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41 results for “soil arthropods”
Variability in soil and litter arthropod populations in the Soil Freezing Study plots at the Hubbard Brook Experimental Forest, 2009-2010
Climate models for the northeastern United States (U.S.) over the next century project an increase in air temperature between 2.8 and 4.3 °C and a decrease in the average number of days per year when a snowpack will cover the forest floor. Warmer temperatures may benefit some litter arthropods by allowing them to expand their ranges and to increase their rates of reproduction. However, a reduction in snowpack depth and duration could offset these changes and lead to increased arthropod mortality because the snowpack plays an important role in insulating arthropods from freezing temperatures. We evaluated these potential changes by measuring arthropod abundance in the Soil Freezing Study plots at the Hubabard Brook Experimental Forest. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Data from: Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta
Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance is correlated with heritable increase of metal excretion efficiency; less pronounced cadmium (Cd) induced growth reduction and, over-expression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and Cd tolerant populations. Many cDNAs responded to Cd exposure in the reference population. Significantly fewer clones were Cd responsive in tolerant animals. Analysis of variance revealed transcripts that interact between Cd exposure and population. Hierarchical cluster analysis of these clones identified two major groups. The first one contained cDNAs that were up regulated by Cd in the reference culture, but non-responsive or down regulated in tolerant animals. This cluster was also characterized by elevated constitutive expression in the tolerant population. Gene ontology analysis revealed that these cDNAs were involved in structural integrity of the cuticle, anti-microbial defense, calcium-channel blocking, sulfur assimilation and chromatin remodeling. The second group consisted of cDNAs down regulated in reference animals but not responding or slightly up regulated in tolerant animals. Their functions involved carbohydrate metabolic processes, Ca2+ dependent stress signaling, redox state, proteolysis and digestion. The reference population showed a strong signature of stress-induced genome-wide perturbation of gene expression, whereas the tolerant animals maintained normal gene expression upon Cd exposure. We confirmed the micro-evolutionary processes occurring in soil arthropod populations and suggest a major contribution of gene regulation to the evolution of a stress-adapted phenotype.
Data from: Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil
Biological communities inhabiting the soil are among the most diversified, complex and yet most poorly studied terrestrial ecosystems. The greatest knowledge gaps apply to the arthropod mesofauna (0·1–2 mm body size) because conventional morphological and molecular approaches are in many cases insufficient for the characterisation of these complex communities. The development of high-throughput sequencing (HTS) methodologies is required to solve current impediments and to further advance our understanding of below-ground biodiversity. We propose a flotation–Berlese–flotation (FBF) protocol for sampling and specimen processing to obtain 'clean' DNA extractions of arthropod mesofauna from the soil. In addition, we developed and tested HTS protocols for the characterisation of arthropod communities from these bulk DNA extractions using cox1 metabarcoding and shotgun metagenomic sequencing on the MiSeq Illumina platform. The FBF protocol provided DNA of soil arthropods from sufficiently large volumes of soil and free from contaminating bacteria and inhibitors. Metabarcoding and metagenomic sequencing on two deep soil samples from Iberian grasslands revealed >100 species of Acari and Collembola from 28 families. Genome assembly straight from shotgun sequencing of bulk specimens produced partial and full mitogenomes for 54 species with average length of >6000 bp. Metabarcoding and metagenomic sequencing resulted in closely congruent OTUs, but species numbers were highest with metabarcoding, while ∼73% of species were confirmed by matching shotgun sequence reads and ∼48% by contig assembly from those shotgun reads. In combination, the FBF protocol together with the PCR-based and shotgun sequencing pipelines addressed most of the challenges of studying soil arthropod mesofauna on the MiSeq Illumina platform. They are powerful, cost-efficient tools for characterising soil diversity in a phylogenetic and community ecology context. These methodological developments of HTS approaches for the study of mesofauna will accelerate ecological and evolutionary studies, biomonitoring of soil arthropods, and progress in both theoretical and applied soil science.
Data from: Hidden island endemic species, and their implications for cryptic speciation within soil arthropods
<p><strong>Aim:</strong> Specialisation to the soil environment is expected to constrain the spatial scale of diversification within animal lineages. In this context, the existence of flightless arthropod lineages, adapted to soil environments, but with broad geographic ranges, represent something of an anomaly. Here we investigate the diversification process within one such 'anomalous' soil specialist: <em>Geomitopsis franzi </em>Coiffait, 1978, an eyeless and flightless beetle species strongly adapted to the endogean environment but distributed across several oceanic islands.</p> <p><strong>Location:</strong> Canary Islands</p> <p><strong>Taxon:</strong> <em>Geomitopsis</em> (Coleoptera, Staphylinidae)</p> <p><strong>Methods:</strong> We performed an integrative study, including molecular phylogenetics, population genomics, and morphometry. Four DNA regions (two mitochondrial and two nuclear) were amplified and sequenced for 159 specimens from 58 localities sampled across five islands for phylogenetic analyses, and a dated phylogenetic tree was obtained using a mitogenome dataset<em>. </em>ddRAD-seq data was generated to evaluate mtDNA lineages in sympatry against the biological species concept.</p> <p><strong>Results:</strong> We found high levels of genetic differentiation (>8% COI gene divergence) among populations from different islands and among geographically coherent lineages within single islands. Lineages within Tenerife presented significant patterns of isolation by distance, with ddRAD-seq providing evidence that lineages represent biological species. Morphometric analyses revealed limited variation, with most lineages lacking diagnostic characters.</p> <p><strong>Main conclusions:</strong> <em>Geomitopsis franzi</em> is comprised of at least seven lineages that merit consideration as biological species, and is best considered as a complex of cryptic species. The limited morphological variation across these lineages is consistent with adaptation to the endogean environment placing strong constraints on morphological change. The evolution of cryptic species should be favoured when such constraints are coupled with limited dispersal ability, which characterises <em>G. franzi</em>, and is a trait that broadly characterises the soil mesofauna. We suggest that cryptic species diversity is likely to be a recurrent feature across soil adapted arthropod species with range sizes that appear inconsistent whith a low potential for dispersal.</p>
Data from: An inventory of the foliar, soil, and dung arthropod communities in pastures of the Southeastern United States
<p>Grassland systems constitute a significant portion of the land area in the U.S. and as a result harbors significant arthropod biodiversity. During this time of biodiversity loss around the world, bioinventories of ecologically important habitats serve as important indicators for the effectiveness of conservation efforts. We conducted a bioinventory of the foliar, soil, and dung arthropod communities in 10 cattle pastures located in the southeastern U.S. during the 2018 grazing season. In sum, 126,251 arthropod specimens were collected. From the foliar community, 13 arthropod orders were observed, with the greatest species richness found in Hymenoptera, Diptera, and Hemiptera. The soil-dwelling arthropod community contained 18 orders. The three orders comprising the highest species richness were Coleoptera, Diptera, and Hymenoptera. Lastly, 12 arthropod orders were collected from cattle dung, with the greatest species richness found in Coleoptera, Diptera, and Hymenoptera. Herbivores were the most abundant functional guild found in the foliar community, and predators were most abundant in the soil and dung communities. Arthropod pests constituted a small portion of the pasture arthropod communities, with 1.01%, 0.34%, and 0.46% pests found in the foliar, soil, and dung communities, respectively. While bioinventories demand considerable time, energy, and resources to accomplish, the information from these inventories has many uses for conservation efforts, land management recommendations, and the direction of climate change science.</p>
Data from: Soil arthropod communities associated with Berberis thunbergii invasion in a temperate deciduous forest harbor more detritivores
<ol> <li><span>Barberry (<em>Berberis</em> <em>thunbergii</em>) is a widely established invasive shrub in temperate forests of the northeastern U.S. with the potential to alter soil arthropod communities through changes to soil nutrient cycling and acidity.</span></li> <li><span>We compared soil arthropod taxa and functional feeding groups between invaded and nearby control areas in a paired observational survey.</span></li> <li><span>Community ordination analysis suggested minimal differences between barberry and control samples. In contrast, pairwise differences revealed elevated densities of multiple taxa in barberry-invaded soils. </span></li> <li><span>Among taxa that were able to be defined by functional feeding group and were collected at higher densities under barberry, all were detritivores. For example, barberry-invaded soils harbored an average of 40% more Isopoda and more than twice as many Diplopoda per unit dry compared to control samples. Differences we observed between barberry and control samples despite the limited study spatiotemporal scope demonstrate the potential for invasions to restructure soil arthropod communities.</span></li> <li><span>Observed patterns potentially reflect elevated leaf litter decomposition rates associated with the invasion; results also highlight the need to integrate site-specific environmental attributes when assessing the impact of invading plants on soil ecosystems.</span></li> </ol>
Urban soil quality is being deteriorated even with low heavy metal levels: An arthropod-based multi-indices approach
<p><span>Urban-induced habitat conversion drastically changes soil life in a variety of ways. Soil sealing, human disturbance, habitat fragmentation, industrial and vehicular pollution are the main causes of urban soil degradation. Soil arthropods, as the most abundant and diverse group of soil fauna, are involved in many soil processes that are of great importance in maintaining soil health and multifunctionality. Nevertheless, soil quality is still mainly characterized by physical, chemical, and microbiological parameters.</span></p> <p><span>Here, we assessed and compared the biological soil quality in woody (REF: reference forest, REM: remnant forest) and non-woody (TURF: public turfgrass, and RUD: ruderal habitat) types of urban green spaces along a disturbance and management intensity gradient in the Budapest metropolitan area (Hungary), using community metrics and soil arthropod-based indicators. Vegetation cover and landscape characteristics of study sites were quantified through vegetation and urbanization indices, respectively. Basic soil properties, total and bioavailable concentrations of the main heavy metals (Cd, Co, Hg, Ni, Zn) were also measured. </span></p> <p><span>Acari, Collembola, and Hymenoptera (mainly Formicidae) were the most abundant groups. Litter-dweller taxa, particularly Protura, proved to be the most sensitive to urban disturbance. Representatives of Hemiptera, Diptera, Symphyla, and Pauropoda were common in low densities. Soil arthropod assemblages in RUD and TURF were more diverse taxonomically than in REM and REF sites. Although the integrated faunal indices showed no differences among soil habitat types, they provided different responses and, consequently, different information. Our findings demonstrated that the biological quality and arthropod community structure of soils were strongly impacted by soil C/N and heavy metal contamination. </span></p> <p><span>We found that low and moderate levels of pollution have adverse effects on edaphic fauna, suggesting biological degradation of soils, even below pollution limits. Nevertheless, more disturbed urban green spaces have been shown to play a significant role in maintaining belowground biodiversity, thereby soil functions.</span></p>
Data from: Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta
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Data from: Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil
Open the record for dataset details and reuse information.
Data from: Soil arthropod communities associated with Berberis thunbergii invasion in a temperate deciduous forest harbor more detritivores
Open the record for dataset details and reuse information.
Data from: Hidden island endemic species, and their implications for cryptic speciation within soil arthropods
Open the record for dataset details and reuse information.
Urban soil quality is being deteriorated even with low heavy metal levels: An arthropod-based multi-indices approach
Open the record for dataset details and reuse information.
Data from: An inventory of the foliar, soil, and dung arthropod communities in pastures of the Southeastern United States
Open the record for dataset details and reuse information.
The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding
<p>Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput-sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multi-hierarchical approach was performed using <span>haplotype-level-COI metabarcoding</span> of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1000 co-distributed species and nearly 3000 haplotypes. Local assemblages were highly distinctive between grasslands and forests, and within each of them showed strong spatial structures and high endemicity at the scale of a few kilometres or less. The local distance-decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was very similar in all three regions, pointing to a significant role of dispersal limitation driving the local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod-diversity on Earth.</p>
Data from: Thermal acclimation and adaptation across populations in a broadly distributed soil arthropod
The relative contributions of phenotypic plasticity and adaptive evolution to the respons-es of species to climate change are poorly understood. It has been suggested that some species or populations will have to rely on their ability to adjust their phenotype rather than on adaptation through evolutionary adaptation. 2. We test the extent of intra- and inter-population patterns of acclimation and genetic varia-tion in multiple traits directly related to environmental tolerance limits in the broadly dis-tributed soil dwelling collembolan Orchesella cincta. 3. Genetic variation in both dynamic and static assays of thermal tolerance was present across seven populations spanning 14° of latitude and both heat and cold tolerance were significantly correlated with latitude. Short term heat and cold acclimation significantly increased thermal tolerance limits across all populations and there was local adaptation for acclimation responses for some traits. Furthermore, results showed large acclimatiza-tion responses in the field within populations for cold tolerance throughout a 13-month period and smaller acclimatization responses for heat tolerance. Acclimatization respons-es were correlated with microhabitat temperature at the site of collection suggesting that plastic responses are highly dynamic and allow organisms to cope with changes in tem-perature. 4. Our findings demonstrate small differences in upper and lower thermal tolerance limits across populations, but substantial local acclimatization effects dictated by microhabitat temperatures, and also highlight the limited scope and strong trade-offs to respond to in-creasing temperatures. These findings demonstrate the need for incorporating infor-mation on species' ability to respond to environmental change using both laboratory and field approaches into climate change models.
FIGURE 5 in Linking burrow morphology to the behaviors of predatory soil arthropods: Applications to continental ichnofossils
FIGURE 5. Burrow-associated activities and behaviors observed among the studied arthropod predators. A) Hysterocrates gigas (at arrow) dwelling within a shallow burrow with an enlarged terminal chamber. B) Two specimens of Pandinus imperator dwelling within a burrow complex. C) Scolopendra polymorpha moving through a burrow complex. D) Scolopendra polymorpha engaged in ambush predation positioned just below the burrow opening. E) Hysterocrates gigas engaged in ambush predation braced within the vertical shaft below the burrow opening. F) Aphonopelma chalcodes (at arrow) waiting within its burrow for prey to enter the tunnel. G) Pandinus imperator (at arrow) waiting within its burrow for prey.
Data from: Thermal acclimation and adaptation across populations in a broadly distributed soil arthropod
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The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding
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Adaptive differences in gene expression associated with stress tolerance in the soil arthropod Orchesella cincta
GEO Series GSE14076. Orchesella cincta. 16 samples. Type: Expression profiling by array.
Transcriptional plasticity of a soil arthropod across different ecological conditions
GEO Series GSE21213. Folsomia candida. 112 samples. Type: Expression profiling by array.
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