arbuscular mycorrhizal fungi and litter depositions to the rhizosphere priming effect induced by grassland species

Abstract: The presence of plants induces strong accelerations in soil organic matter (SOM) mineralization by stimulating soil microbial activity a phenomenon known as the rhizosphere priming effect (RPE). The RPE could be induced by several mechanisms including root exudates, arbuscular mycorrhizal fungi (AMF) and root litter. However the contribution of each of these to rhizosphere priming is unknown due to the complexity involved in studying rhizospheric processes. In order to determine the role of each of these mechanisms, we incubated soils enclosed in nylon meshes that were permeable to exudates, or exudates & AMF or exudates, AMP and roots under three grassland plant species grown on sand. Plants were continuously labeled with C-13 depleted CO2 that allowed distinguishing plant-derived CO2 from soil-derived CO2. We show that root exudation was the main way by which plants induced RPE (58-96% of total RPE) followed by root litter. AMP did not contribute to rhizosphere priming under the two species that were significantly colonized by them i.e. Poa trivialis and Trifolium repens. Root exudates and root litter differed with respect to their mechanism of inducing RPE. Exudates induced RPE without increasing microbial biomass whereas root litter increased microbial biomass and raised the RPE mediating saprophytic fungi. The RPE efficiency (RPE/unit plant-C assimilated into microbes) was 3-7 times higher for exudates than for root litter. This efficiency of exudates is explained by a microbial allocation of fresh carbon to mineralization activity rather than to growth. These results suggest that root exudation is the main way by which plants stimulated mineralization of soil organic matter. Moreover, the plants through their exudates not only provide energy to soil microorganisms but also seem to control the way the energy is used in order to maximize soil organic matter mineralization and drive their own nutrient supply. (C) 2014 Elsevier Ltd. All rights reserved.

Microbial consortium-mediated plant defense against phytopathogens: Readdressing for enhancing efficacy

Abstract: Microorganisms under natural habitats live in communities and some provides benefits to plant. Further, microbes when introduced to soil as consortium and interact with a host plant, partially mimic the natural soil conditions. The current research trend has therefore oriented towards investigating the role of small microbial consortia in promoting plant growth and health against various invading pathogens. This is a paradigm shift from the original investigations involving a single microbe. In the recent past, information on various mechanisms by which microbial consortia promoted plant growth and triggered defense responses in host plants during pathogen ingress have become available. It was also unveiled that microbes in small consortia enhance the defense signaling cascades leading to enhanced transcriptional activation of several metabolic pathways. However, an additive or synergistic effect is not achieved every time a microbial consortium is used. With progress in time a sizable understanding on microbial consortium-induced plant defense responses had been reached. Further generation of information on host's responses to pathogenic challenge in the presence of diverse microbial consortia at functional level is underway. In this review, we have presented the outcomes of small microbial consortia used so far to protect crop plants from various pathogens. We have also provided possible explanations for reduction in diseases when a microbial consortium was used, compared the effects of microbes when used alone as well as in consortium, possible shortcomings for not obtaining desired outcome from the introduced consortia, and provided the rationale for development of effective microbial consortia capable of inducing enhanced systemic resistance. Finally, we have suggested some potential biotechnological applications to sustain the effect of microbe-induced defense responses in host plants.

The effects of simulated nitrogen deposition on plant root traits: A meta-analysis

Abstract: Global atmospheric nitrogen deposition has increased steadily since the 20th century, and has complex effects on terrestrial ecosystems. This work synthesized results from 54 papers and conducted a meta-analysis to evaluate the general response of 15 variables related to plant root traits to simulated nitrogen deposition. Simulated nitrogen deposition resulted in significantly decreasing fine root biomass (

Shifts in microbial community and water-extractable organic matter composition with biochar amendment in a temperate forest soil

Abstract: Biochar amendment in soil has been proposed as a carbon sequestration strategy which may also enhance soil physical and chemical properties such as nutrient and water holding capacity as well as soil fertility and plant productivity. However, biochar may also stimulate microbial activity which may lead to increased soil CO2 respiration and accelerated soil organic matter (OM) degradation which could partially negate these intended benefits. To investigate short-term soil microbial responses to biochar addition, we conducted a 24 week laboratory incubation study. Biochar produced from the pyrolysis of sugar maple wood at 500 °C was amended at concentrations of 5, 10 and 20 t/ha in a phosphorus-limited forest soil which is under investigation as a site for biochar amendment. The cumulative soil CO2 respired was higher for biochar-amended samples relative to controls. At 10 and 20 t/ha biochar application rates, the concentration of phospholipid fatty acids (PLFAs) specific to Gram-positive and Gram-negative bacteria as well as actinomycetes were lower than controls for the first 16 weeks, then increased between weeks 16–24, suggesting a gradual microbial adaptation to altered soil conditions. Increases in the ratio of bacteria/fungi and lower ratios of Gram-negative/Gram-positive bacteria suggest a microbial community shift in favour of Gram-positive bacteria. In addition, decreasing ratios of cy17:0/16:1ω7 PLFAs, a proxy used to examine bacterial substrate limitation, suggest that bacteria adapted to the new conditions in biochar-amended soil over time. Concentrations of water-extractable organic matter (WEOM) increased in all samples after 24 weeks and were higher than controls for two of the biochar application rates. Solution-state 1H NMR analysis of WEOM revealed an increase in microbial-derived short-chain carboxylic acids, lower concentrations of labile carbohydrate and peptide components of soil OM and potential accumulation of more recalcitrant polymethylene carbon during the incubation. Our results collectively suggest that biochar amendment increases the activity of specific microorganisms in soil, leading to increased CO2 fluxes and degradation of labile soil OM constituents.

Organic acid induced release of nutrients from metal-stabilized soil organic matter – The unbutton model

Abstract: Processes of soil organic matter (SOM) stabilization and the reverse, destabilization of SOM resulting in subsequent release and mobilization of nutrients from SOM, remain largely unresolved. The perception of SOM as supramolecular aggregates built of low molecular mass biomolecules is currently emerging. Polyvalent metal cations contribute to SOM tertiary structure by bridging functional groups of such molecules (Simpson et al., 2002). The strong bond to metals protects high quality organic material from being immediately accessed and decomposed. Here we propose a three-step process by which low molecular mass organic acids (LMMOAs) and hydrolytic enzymes act in series to destabilize SOM supramolecules to release organic nitrogen (N) and phosphorus (P) for local hyphal and root uptake. Complexation of the stabilizing metals by fungal-released LMMOA gives fungal-root consortia direct access to organic substrates of good quality. Because of their small sizes and carboxyl group configuration, citric and oxalic acids are the most effective LMMOAs forming stable complexes with the main SOM bridging metals Ca and Al in SOM. Citrate, forming particularly strong complexes with the trivalent cations Al and Fe, is dominant in soil solutions of low-productive highly acidic boreal forest soils where mycorrhizal associations with roots are formed predominantly by fungi with hydrophobic hyphal surfaces. In these systems mycelia participate in the formation of N-containing SOM with a significant contribution from strong Al bridges. In less acidic soils of temperate forests, including calcareous influenced soils, SOM is stabilized predominantly by Ca bridges. In such systems mycorrhizal fungi with more hydrophilic surfaces dominate, and oxalic acid, forming strong bidentate complexes with Ca, is the most common LMMOA exuded. A plant-fungus driven biotic mechanism at the supramolecular aggregate level (103–105 Da) resolves micro-spatial priming of SOM, where the destabilization step is prerequisite for subsequent release of nutrients.

Assessment of gross and net mineralization rates of soil organic phosphorus – A review

Abstract: The quantification of net soil organic P mineralization rates is hampered by the potentially rapid sorption of released phosphate. Here, isotopic dilution approaches to assess gross and net organic P mineralization rates under steady-state conditions are reviewed, including different analytical and numerical solutions to assess P transformation rates based on incubation experiments with 32P- or 33P-labeled soils. Non-isotopic approaches are also commented on. Published isotopic dilution studies show that isotopically exchangeable P during incubation can partly or even predominantly (20–90%) result from biological and biochemical rather than physicochemical processes. The relative contribution of biological and biochemical processes tends to be lower in arable soils than under grassland and forests and is negatively related to the availability of inorganic P and positively to concentrations of soil organic carbon. Typical basal gross organic P mineralization rates range between 0.1 and 2.5 mg P kg−1 d−1, but rates up to 12.6 mg P kg−1 d−1 have been observed in grassland and forest soils. The further partitioning of gross organic P mineralization remains uncertain, but a dominance of microbial immobilization and remineralization is likely under most conditions, at least during the initial weeks of incubation. Over longer time periods, the relative importance of mineralization of non-living soil organic P increases, with the contribution of extracellular hydrolysis remaining to be elucidated. This requires other approaches than enzyme activity assays, since measurements of phosphomonoesterase activity in soil render organic P mineralization rates that are one to two orders of magnitude greater than those determined by isotopic dilution. The numerical modeling approach will enable assessment of soil P transformation rates under non-steady-state conditions, where P fluxes are likely to be greater than under steady-state conditions. Ultimately, an improved understanding of the biological and biochemical processes in soil P dynamics may help to improve P management in agroecosystems.

Impact of conservation tillage and organic farming on the diversity of arbuscular mycorrhizal fungi

Abstract: Communities of arbuscular mycorrhizal fungi (AMF) are strongly affected by land use intensity and soil type. The impact of tillage practices on AMF communities is still poorly understood, especially in organic farming systems. Our objective was to investigate the impact of soil cultivation on AMF communities in organically managed clay soils of a long-term field experiment located in the Sissle valley (Frick, Switzerland) where two different tillage (reduced and conventional mouldboard plough tillage) and two different types of fertilization (farmyard manure & slurry, or slurry only) have been applied since 2002. In addition, a permanent grassland and two conventionally managed croplands situated in the neighborhood of the experiment were analyzed as controls. Four different soil depths were studied including top-soils (0–10 and 10–20 cm) of different cultivation regimes and undisturbed sub-soils (20–30 and 30–40 cm). The fungi were directly isolated from field soil samples, and additionally spores were periodically collected from long-term trap culture (microcosm) systems. In total, >50,000 AMF spores were identified on the species level, and 53 AMF species were found, with 38 species in the permanent grassland, 33 each in the two reduced till organic farming systems, 28–33 in the regularly plowed organic farming systems, and 28–33 in the non-organic conventional farming systems. AMF spore density and species richness increased in the top-soils under reduced tillage as compared to the ploughed plots. In 10–20 cm also the Shannon–Weaver AMF diversity index was higher under reduced tillage than in the ploughed plots. Our study demonstrates that AMF communities in clay soils were affected by land use type, farming system, tillage as well as fertilization strategy and varying with soil depth. Several AMF indicator species especially for different land use types and tillage strategies were identified from the large data set.

Heterotrophic nitrification of organic N and its contribution to nitrous oxide emissions in soils

Abstract: Nitrous oxide (N 2 O) is one of the key trace gases playing an important role in global climate change. Soils are the most important source of global N 2 O. A large number of studies have been conducted to quantify soil-based N 2 O emissions, including processes of N 2 O production, microbial mechanisms of N 2 O production, and the prediction of N 2 O emissions via various modeling approaches on various spatial scales. However, a considerable uncertainty still exists regarding the spatial and temporal variability of N 2 O emissions in natural and managed habitats. In this review, we summarize the nitrogen (N) pools related with N 2 O production and the methods quantifying the gross heterotrophic nitrification of organic N and its contribution to N 2 O emissions in soils, with the aim to derive a simplified conceptual approach for N 2 O emissions. We show that with current stable isotopes techniques such a quantification is possible and can propose more information to understand N 2 O emissions from a wide range of soil and ecosystems. The gross heterotrophic nitrification of organic N rate may be generally significant in acidic forest soils with high C/N ratio. However, the contribution of heterotrophic nitrification of organic N process to total N 2 O emissions seems to be dependent on soil pH, C/N ratio and land use. Therefore, we propose introducing N 2 O production via heterotrophic nitrification of organic N into the conceptual “hole-in-the-pipe” (HIP) model of N 2 O emission, originally developed by Firestone and Davidson (1989).

A review of soil NO transformation: associated processes and possible physiological significance on organisms.

Abstract: NO emissions from soils and ecosystems are of outstanding importance for atmospheric chemistry. Here we review the current knowledge on processes involved in the formation and consumption of NO in soils, the importance of NO for the physiological functioning of different organisms, and for inter- and intra-species signaling and competition, e.g. in the rooting zone between microbes and plants. We also show that prokaryotes and eukaryotes are able to produce NO by multiple pathways and that unspecific enzymo-oxidative mechanisms of NO production are likely to occur in soils. Nitric oxide production in soils is not only linked to NO production by nitrifying and denitrifying microorganisms, but also linked to extracellular enzymes from a wide range of microorganisms. Further investigations are needed to clarify molecular mechanisms of NO production and consumption, its controlling factors, and the significance of NO as a regulator for microbial, animal and plant processes. Such process understanding is required to elucidate the importance of soils as sources (and sinks) for atmospheric NO.

Arbuscular mycorrhizal contribution to copper, manganese and iron nutrient concentrations in crops – A meta-analysis

Abstract: The micronutrients copper (Cu), manganese (Mn) and iron (Fe) are essential for crop plant development and productivity. However, a quantitative, data-based consensus has yet to be reached on the role of arbuscular mycorrhizal fungi (AMF) in Cu, Mn and Fe nutrition in crops. Thus, we performed a meta-analysis to quantitatively synthesize the findings of 233 single publications and to test the impact of 10 moderator variables on the AM fungal mediated Cu, Mn and Fe aboveground tissue concentration. AMF had overall a significantly positive effect on crop Cu nutrition (on average 29%). For Fe, a positive AM fungal mediated effect was detectable only for intermediate ‘experimental duration’ (lasting 56–112 days). AMF only produced a positive effect on Mn nutrition in herbs, while for other plant types, edaphic and study-related factors we documented neutral or negative results. The application of AMF for crop plant fortification is still in its infancy. Here we found evidence for a significant role of AMF for Cu, Fe and (to a limited extent) Mn crop plant nutrition. This highlights that more efforts should be devoted to harnessing the potential beneficial effects of these symbionts not just for yield but also nutritional quality, especially considering increasing demands for food quality in the future.

Responses of wheat to arbuscular mycorrhizal fungi: A meta-analysis of field studies from 1975 to 2013

Abstract: Arbuscular mycorrhizal fungi (AMF) can benefit growth and yield of agriculturally significant crops by increasing mineral nutrient uptake, disease resistance and drought tolerance of plants. We conducted a meta-analysis of 38 published field trials with 333 observations to determine the effects of inoculation and root colonization by inoculated and non-inoculated (resident) AMF on P, N and Zn uptake, growth and grain yield of wheat. Field AMF inoculation increased aboveground biomass, grain yield, harvest index, aboveground biomass P concentration and content, straw P content, aboveground biomass N concentration and content, grain N content and grain Zn concentration. Grain yield was positively correlated with root AMF colonization rate, whereas straw biomass was negatively correlated. The most important drivers of wheat growth response to AMF were organic matter concentration, pH, total N and available P concentration, and texture of soil, as well as climate and the AMF species inoculated. Analysis showed that AMF inoculation of wheat in field conditions can be an effective agronomic practice, although its economic profitability should still be addressed for large-scale applications in sustainable cropping systems.

Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils

Abstract: Root-derived carbon (C) is considered as critical fuel supporting the interaction between plant and rhizosphere microbiome, but knowledge of how plant–microbe association responds to soil fertility changes in the agroecosystem is lacking. We report an integrative methodology in which stable isotope probing (SIP) and high-throughput pyrosequencing are combined to completely characterize the root-feeding bacterial communities in the rhizosphere of wheat grown in historical soils under three long-term (32-year) fertilization regimes. Wheat root-derived 13 C was dominantly assimilated by Actinobacteria and Proteobacteria (notably Burkholderiales), accounting for nearly 70% of root-feeding microbiome. In contrast, rhizosphere bacteria utilizing original soil organic matter (SOM) possessed a higher diversity at phylum level. Some microbes (e.g. Bacteroidetes and Chloroflexi) enhancing in the rhizosphere were not actively recruited through selection by rhizodeposits, indicating a limited range of action of root exudates. Inorganic fertilization decreased the dependence of Actinobacteria on root-derived C, but significantly increased its proportion in SOM-feeding microbiome. Furthermore, significantly lower diversity of the root-feeding microbiome, but not the SOM-feeding microbiome, was observed under both organic and inorganic fertilizations. These results revealed that long-term fertilizations with increasing nutrients availability would decrease the preference of rhizosphere microbiome for root-derived substrates, leading to a simpler crop–microbe association.

Effects of nitrogen enrichment on belowground communities in grassland: Relative role of soil nitrogen availability vs. soil acidification

Abstract: Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide range of impacts on the above- and belowground communities. An increase in high N availability has been assumed to be a major mechanism enhancing the abundance of above- and belowground communities. In addition to increasing available N, however, N enrichment causes soil acidification, which may negatively affect above- and belowground communities. The relative importance of increased N availability vs. increased soil acidity for above- and belowground communities in natural ecosystems experiencing N enrichment is unclear. In a 12-year N enrichment experiment in a semi-arid grassland, N enrichment substantially increased both above- and belowground plant biomass mainly via the N availability-induced increase in biomass of perennial rhizome grasses. N enrichment also dramatically suppressed bacterial, fungal, and actinobacteria biomass mainly via the soil acidification pathway (acidification increased concentrations of H+ ions and Al3+ and decreased concentrations of mineral cations). In addition, N enrichment also suppressed bacterial-, fungal-feeding, and omnivorous + carnivorous nematodes mainly via the soil acidification pathway (acidification reduced nematode food resources and reduced concentrations of mineral cations). The positive effects resulting from the increase in belowground carbon allocation (via increase in quantity and quality of plant production) on belowground communities were outweighed by the negative effects resulting from soil acidification, indicating that N enrichment weakens the linkages between aboveground and belowground components of grassland ecosystems. Our results suggest that N enrichment-induced soil acidification should be included in models that predict biota communities and linkages to carbon and nitrogen cycling in terrestrial ecosystems under future scenarios of N deposition.

Distinctive effects of TiO2 and CuO nanoparticles on soil microbes and their community structures in flooded paddy soil

Abstract: The wide use of metal oxide nanoparticles (MNPs) will inevitably increase their environmental release into soil, which consequently raises concerns about their environmental impacts and ecological risks. In this study, two typical MNPs (TiO 2 and CuO NPs) in different doses (0, 100, 500 and 1000 mg kg −1 soil) were applied to evaluate their effects on microbes in flooded paddy soil. The negative effects of CuO NPs were stronger than that of TiO 2 NPs on soil microbes, as reflected by the significant decline in soil microbial biomass (as indicated by the reduced microbial biomass carbon [MBC] and the total phospholipid fatty acids [PLFAs]) and enzyme activities including urease, phosphatase and dehydrogenase. The principle component analysis (PCA) of the PLFAs and the diversity indices reveal that not TiO 2 NPs but CuO NPs reduced the composition and diversity of the paddy soil microbial community. The reduced impact of TiO 2 NPs may be due to their particle characteristics. The bioavailability of CuO NPs is thought to induce the major toxicity to microbes in the flooded paddy soil, as determined by the increased Cu contents in the soil extractions and the microbial cells. The elevated stress ratio values demonstrate that CuO NPs may also indirectly affect soil microbes by changing nutrient bioavailability. Over all, both TiO 2 NPs and CuO NPs may induce perturbations on the microbes in flooded paddy soil and showed potential risks to the paddy soil ecosystem. Therefore, attentions toward the effects of MNPs to the ecological environment should be paid from now on.

Biochar suppresses N2O emissions while maintaining N availability in a sandy loam soil

Abstract: Nitrous oxide (N2O) from agricultural soil is a significant source of greenhouse gas emissions. Biochar amendment can contribute to climate change mitigation by suppressing emissions of N2O from soil, although the mechanisms underlying this effect are poorly understood. We investigated the effect of biochar on soil N2O emissions and N cycling processes by quantifying soil N immobilisation, denitrification, nitrification and mineralisation rates using 15N pool dilution techniques and the FLUAZ numerical calculation model. We then examined whether biochar amendment affected N2O emissions and the availability and transformations of N in soils. Our results show that biochar suppressed cumulative soil N2O production by 91% in near-saturated, fertilised soils. Cumulative denitrification was reduced by 37%, which accounted for 85–95 % of soil N2O emissions. We also found that physical/chemical and biological ammonium (NH4+) immobilisation increased with biochar amendment but that nitrate (NO3−) immobilisation decreased. We concluded that this immobilisation was insignificant compared to total soil inorganic N content. In contrast, soil N mineralisation significantly increased by 269% and nitrification by 34% in biochar-amended soil. These findings demonstrate that biochar amendment did not limit inorganic N availability to nitrifiers and denitrifiers, therefore limitations in soil NH4+ and NO3− supply cannot explain the suppression of N2O emissions. These results support the concept that biochar application to soil could significantly mitigate agricultural N2O emissions through altering N transformations, and underpin efforts to develop climate-friendly agricultural management techniques.

Soil methane oxidation and land-use change – from process to mitigation

Abstract: Global atmospheric methane (CH4) concentrations are now approaching 1800 ppbv as a result of the growing imbalance between the net CH4 emissions from natural and anthropogenic sources of this potent greenhouse gas, and its consumption by physical and biological processes. The main focus of this review is on how land-use change and soil management can be used to correct this imbalance. Currently, the main terrestrial source for CH4 is from natural wetlands and irrigated rice cultivation, although improvements in water management during rice production have resulted in major reductions of CH4 emissions from this source. Afforestation and reforestation can also enhance soil CH4 oxidation by influencing the composition and activity of the soil methanotroph (aerobic proteobacteria) community. The effects of these and other land-use changes on soil CH4 oxidation are not generally well understood, but are known to influence this process through their effects on a range of soil properties such as soil moisture, nitrogen status, and pH that also affects methanotroph community structure and function. Recent advances in molecular techniques have confirmed the central role of methanotroph communities in regulating soil CH4 consumption by revealing how they respond to land-use change. Community-level molecular analyses of methanotroph populations under different conditions now provide new insights into the distinct traits of the different subgroups and their ecology. These advances in understanding the abiotic and biological processes regulating soil CH4 oxidation now offers the possibility of being able to predict which land-use and management practices, especially for afforestation and reforestation, will achieve high soil CH4 oxidation rates They also improve the prospects for integrated assessment of the atmospheric impacts on the global greenhouse gas budget from net soil emissions of CH4, N2O, and CO2 with land use and management change.

Microbial community structure mediates response of soil C decomposition to litter addition and warming

Abstract: Microbial activity has been highlighted as one of the main unknowns controlling the fate and turnover of soil organic matter (SOM) in response to climate change. How microbial community structure and function may (or may not) interact with increasing temperature to impact the fate and turnover of SOM, in particular when combined with changes in litter chemistry, is not well understood. The primary aim of this study was to determine if litter chemistry impacted the decomposition of soil and litter-derived carbon (C), and its interaction with temperature, and whether this response was controlled by microbial community structure and function. Fresh or pre-incubated eucalyptus leaf litter (13C enriched) was added to a woodland soil and incubated at 12, 22, or 32 �C. We tracked the movement of litter and soilderived C into CO2, water-extractable organic carbon (WEOC), and microbial phospholipids (PLFA). The litter additions produced significant changes in every parameter measured, while temperature, interacting with litter chemistry, predominately affected soil C respiration (priming and temperature sensitivity), microbial community structure, and the metabolic quotient (a proxy for microbial carbon use efficiency [CUE]). The direction of priming varied with the litter additions (negative with fresh litter, positive with pre-incubated litter) and was related to differences in the composition of microbial communities degrading soil-C, particularly gram-positive and gram-negative bacteria, resulting from litter addition. Soil-C decomposition in both litter treatments was more temperature sensitive (higher Q10) than in the soil-only control, and soil-C priming became increasingly positive with temperature. However, microbes utilizing soil-C in the litter treatments had higher CUE, suggesting the longer-term stability of soil-C may be increased at higher temperature with litter addition. Our results show that in the same soil, the growth of distinct microbial communities can alter the turnover and fate of SOM and, in the context of global change, its response to temperature.