Perennial cropping systems are known to highly support soil fauna and its diversity. This has already been investigated for grassland and bioenergy systems. Recently, perennial wheat (Kernza®) is increasingly recognised throughout European agriculture. However, the detailed impacts of perennial grain on soil functioning are not well investigated yet.Within the EU-Biodiversa project NAPERDIV nematode communities, among other research areas, were investigated in a Pan-European transect from South France to Belgium to South Sweden representing a climatic gradient from south to north and variations in soil conditions. Additionally, two soil depths (5-15 cm; 25-35 cm) were investigated.In total, nematodes from 31 families were identified, with the perennial cropping system having a greater number of taxa and biomass. Additionally, this cropping system was characterised with system stability and food web complexity due to greater proportions of predators and omnivores and a higher maturity index, channel index and structure index as compared to annual wheat. In contrast, the enrichment index was highest in the annual cropping system, representing nutrient enrichment and rapid responses of opportunistic nematodes. Nematode diversity was greater for the upper soil depth.In summary, nematode communities mainly reflect the impact of land-use, tillage, fertilisation, and soil organic matter on their feeding behaviour. The promotion in diversity for the perennial cropping system for all study sites shows that differences in soil and climate conditions do not interfere with the beneficial effects of perennnial wheat.

The fog harvesting grass Stipagrostis sabulicola is one of the few plants able to cope with the hostile conditions in dune fields of the hyper-arid Namib Desert. S. sabulicola tussocks modify the substrate and atmospheric conditions leading to the formation of fog plant oases (FPO). Average air temperature within FPO canopies was reduced by up to 7.5 degrees C and air humidity raised by 11 % compared to the bare sand, inducing a lowering of vapor pressure deficit (VPD) by up to 1.5 kPa. Stomatal conductance showed a negatitive correlation with VPD, rising to an average of 435 mmol.m-2 s-1 in the forenoon of foggy days. Due to leaf water runoff during fog events, substrate moisture at the plant basis increased locally to values of up to 16% ensuring adequate plant water supply during fogless days. FPO substrates had finer grain sizes and doubled concentration of organic particles, thus improving water storage capacity. Fog interception rate of the sand increased by up to 109 % with steepening of S. sabulicola mounds. Improved water availability, balanced temperature conditions and the presence of digestible plant material promote niche-building for substrate life, which in turn is a prerequisite for the functioning of fog-driven oases ecosystems.

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The Namib Desert is a hyperarid coastal desert where fog is a major moisture source. We hypothesized that the fog-harvesting grass Stipagrostis sabulicola establishes an important ecological niche, termed the "Fog-Plant-Oases" (FPOs), and serves as the primary carbon source for the invertebrate community. To determine this, we measured the natural variations of the stable carbon and nitrogen isotopes (δ13C and δ15N) of invertebrates as well as that of plant biomass and belowground detritus and estimated the contributions of the fog plants in their diets. Our findings revealed a complex trophic structure and demonstrated that S. sabulicola fuels carbon flow from lower to higher trophic levels in the aboveground food web. The distinct δ13C values of bacterial- and fungal-feeding nematodes indicated however the separation of the aboveground niche, which is primarily sustained by S. sabulicola, from the belowground niche, where wind-blown sediments may serve as the main energy source for the soil biota. Our findings further accentuate the critical role of S. sabulicola FPOs in establishing complex trophic dynamics and a distinctive food web within the hyperarid Namib dunes.

AbstractIntroductionConventional agricultural land‐use may negatively impact biodiversity and the environment due to the increased disturbances to the soil ecosystem by tillage, for example. Cultivation of the perennial grain intermediate wheatgrass (Thinopyrum intermedium, IWG, Kernza®) is a nature‐based solution for sustainable agriculture, improving nutrient retention mainly through its extensive root system. Nematodes serve as sensitive bioindicators, detecting early changes in the soil food web, reflecting in changes in their community structure.Materials and MethodsIWG and annual wheat sites in South France, Belgium and South Sweden were investigated in April 2022 for two depths (5–15 cm; 25–35 cm) to evaluate the difference in nematode community structure among the cropping systems.ResultsSites with IWG cultivation held an accumulation of structure indicators (c‐p 3–5 nematodes) compared to sites with annual wheat cultivation. A generalised linear mixed model revealed significantly more root feeders, especially for the subsoil, under IWG as a result of the perennial cultivation. The maturity index, plant‐parasitic index, channel index and structure index were greater for IWG sites. The enrichment index was greater for annual wheat sites due to the dominance of bacterivores and enrichment indicators (c‐p 1 nematodes). The nematode community structure (weighted faunal profile analysis) indicates IWG sites as being a generally undisturbed system with efficient nutrient cycling and balanced distribution of feeding types, as well as higher metabolic footprint values for root feeders (including plant‐parasitic nematodes) and fungivores. Annual wheat sites, on the other hand, held indicators of a disturbed system with increased occurrence of opportunistic species and a more bacterial driven pathway. The topsoil had an increased occurrence of structure indicators in both cropping systems.ConclusionIWG creates favourable conditions for a diverse food web, including improved nutrient cycling and a heterogeneous resource environment, regardless of climatic conditions, establishing it as a stable and resilient agricultural management system.

Soil and soil-biodiversity protection are increasingly important issues in environmental science and policies, requiring the availability of high-quality empirical data on soil biodiversity. Here we present a publicly available data warehouse for the soil-biodiversity domain, Edaphobase 2.0, which provides a comprehensive toolset for storing and re-using international soil-biodiversity data sets, following the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. A major strength is the possibility of annotating biodiversity data with exhaustive geographical, environmental and methodological metadata, allowing a wide range of applications and analyses. The system harmonises and integrates heterogeneous data from diverse sources into standardised formats, which can be searched together using numerous filter possibilities, and offers data exploration and analysis tools. Edaphobase features a strict data transparency policy, comprehensive quality control, and DOIs can be provided for individual data sets. The database currently contains >450,000 data records from >35,0000 sites and is accessed nearly 14,000 times/year. The data curated by Edaphobase 2.0 can greatly aid researchers, conservationists and decision makers in understanding and protecting soil biodiversity.

Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.

Soils, just like all other ecosystem compartments, change over time and, consequently, conditions for soil-inhabiting organisms are also changing, affecting their composition and diversity. Soil biodiversity is a critical component of ecosystems that supports many essential ecosystem functions and services, such as nutrient cycling, carbon sequestration, water regulation and biomass production for food, fodder, fibre and energy. However, and despite the importance of soil biodiversity for ecosystem health and human well-being, neither current state, drivers, potential consequences for ecosystem services nor options for sustainable governance of soil biodiversity are well understood. Here, we provide a framework for and argue that conducting a national assessment of soil biodiversity, albeit being a complex endeavour, is fundamental to building a baseline to understand the current state and trends of soil biodiversity, but also to identify the main drivers of change, the impacts of soil biodiversity loss and the potential pathways for conservation and sustainable governance of soil biodiversity.

Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.

Lignocellulose is a major component of plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered as primary decomposers and evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 cellulases in a collection of soil invertebrate genomes and found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently from microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.

Lignocellulose is a major component of plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered as primary decomposers and evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 cellulases in a collection of soil invertebrate genomes and found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently from microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.

Although soil ecology has benefited from recent advances in describing the functional and trophic traits of soil organisms, data reuse for large-scale soil food-web reconstructions still faces challenges. These obstacles include: (1) most data on the trophic interactions and feeding behaviour of soil organisms being scattered across disparate repositories, without well-established standard for describing and structuring trophic datasets; (2) the existence of various competing terms, rather than consensus, to delineate feeding-related concepts such as diets, trophic groups, feeding processes, resource types, leading to ambiguities that hinder meaningful data integration from different studies; (3) considerable divergence in the trophic classification of numerous soil organisms, or even the lack of such classifications, leading to discrepancies in the resolution of reconstructed food webs and complicating the reuse and comparison of food-web models within synthetic studies. To address these issues, we introduce the Soil Food Web Ontology, a novel formal conceptual framework designed to foster agreement on the trophic ecology of soil organisms. This ontology represents a collaborative and ongoing endeavour aimed at establishing consensus and formal definitions for the array of concepts relevant to soil trophic ecology. Its primary objective is to enhance the accessibility, interpretation, combination, reuse, and automated processing of trophic data. By harmonising the terminology and fundamental principles of soil trophic ecology, we anticipate that the Soil Food Web Ontology will improve knowledge management within the field. It will help soil ecologists to better harness existing information regarding the feeding behaviours of soil organisms, facilitate more robust trophic classifications, streamline the reconstruction of soil food webs, and ultimately render food-web research more inclusive, reusable and reproducible.

Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes and genome assemblies. We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades and potworms. We shotgun-sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes. We recovered 90% of the species, and observed relatively high false positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g. springtails) consistently attracting more hits than others (e.g. enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We provide a roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing, and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

Punctoribates is one of few genera in Poronota (Acari: Oribatida) containing species with porose areas and species with saccules, the two types of the octotaxic system. These porose organs are the main difference between two morphologically similar species, P. punctum with porose areas and P. zachvatkini with saccules. As the octotaxic system can vary within species, species separation solely based on this trait might be insufficient. To assess the species status of P. zachvatkini, we investigated additional differences from P. punctum by comparing habitat preferences of the two species regarding nature reserves and agricultural landscapes during a field study in the German Eifel region, and by examining Punctoribates material from four large German natural history museums. We also performed scanning electron microscopy (SEM) and a genetic analysis using the D3 marker of the nuclear 28S rDNA gene. In the field study, P. zachvatkini had higher densities in the nature reserves and P. punctum in the agricultural landscapes. Evaluation of the museum material revealed P. punctum occurred more regularly in disturbed sites such as urban, agricultural and post-mining areas compared to P. zachvatkini. Pairwise distances of the 28S D3 genetic marker as well as an additional base pair in P. zachvatkini further support the separation of the two species, and SEM investigations revealed new details regarding the punctulation of P. zachvatkini. The review of the museum material showed that P. zachvatkini already occurred in Germany in 1967 and has a wider distribution than previously known.

The present study gives the first detailed results on the partner-finding behaviour of tardigrades. We investigated whether the finding of mating partners by Isohypsibius dastychi followed certain criteria that are expected if pheromone signals are involved. For this purpose, tardigrade pairs were positioned in an arena, at a range of distances from each other. Only those females that were ready for mating attracted the male. The smaller the initial distance between them, the more directly the male headed for the female. The route travelled and time taken increased exponentially with increasing initial distance between partners, which means that the male lost orientation with respect to the female the larger the distance between the pair became. The findings indirectly suggest a yet undetermined female pheromone, which produces a concentration gradient in the water and loses strength quickly in terms of distance. Our assumption is supported by rare observations of sperm release without direct contact between partners that nevertheless resulted in fertile offspring. The observation that the female partners in this no-contact mating behaviour then deposited their eggs (a behaviour that was never seen when males were absent) suggests that they, likewise, can sense a fresh ejaculate of spermatozoa in their direct vicinity.

Open-cast coal-mining creates a severe disturbance of ecological systems, resulting in post-mining areas that have lost their soils entirely and are exposed to extreme conditions. Nonetheless, these areas allow us to investigate the process of primary succession. We studied the first 12 years of soil tardigrade succession at ` Chicken Creek', an experimental site within the open-cast coal-mining area in Welzow Sud, Germany. A total of ten tardigrade genera and 13 species or species groups were identified at the site. Over time, the organic carbon content, proportion of silt and nutrient availability in the soil increased, and the soil particle size distribution and pH value changed significantly. The vegetation cover and nematode abundance increased, whereas tardigrade densities peaked in 2008 and decreased thereafter, as did their mean body size. Species replacement was obvious within this 12 year study period, and tardigrade species diversity increased, indicating that ecological niche diversity also increased throughout this time. Vegetation cover, soil particle size distribution and time were the most important factors influencing the tardigrade community. We also discuss further potential factors and the ability of terrestrial tardigrades to persist despite many environmental constraints, such as fluctuations in pH and moisture, and to colonize new habitats faster than most other animal groups.

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

ZusammenfassungNematoden spielen nicht nur als Parasiten in Mensch, Tier und Pflanze eine – wenn auch negative – so doch herausragende Rolle. Sie wirken vor allem als ausgesprochene Nützlinge für uns: Sie sind als wichtiger, natürlicher Bestandteil des Nahrungsnetzes maßgeblich und unverzichtbar am Nährstoffkreislauf beteiligt. Außerdem setzen wir sie in zunehmendem Maße gewinnbringend in der biologischen Schädlingsbekämpfung, der ökotoxikologischen Bewertung von Böden und Sedimenten und als ausgezeichnete Modellorganismen für die Forschung ein.

To examine physiological adaptations to the two combined stressors O2 deprivation and extreme CO2 concentrations, we compared respiratory responses of two nematode species occurring in natural CO2 springs. The minimum O2 concentration allowing maintenance of respiration in both species was 0.0176μmol O2ml-1 (corresponds to 1.4% O2 in air). After exposure to anoxia, individuals resumed respiration immediately when O2 was added, but on a lower level compared to control and without showing a respiratory overshoot. A species-specific response was found in respiration rate during 20% CO2: the more tolerant species maintained respiration rates, whereas the sensitive species showed a decreased respiration rate as low as after anoxia. The results indicate that during 20% CO2 the sensitive species undergo a survival state. We conclude, that the ability to maintain respiration even under low oxygen and high CO2 concentrations may allow the better adapted species to occupy an ecological niche in the field, where others cannot exist.

The present paper aims at providing a practical identification tool for soil zoologists. It shall facilitate taxonomic examination of tardigrade communities in order to encourage further investigations and by this expand our scarce knowledge on soil tardigrades. From faunistic studies on soil tardigrades a list of the eutardigrade species presently known from European soils was gathered comprising 22 genera, 58 species, 3 species groups. Based on the most important standard works and on up-to-date nomenclature an illustrated key to the eutardigrade genera of European soils was created. Genus descriptions and identification keys to the soil species were added while those genera that hold only one or two soil species were accomplished with short species descriptions. Additional information is given on the relevant determination features, such as claws and bucco-pharyngeal apparatus. Difficulties in tardigrade identification and taxonomy are discussed. Due to the comparably small number of studies that so far exist on soil tardigrades, the key will most likely not cover all species present in European soils, but shall provide a basis to facilitate further research.