Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes.

Whether or not communities of microbial eukaryotes are structured in the same way as bacteria is a general and poorly explored question in ecology. Here, we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted selection driven by the salinity gradient in bacterial communities (explaining ∼ 72% of taxa turnover), while microeukaryotic counterparts were predominantly structured by ecological drift (∼72% of the turnover). Nevertheless, we also detected a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, selection has had a role in the structuring of specific members of their communities. In sum, we conclude that microeukaryotes and bacteria inhabiting the same communities can be structured predominantly by different processes. This should be considered in future studies aiming to understand the mechanisms that shape microbial assemblages.

Combined effects of agrochemicals and ecosystem services on crop yield across Europe.

Simultaneously enhancing ecosystem services provided by biodiversity below and above ground is recommended to reduce dependence on chemical pesticides and mineral fertilisers in agriculture. However, consequences for crop yield have been poorly evaluated. Above ground, increased landscape complexity is assumed to enhance biological pest control, whereas below ground, soil organic carbon is a proxy for several yield-supporting services. In a field experiment replicated in 114 fields across Europe, we found that fertilisation had the strongest positive effect on yield, but hindered simultaneous harnessing of below- and above-ground ecosystem services. We furthermore show that enhancing natural enemies and pest control through increasing landscape complexity can prove disappointing in fields with low soil services or in intensively cropped regions. Thus, understanding ecological interdependences between land use, ecosystem services and yield is necessary to promote more environmentally friendly farming by identifying situations where ecosystem services are maximised and agrochemical inputs can be reduced.

NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction.

UNLABELLED: The nucleotide binding site leucine-rich repeats (NBSLRRs) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms have explained the regulation of plant immunity, but still, we have limited understanding about plant defence against different pathogens. Identification of R-proteins and proteins having R-protein-like features across the genome, transcriptome and proteome would be highly useful to develop the global understanding of plant defence mechanisms, but it is laborious and time-consuming task. Therefore, we have developed a support vector machine-based high-throughput pipeline called NBSPred to differentiate NBSLRR and NBSLRR-like protein from Non-NBSLRR proteins from genome, transcriptome and protein sequences. The pipeline was tested and validated with input sequences from three dicot and two monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays. AVAILABILITY AND IMPLEMENTATION: The NBSPred pipeline is available at http://soilecology.biol.lu.se/nbs/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: sandeep.kushwaha@biol.lu.se.

Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange.

Agricultural fertilization significantly affects arbuscular mycorrhizal fungal (AMF) community composition. However, the functional implications of community shifts are unknown, limiting understanding of the role of AMF in agriculture. We assessed AMF community composition at four sites managed under the same nitrogen (N) and phosphorus (P) fertilizer regimes for 55 yr. We also established a glasshouse experiment with the same soils to investigate AMF-barley (Hordeum vulgare) nutrient exchange, using carbon (13 C) and 33 P isotopic labelling. N fertilization affected AMF community composition, reducing diversity; P had no effect. In the glasshouse, AMF contribution to plant P declined with P fertilization, but was unaffected by N. Barley C allocation to AMF also declined with P fertilization. As N fertilization increased, C allocation to AMF per unit of P exchanged increased. This occurred with and without P fertilization, and was concomitant with reduced barley biomass. AMF community composition showed no relationship with glasshouse experiment results. The results indicate that plants can reduce C allocation to AMF in response to P fertilization. Under N fertilization, plants allocate an increasing amount of C to AMF and receive relatively less P. This suggests an alteration in the terms of P-C exchange under N fertilization regardless of soil P status.

Soil food web properties explain ecosystem services across European land use systems.

Intensive land use reduces the diversity and abundance of many soil biota, with consequences for the processes that they govern and the ecosystem services that these processes underpin. Relationships between soil biota and ecosystem processes have mostly been found in laboratory experiments and rarely are found in the field. Here, we quantified, across four countries of contrasting climatic and soil conditions in Europe, how differences in soil food web composition resulting from land use systems (intensive wheat rotation, extensive rotation, and permanent grassland) influence the functioning of soils and the ecosystem services that they deliver. Intensive wheat rotation consistently reduced the biomass of all components of the soil food web across all countries. Soil food web properties strongly and consistently predicted processes of C and N cycling across land use systems and geographic locations, and they were a better predictor of these processes than land use. Processes of carbon loss increased with soil food web properties that correlated with soil C content, such as earthworm biomass and fungal/bacterial energy channel ratio, and were greatest in permanent grassland. In contrast, processes of N cycling were explained by soil food web properties independent of land use, such as arbuscular mycorrhizal fungi and bacterial channel biomass. Our quantification of the contribution of soil organisms to processes of C and N cycling across land use systems and geographic locations shows that soil biota need to be included in C and N cycling models and highlights the need to map and conserve soil biodiversity across the world.

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.

BACKGROUND: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. RESULTS: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 [corrected] publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ . CONCLUSION: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.

Intensive agriculture reduces soil biodiversity across Europe.

Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects biodiversity of the soil food web as a whole, and whether or not these effects may be generalized across regions. We examined biodiversity in soil food webs from grasslands, extensive, and intensive rotations in four agricultural regions across Europe: in Sweden, the UK, the Czech Republic and Greece. Effects of land-use intensity were quantified based on structure and diversity among functional groups in the soil food web, as well as on community-weighted mean body mass of soil fauna. We also elucidate land-use intensity effects on diversity of taxonomic units within taxonomic groups of soil fauna. We found that between regions soil food web diversity measures were variable, but that increasing land-use intensity caused highly consistent responses. In particular, land-use intensification reduced the complexity in the soil food webs, as well as the community-weighted mean body mass of soil fauna. In all regions across Europe, species richness of earthworms, Collembolans, and oribatid mites was negatively affected by increased land-use intensity. The taxonomic distinctness, which is a measure of taxonomic relatedness of species in a community that is independent of species richness, was also reduced by land-use intensification. We conclude that intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms. Land-use intensification results in fewer functional groups of soil biota with fewer and taxonomically more closely related species. We discuss how these changes in soil biodiversity due to land-use intensification may threaten the functioning of soil in agricultural production systems.

Agent-Based Life Cycle Assessment enables joint economic-environmental analysis of policy to support agricultural biomass for biofuels.

Production of agricultural biofuels is expected to rise due to increasing climate change mitigation ambitions. Policy interventions promoting targeted bioenergy solutions can be motivated by the large environmental externalities present in agricultural systems and the local context of biomass production co-benefits. Introducing energy crops in crop rotations in arable land with depleted Soil Organic Carbon (SOC) levels offers the potential to increase SOC stocks and future crop yields as a step towards more sustainable agricultural systems. However, the environmental performance of a policy incentive for energy crops with SOC co-benefits is less evident when considering its land-use effects within and outside of the target agricultural system. We study the potential impacts of a change in agricultural policy on regional agricultural structure and production, and the environment with an Agent-Based Life Cycle Assessment approach. We simulate a policy payment that would achieve adoption of grass leys in crop rotations corresponding to 25 % of the highly productive land in an intensive farming region of southern Sweden. Although enhancing soil health in SOC-depleted farming regions is a desirable environmental objective, its significance is limited within the life-cycle performance of the payment. Instead, crop-displacement impacts and the grass potential as biofuel feedstock are the main drivers. The active utilisation of grasses for biofuel purposes is key in reaching a positive environmental evaluation of the policy instrument. Our environmental evaluation is likely generalisable to other regions with similar technological levels and farming intensity, while our analysis on structural shifts is specific to the policy instrument and agricultural production system under study. Overall, our work provides a method to contrast regional effects and global environmental impacts of policy instruments supporting agricultural biomass for biofuels prior to implementation. This contributes to the environmental assessment of land-based biofuels at a time when their sustainability is highly debated.

Primary assembly of soil communities: disentangling the effect of dispersal and local environment.

It has long been recognised that dispersal abilities and environmental factors are important in shaping invertebrate communities, but their relative importance for primary soil community assembly has not yet been disentangled. By studying soil communities along chronosequences on four recently emerged nunataks (ice-free land in glacial areas) in Iceland, we replicated environmental conditions spatially at various geographical distances. This allowed us to determine the underlying factors of primary community assembly with the help of metacommunity theories that predict different levels of dispersal constraints and effects of the local environment. Comparing community assembly of the nunataks with that of non-isolated deglaciated areas indicated that isolation of a few kilometres did not affect the colonisation of the soil invertebrates. When accounting for effects of geographical distances, soil age and plant richness explained a significant part of the variance observed in the distribution of the oribatid mites and collembola communities, respectively. Furthermore, null model analyses revealed less co-occurrence than expected by chance and also convergence in the body size ratio of co-occurring oribatids, which is consistent with species sorting. Geographical distances influenced species composition, indicating that the community is also assembled by dispersal, e.g. mass effect. When all the results are linked together, they demonstrate that local environmental factors are important in structuring the soil community assembly, but are accompanied with effects of dispersal that may "override" the visible effect of the local environment.

Conventional agriculture and not drought alters relationships between soil biota and functions.

Soil biodiversity constitutes the biological pillars of ecosystem services provided by soils worldwide. Soil life is threatened by intense agricultural management and shifts in climatic conditions as two important global change drivers which are not often jointly studied under field conditions. We addressed the effects of experimental short-term drought over the wheat growing season on soil organisms and ecosystem functions under organic and conventional farming in a Swiss long term trial. Our results suggest that activity and community metrics are suitable indicators for drought stress while microbial communities primarily responded to agricultural practices. Importantly, we found a significant loss of multiple pairwise positive and negative relationships between soil biota and process-related variables in response to conventional farming, but not in response to experimental drought. These results suggest a considerable weakening of the contribution of soil biota to ecosystem functions under long-term conventional agriculture. Independent of the farming system, experimental and seasonal (ambient) drought conditions directly affected soil biota and activity. A higher soil water content during early and intermediate stages of the growing season and a high number of significant relationships between soil biota to ecosystem functions suggest that organic farming provides a buffer against drought effects.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities.

Effects of simulated drought on biological soil quality, microbial diversity and yields under long-term conventional and organic agriculture.

Drought and agricultural management influence soil microorganisms with unknown consequences for the functioning of agroecosystems. We simulated drought periods in organic (biodynamic) and conventional wheat fields and monitored effects on soil water content, microorganisms and crops. Above the wilting point, water content and microbial respiration were higher under biodynamic than conventional farming. Highest bacterial and fungal abundances were found in biodynamically managed soils, and distinct microbial communities characterised the farming systems. Most biological soil quality parameters and crop yields were only marginally affected by the experimental drought, except for arbuscular mycorrhizal fungi (AMF), which increased in abundance under the experimental drought in both farming systems. AMF were further strongly promoted by biodynamic farming resulting in almost three times higher AMF abundance under experimental drought in the biodynamic compared with the conventional farming system. Our data suggest an improved water storage capacity under biodynamic farming and confirms positive effects of biodynamic farming on biological soil quality. The interactive effects of the farming system and drought may further be investigated under more substantial droughts. Given the importance of AMF for the plant's water supply, more in-depth studies on AMF may help to clarify their role for yields under conditions predicted by future climate scenarios.

Landscape configuration affects herbivore-parasitoid communities in oilseed rape.

It is crucial to consider the effects of large-scale drivers on species presences and ecological interactions to understand what structures communities. In our study, we investigated how the species composition and the potential interaction networks of herbivore and parasitoid communities in oilseed rape fields are affected by agricultural landscape characteristics. Insect communities of 26 winter oilseed rape fields in southern Sweden were captured in water traps over a continuous time span of 30 ± 2 days. In total, 31% of the variation in the composition of herbivore host communities was explained by a combination of the surrounding oilseed rape area in the study year and the previous year and distance to the nearest forest. The oilseed rape area in the study year and distance to forest also explained 14% of the variation in the composition of parasitoid communities. Distance to the nearest forest together with the area of oilseed rape in the previous year explained 45% of the variation in asymmetry of interaction webs. These results indicate that several measures of landscape configuration are important both for the composition of host and parasitoid communities and also for the structure of interaction networks. Our results support the view that it is an appropriate strategy to cultivate oilseed rape in landscapes that are far away from forests, in order to minimize recolonization by pest species and at the same time to attract parasitoid species from the open landscape.

Long-term effects of short-term perturbation in a subalpine grassland.

Theoretical advances and short-term experimental studies have furthered our understanding of how ecosystems respond to perturbation. However, there are few well-replicated experimental studies that allow an assessment of long-term responses. Results from a controlled, large-scale field experiment in a subalpine grassland near Interlaken, Switzerland, show that 2-4 years of liming (Ca: 40 g x m(-2) x yr(-1)) still significantly affected the composition of the vegetation and the soil microbial community nearly 70 years after the treatments were imposed, whereas NPK fertilization (8 g x m(-2) x yr(-1)) only marginally affected vegetation composition. The exchangeable content of Ca ions and soil pH were higher in limed plots but were unaffected in fertilized plots. Plant species and PLFAs (phospholipid fatty acids) indicating low pH values were found in higher abundance in the unlimed plots, suggesting that the long-lasting effects of liming on the above- and belowground communities were mediated through changes in soil pH. The results of this long-term study indicate that the resilience of mountain ecosystems may be particularly low in response to perturbations that substantially alter soil pH or other key determinants of belowground processes.

The benefits of systematic mapping to evidence-based environmental management.

Reviews of evidence are a vital means of summarising growing bodies of research. Systematic reviews (SRs) aim to reduce bias and increase reliability when summarising high priority and controversial topics. Similar to SRs, systematic maps (SMs) were developed in social sciences to reliably catalogue evidence on a specific subject. Rather than providing answers to specific questions of impacts, SMs aim to produce searchable databases of studies, along with detailed descriptive information. These maps (consisting of a report, a database, and sometimes a geographical information system) can prove highly useful for research, policy and practice communities, by providing assessments of knowledge gaps (subjects requiring additional research), knowledge gluts (subjects where full SR is possible), and patterns across the research literature that promote best practice and direct research resources towards the highest quality research. Here, we introduce SMs in detail using three recent case studies that demonstrate their utility for research and decision-making.

Agricultural Land Use Determines the Trait Composition of Ground Beetle Communities.

In order to improve biological control of agricultural pests, it is fundamental to understand which factors influence the composition of natural enemies in agricultural landscapes. In this study, we aimed to understand how agricultural land use affects a number of different traits in ground beetle communities to better predict potential consequences of land-use change for ecosystem functioning. We studied ground beetles in fields with different agricultural land use ranging from frequently managed sugar beet fields, winter wheat fields to less intensively managed grasslands. The ground beetles were collected in emergence tents that catch individuals overwintering locally in different life stages and with pitfall traps that catch individuals that could have a local origin or may have dispersed into the field. Community weighted mean values for ground beetle traits such as body size, flight ability and feeding preference were estimated for each land-use type and sampling method. In fields with high land-use intensity the average body length of emerging ground beetle communities was lower than in the grasslands while the average body length of actively moving communities did not differ between the land-use types. The proportion of ground beetles with good flight ability or a carnivorous diet was higher in the crop fields as compared to the grasslands. Our study highlights that increasing management intensity reduces the average body size of emerging ground beetles and the proportion of mixed feeders. Our results also suggest that the dispersal ability of ground beetles enables them to compensate for local management intensities.

Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.

Patchiness and compensatory growth in a fungus-Collembola system.

The compensatory growth potential of a grazed fungal biomass was mathematically expressed as a function of patchiness in its distribution and demonstrated in an experiment using the fungivorous collembolan Onychiurus armatus and the soil fungi Verticillium bulbillosum and Penicillium spinulosum. The model addresses the regrowth potential in relation to patch fragmentation, travelling time and consumption rate of the collembolan and the mean relative growth rate of the fungus. It suggests that the mean relative growth rate required for regrowth decreases with patch fragmentation and increases with the mean growth rate of the fungus. The experiments were performed with a system of soil-filled vials provided with fungi and collembolans. The size of the vials and the length of the tubes connecting them were varied to give different patch sizes and travelling times. The respiratory activity of fungi after grazing increased as a unit of mycelium was distributed into smaller connected vials. The slow growing species V. bulbillosum showed a greater but delayed response to grazing in comparison with the fast growing P. spinulosum. An increased travelling time delayed the growth response in both species.

Seasonal changes in lipid composition and glycogen storage associated with freeze-tolerance of the earthworm, Dendrobaena octaedra.

The earthworm, Dendrobaena octaedra, is a common species in the uppermost soil and humus layers of coniferous forests and tundra in temperate and subarctic regions. The species is freeze-tolerant and may survive several months in a frozen state. Upon freezing, glycogen reserves are rapidly converted to glucose serving as a cryoprotectant and fuel for metabolism. In the present study we investigated the induction of freeze-tolerance under field conditions, and sought to find relationships between temperature, glycogen and fat reserves, membrane phospholipid composition and the degree of freeze-tolerance. Freeze-tolerance was induced when worms had experienced temperatures below 5 degrees C for 2 weeks or more. Freeze-tolerance was linked to the magnitude of glycogen reserves, which also fluctuated with field temperatures being highest in autumn and winter. On the other hand fat reserves seemed not to be linked with freeze-tolerance at all. However, high glycogen alone did not confer freeze-tolerance; alterations in the membrane phospholipid fatty acid composition (PLFA) were also necessary in order to secure freeze-tolerance. The changes in PLFA composition were generally similar to changes occurring in other ectothermic animals during winter acclimation with an increased degree of unsaturation of the PLFAs.