N-cycling Communities Research Articles

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16–0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41–69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from “nitrification-denitrification” in the recharge area to “partial nitrification-anammox” in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.

The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.

Combined application of organic manure and chemical fertilizers stabilizes soil N-cycling microflora

• The abundance of N-cycling genes differently responded to NPK application.• Chemical NPK application greatly altered the N-cycling microbial community structure.• Soil acidification was the main driver for the variation in the N-cycling microbial community.• Manure addition was beneficial for stabilizing the N-cycling microbial community.Straw and manure are widely applied to agricultural systems, and greatly shape soil N-cycling microflora. However, we still lack a comprehensive understanding of how these organic materials structure soil N-cycling microbial communities. In this study, metagenomic analysis was performed to investigate the compositional variation in N-cycling microbial communities in a 30-year long-term experiment under five fertilization regimes: no fertilization (Control), chemical fertilization only (NPK), and NPK with wheat straw (NPK + HS), pig manure (NPK + PM), and cow manure (NPK + CM). Long-term NPK application differentially changed N-cycling gene abundance and greatly altered N-cycling microbial community structure. NPK + HS resulted in a similar pattern to NPK in terms of gene abundance and community structure. However, NPK + PM and NPK + CM significantly increased most genes and resulted in a community similar to that of the Control. Further analysis revealed that serious soil acidification caused by long-term NPK fertilization was a major factor for the variation in N-cycling microbial communities. The addition of alkaline manure, rather than wheat straw, stabilized the N-cycling microbial community structure presumably by alleviating soil acidification. These results revealed the strong impact of soil acidification on microbial N-cycling communities and illustrated the possibility of resolving nitrogen-related environmental problems by manipulating pH in acidified agricultural soils.

Stable nitrogen-cycling capacity in relation to fertilization and intercropping in a sub-boreal grassland

Grasslands are important in sub-boreal climate agricultural systems and are managed with various combinations of N fertilization and plant species. Ammonia-oxidizing and denitrifying microorganisms are key players in determining the fate of nitrogen (N) and thereby also the yield in grassland systems and their impact on gaseous N losses and leaching. We established a three-year field study in southern Finland with fertilizer treatment as a main-plot factor, including organic and synthetic fertilizers and plant species and mixtures thereof as the sub-plot factor. We quantified six genes encoding key N-cycling enzymes by quantitative PCR to determine the abundance of the communities involved in N-transformation processes and also included previously published data on crop yield, soil properties and the overall bacterial community composition. With the exception of ammonia oxidizing bacteria (AOB), which were primarily affected by fertilization, the abundances of all other N-cycling communities changed over time with either an increase or decrease from summer to autumn. Differences in gene abundances between plant species treatments and in fertilizer by plant species interactions were detected mainly in the beginning of the cropping season during the first year. The nirS-type denitrifiers and nosZII nitrous oxide reducers responded more to changes in soil properties than their functional counterpart nirK and nosZI communities. Using structural equation modeling, we show that the overall microbial community composition and diversity played an important role in mediating the management effects on crop yield, genetic potential for N retention and N2O sink capacity. However, a trade-off between the genetic potential for N retention and N2O sink capacity was detected, indicating the challenges in managing grasslands in a sustainable way.

Cover crop composition drives changes in the abundance and diversity of nitrifiers and denitrifiers in citrus orchards with critical effects on N2O emissions

• Cover crop C and N effects linked to N-cycling community abundance and diversity. • Lower soil N 2 O fluxes with legume + non-legume cover crops vs non-legumes. • Cover crop mixture had significant effects on nirK and nosZ I community diversity. • nirK and nosZ I community composition attributed to soil properties and CC mixtures. • amoA AOA, nirK, and nosZ I species potential indicators of CC N 2 O changes. Tree crops contribute to global agriculture production, but they are usually cultivated in soils with low nutrient availability. Cover crops (CCs) have been reported as a sustainable management strategy to improve soil nutrient availability for vegetable systems, but less is known about their influence on soil nutrient cycling, greenhouse gas emissions (GHG), and the soil microbiome in tree crops. We examined the effect of replacing the traditional weedy row middles of a commercial Florida citrus orchard with two different mixtures of CCs (legumes and non-legumes, LG + NL; and non-legumes only, NL) compared to a grower standard control (GSC) over a period of two years. Both CC mixtures significantly increased soil carbon (C) availability, microbial abundance, and soil respiration in the row middles compared to the GSC. Significant increases in soil nitrogen (N) concentrations and abundance of genes associated with N-fixation and nitrification were observed in soils treated with LG + NL. Planting LG + NL significantly increased the abundance of nosZ -type denitrifiers compared to NL and the GSC treatments, and significantly reduced nitrous oxide (N 2 O) emissions. The use of both CC mixtures reduced bacterial diversity and affected the composition of nirK and nosZ I communities. The composition of nosZ I communities differed between CC mixtures, possibly due to changes in soil moisture and carbon. Specific amoA ammonia-oxidizing archaea, nirK, and nosZ I species were identified as potential indicators for changes in N 2 O emissions after planting CCs. Our results show that CCs can be a good strategy to improve soil nutrient cycling in the row middles of tree crops and that CC composition drives changes in the abundance and diversity of N-cycling communities which ultimately impact GHG emissions.

Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures.

Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems.

Linking long-term soil phosphorus management to microbial communities involved in nitrogen reactions

The influence of soil phosphorous (P) content on the N-cycling communities and subsequent effects on N2O emissions remains unclear. Two laboratory incubation experiments were conducted on soils collected from a long-term (est. 1995) P-addition field trial sampled in summer 2018 and winter 2019. Incubations were treated with a typical field amendment rate of N as well as a C-amendment to stimulate microbial activity. Throughout both incubations, soil subsamples were collected prior to fertiliser amendment and then throughout the incubations, to quantify the abundance of bacteria (16S rRNA), fungi (ITS) and Thaumarcheota (16S rRNA) as well as functional guilds of genes involved in nitrification (bacterial and archaeal amoA, and comammox) and denitrification (nirS, nirK, nosZ clade I and II) using quantitative PCR (qPCR). We also evaluated the correlations between each gene abundance and the associated N2O emissions depending on P-treatments. Our results show that long-term P-application influenced N-cycling genes abundance differently. Except for comammox, overall nitrifiers’ genes were most abundant in low P while the opposite trend was found for denitrifiers’ genes. C and N-amendments strongly influenced the abundance of most genes with changes observed as soon as 24 h after application. ITS was the only gene correlated to N2O emissions in the low P-soils while microbes were mostly correlated to emissions in high P, suggesting possible changes in the organisms involved in N2O production depending on soil P-content. This study highlights the importance of long-term P addition on shaping the microbial community function which in turn stimulates a direct impact on the subsequent N emissions.

Loss in soil microbial diversity constrains microbiome selection and alters the abundance of N-cycling guilds in barley rhizosphere

Plant roots are shaping microbial communities that are distinct from the surrounding soil. These root-associated microbial communities can have both positive and negative effects on the host nutrient acquisition and thereby growth, yet how loss of soil microbial diversity will constrain the plant microbiome selection is relatively unknown. In this study, we manipulated the soil microbial community using a removal-by-dilution approach to examine how microbial diversity modulates microbiome selection in barley, including microbial guilds involved in nitrogen (N) cycling processes causing N loss, and its consequences for plant performance. We found that microbial diversity loss reduced the barley's ability to recruit specific microorganisms from the soil and only members of the Alphaproteobacteria and Bacteroidetes were enriched in both rhizosphere and root-associated compartments irrespective of dilution level. Loss in soil microbial diversity and the presence of plants affected the N-cycling communities, with the abundance of nitrous oxide reducers being 2–4 times higher in both barley compartments in the lower diversity soils. In these soils, the low abundance of bacterial ammonia oxidizers (close or below detection level in the barley compartments) was concomitant with an increase in leaf greenness (ca. 12%), an indicator of the plant N status. The reduction in soil microbial diversity was thus coupled to a change in functional traits of rhizosphere and root-associated communities, with consequences for plant performance. This work contributes to our understanding of plant-microbe interactions, which is needed to steer the crop microbiome towards increased N-use efficiency while minimizing negative environmental impact.

Distribution of nitrogen-cycling genes in an oxygen-depleted cyclonic eddy in the Alfonso Basin, Gulf of California

The marine N cycle is driven mainly by microorganisms whose distribution can be shaped by mesoscale eddies. Recently, eddies containing oxygen minimum zones (OMZs) have been recognised as N-loss hotspots, complicating even more the calculations of the marine N budgets. As a contribution to this understanding, we investigated the effect of a cyclonic eddy confined in an oxygen-depleted basin on the distribution of the N-cycling communities. We measured hydrographic properties of the water column, nutrient concentrations, and the abundance of key genes involved in the processes of nitrification (archaeal and bacterial amoA), denitrification (nirS and nirK), dissimilatory nitrate reduction to ammonia (DNRA; nrfA) and anammox (hzo) within the eddy. Our results indicated that the cyclonic circulation affected the distribution of nutrients and the abundance of amoA and nirS genes, whereas oxygen influenced the distribution of nirK, nrfA, and hzo genes. Additionally, the aerobic ammonium oxidation by archaea seems to be an important source of nitrite, which might fuel denitrifier, DNRA, and anammox communities in this basin. These findings along with the high N deficit in the OMZ suggest the existence of an active N cycling that might enhance the N-loss in this oxygen-depleted basin.

The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry

Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.

Linking soil N2O emissions with soil microbial community abundance and structure related to nitrogen cycle in two acid forest soils

Tree species and seasonal change influence N2O flux and microbial communities, but the mechanisms are unclear. We studied N2O flux in soils planted with slash pine and oil-seed camellia trees. We sampled on typical days of the four seasons. We tested whether N-cycling communities respond more to tree species or seasonal change. We assessed how tree species affect N2O flux. We used qPCR and RFLP to determine abundance and community composition of amoA-containing bacteria (AOB) and archaea (AOA), and denitrifiers that contain the narG, nirK, nirS, and nosZ genes. N2O flux rate and soil characteristics varied significantly between forest soils and sampling seasons. Abundance of all detected genes, but not of the nirS gene, was significantly affected by tree species. Differences in gene abundance between days in different seasons were found only for narG, nirK, and nosZ. Functional microbial community composition in the soil varied between the tree species for most of the genes studied, but varied, not significantly, slightly among sampling days. Differences in the abundance and community composition of nitrifiers and denitrifiers between tree species depended on soil concentration of NH4+, NO3−, and dissolved organic carbon (DOC). N2O flux rate was affected by community composition, but not abundance of nitrifiers and denitrifiers. Temperature, NO3−, and DOC concentrations significantly affected N2O flux. Tree species influenced N2O flux more than seasonal change, by altering community composition and environmental factors rather than nitrifier/denitrifier abundance.

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

The effect of intercropping on the genetic potential for N-cycle pathways promoting either retention or loss of N by the microbial communities associated to the roots or present in the bulk soil for two forage crops was studied in a greenhouse experiment. Medicago sativa (‘lucerne’) and Dactylis glomerata (‘cocksfoot’) were grown as sole crops or intercropped in soils with or without addition of biogas digestate to also evaluate fertilizer effects. Eight genes involved in inorganic N-cycling were quantified using real-time PCR to determine the genetic potential for different N-cycling pathways. Both plant species and intercropping affected the abundance of root-associated microbial-derived genes involved in N-cycling processes, while there was no effect of amendment with biogas digestate. The genetic potential for the various pathways differed between bulk soil and roots, as well as between the roots of the two plant species, suggesting that organisms involved in different N-cycling processes were favored in different compartments in the soil-root environment. Ammonia oxidizers involved in nitrification, a pathway resulting in N-leaching, dominated in soil whereas those related to N2 fixation and gaseous N losses (denitrification) were more abundant on roots. We also observed niche differentiation between the two major groups of organisms with the capacity to reduce N2O in the root- and soil compartment. Legume-grass intercropping resulted in a decreasing trend for several root-associated functional communities. More specifically, the legume exerted an effect on the N-cycling communities on the roots of both the legume and grass species, which suggests altered plant-microbial or microbial-microbial interactions during intercropping.

Spatial and temporal dynamics of nitrogen fixing, nitrifying and denitrifying microbes in an unfertilized grassland soil

The microbial groups of nitrogen fixers, ammonia oxidizers, and denitrifiers largely drive the inorganic nitrogen cycle in temperate terrestrial ecosystems. Their spatial and temporal dynamics, however, vary depending on the studied scale. The present study aimed to fill a knowledge gap by providing an explicit picture of spatial and temporal dynamics of a subset of these soil microorganisms at the plot scale. We selected an unfertilized perennial grassland, where nitrogen cycling is considered to be efficient and tightly coupled to plant growth. At six times over one growing season 60 soil samples were taken from a 10 m × 10 m area and abundances of marker genes for total archaea and bacteria (16S rRNA), nitrogen fixing bacteria (nifH), ammonia oxidizing archaea (amoA AOA) and bacteria (amoA AOB), and denitrifying bacteria (nirS, nirK and nosZ) were determined by qPCR. Potential nitrification activity (PNA) and denitrifying enzyme activity (DEA) were determined. Seasonal changes in abundance patterns of marker genes were detected, and were associated with changes in substrate availability associated with plant growth stages. Potential nitrification and denitrification enzyme activities were strongly spatially structured at the studied scale, corresponding to periods of rapid plant growth, June and October, and their spatial distributions were similar, providing visual evidence of highly localized spatial and temporal conditions at this scale. Temporal variability in the N-cycling communities versus the stability of their respective potential activities provided evidence of both short-lived temporal niche partitioning and a degree of microbial functional redundancy. Our results indicate that in an unfertilized grassland, at the meter scale, abundances of microbial N-cycling organisms can exhibit transient changes, while nitrogen cycling processes remain stable.

Soil microbial communities as potential regulators of in situ N2O fluxes in annual and perennial cropping systems

Significant reductions in nitrous oxide (N2O) fluxes have been observed with perennial cropping systems compared to annual crops. However, it is unclear if this reduction in N2O flux is linked to soil microbial communities due to plant-specific characteristics stimulating changes in microbial community structure. The response of microbial communities involved in N2O production to liquid dairy manure (LDM) application and tillage in annual and perennial systems has also not been assessed. Our objectives were to contrast changes in the population sizes and community structures of ammonia oxidizer (represented by amoA and crenamoA gene targets) and denitrifier (nirK, nirS, and nosZ gene targets) communities in differently managed annual and perennial fields, and to determine if differences in these microbial communities were related to observed variation in N2O fluxes. Soil was sampled in 2012 and in 2014 in a 4-ha spring-applied LDM grass-legume (perennial) field and two 4-ha corn (annual) fields under fall or spring LDM application. Soil DNA was extracted and used to target N-cycling genes via qPCR (n = 6) and for next-generation sequencing (Illumina Miseq) (n = 3). Significantly higher field-scale N2O fluxes were observed in the annual fields compared to the perennial system; however N2O fluxes increased 10-fold after plough down of the perennial field. Nonmetric multidimensional scaling (NMS) and multi-response permutation procedure (MRPP) indicated statistical differences in N-cycling communities between annual and perennial cropping systems, and in some cases, communities became indistinct in ordination space between annual and perennial fields after ploughing. Indicator species analysis was used to identify sequences clustered into operational taxonomic units (OTUs) most responsible for community shifts related to management. The abundance of N2O-reducing soil microbial communities (nosZ gene copies) and specific nirK, nirS and nosZ OTUs were proposed as important with respect to the production and consumption of N2O in these soils. Our results illustrate that ammonia oxidizer and denitrifier soil bacterial communities are sensitive to agricultural management (annual or perennial crop type, LDM management, and ploughing), highlighting their significance for the development of effective N2O mitigation strategies.

Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils

This study aims to provide first insights on the impact of land-use intensification and soil properties in shaping the composition of N-cycling microbial communities in Mediterranean peaty soils drained for agricultural purposes. An intensively cultivated peaty soil represented by an intensive maize cropping system was compared with an extensive grassland and an agricultural soil left abandoned for 15 years. Clone-library sequencing based on partial amoA and nirK functional genes was used to characterize the composition of ammonia-oxidizer microorganisms and nirK-type bacterial denitrifiers, respectively. The relative roles of land-use intensification and soil physico-chemical properties in community composition shaping were quantified by multivariate analyses. Phylogenetic and multivariate analyses showed that (i) the majority of sequences of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) grouped within the Nitrosotalea and Nitrosospira clusters, respectively; (ii) uncultured denitrifying bacteria were unique to our soil; (iii) land-use intensification shaped the composition of N-cycling communities; (iv) ammonia-oxidizing communities were driven by clay (AOA), bulk density (AOB), and exchangeable calcium (both AOA and AOB); and (v) nirK-type denitrifier bacteria were shaped by silt, ammonium, and exchangeable potassium. Based on the variation partitioning, soil properties were the primary determinants of the AOA and nirK-type denitrifier community composition, while land-use intensification was the major factor shaping the community composition of AOB. These findings improve the knowledge on such vulnerable agrosystems aiming to optimize the management of soil microbes in order to enhance the sustainability of N fertilization.

Organic nitrogen cycling microbial communities are abundant in a dry Australian agricultural soil

Some microbial nitrogen (N) cycling processes continue under low soil moisture levels in drought-adapted ecosystems. These processes are of particular importance in winter cropping systems, where N availability during autumn sowing informs fertilizer practices and impacts crop productivity. We evaluated the organic and inorganic N-cycling communities in a key cropping soil (Vertosol), using a controlled-environment incubation study that was designed to model the autumn break in south Australian grain growing regions. Soils from wheat, lucerne, and green manure (disced-in vetch) rotations of the Sustainable Cropping Rotations in Mediterranean Environments trial (Victoria, Australia) were collected during the summer when soil moisture was low. Microbial community structure and functional capacity were measured both before and after wetting (21, 49, and 77 days post-wetting) using terminal restriction fragment length polymorphism measures of bacterial and fungal communities, and quantitative PCR of nitrogen cycling genes. Quantified genes included those associated with organic matter decomposition (laccase, cellobiohydrolase), mineralization of N from organic matter (peptidases) and nitrification (bacterial and archaeal ammonia monooxygenase and nitrite oxidoreductase). In general, the N cycling functional capacity decreased with soil wetting, and there was an apparent shift from organic-N cycling dominance to autotrophic mineral-N cycling dominance. Soil nitrate levels were best predicted by laccase and neutral peptidase genes under drought conditions, but by neutral peptidase and bacterial ammonia monooxygenase genes under moist conditions. Rotation history affected both the structural and functional resilience of the soil microbial communities to changing soil moisture. Discing in green manure (vetch) residues promoted a resilient microbial community, with a high organic-N cycling capacity in dry soils. Although this was a small-scale microcosm study, our results suggest that management strategies could be developed to control microbial organic-N processing during the summer fallow period and thus improve crop-available N levels at sowing.

Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils

A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type denitrifiers to scales >14 m for nirK-type denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type denitrifiers increased in high LUI, but decreased for biogeochemical properties, suggesting that biotic and/or abiotic factors other than those measured are driving the spatial distribution of these microorganisms at the plot scale. Furthermore, ammonia oxidizers (amoA ammonia-oxidizing archaea and amoA ammonia-oxidizing bacteria) and nitrate reducers (napA and narG) showed spatial coexistence, whereas niche partitioning was found between nirK- and nirS-type denitrifiers. Together, our results indicate that spatial analysis is a useful tool to characterize the distribution of different functional microbial guilds with respect to soil biogeochemical properties and land-use management. In addition, spatial analyses allowed us to identify distinct distribution ranges indicating the coexistence or niche partitioning of N-cycling communities in grassland soil.

Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment

The relative importance of size and composition of microbial communities in ecosystem functioning is poorly understood. Here, we investigated how community composition and size of selected functional guilds in the nitrogen cycle correlated with agroecosystem functioning, which was defined as microbial process rates, total crop yield and nitrogen content in the crop. Soil was sampled from a 50-year fertilizer trial and the treatments comprised unfertilized bare fallow, unfertilized with crop, and plots with crop fertilized with calcium nitrate, ammonium sulfate, solid cattle manure or sewage sludge. The size of the functional guilds and the total bacterial community were greatly affected by the fertilization regimes, especially by the sewage sludge and ammonium sulfate treatments. The community size results were combined with previously published data on the composition of the corresponding communities, potential ammonia oxidation, denitrification, basal and substrate-induced respiration rates, in addition to crop yield for an integrated analysis. It was found that differences in size, rather than composition, correlated with differences in process rates for the denitrifier and ammonia-oxidizing archaeal and total bacterial communities, whereas neither differences in size nor composition was correlated with differences in process rates for the ammonia-oxidizing bacterial community. In contrast, the composition of nitrate-reducing, denitrifying and total bacterial communities co-varied with primary production and both were strongly linked to soil properties.