Background Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.ResultsWe applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster.ConclusionsThe expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3852-x) contains supplementary material, which is available to authorized users.

Predicted changes in soil water availability regimes with climate and land-use change will impact the community of functionally important soil organisms, such as macro-detritivores. Identifying and quantifying the functional traits that underlie interspecific differences in desiccation resistance will enhance our ability to predict both macro-detritivore community responses to changing water regimes and the consequences of the associated species shifts for organic matter turnover. Using path analysis, we tested (1) how interspecific differences in desiccation resistance among 22 northwestern European terrestrial isopod species could be explained by three underlying traits measured under standard laboratory conditions, namely, body ventral surface area, water loss rate and fatal water loss; (2) whether these relationships were robust to contrasting experimental conditions and to the phylogenetic relatedness effects being excluded; (3) whether desiccation resistance and hypothesized underlying traits could explain species distribution patterns in relation to site water availability. Water loss rate and (secondarily) fatal water loss together explained 90% of the interspecific variation in desiccation resistance. Our path model indicated that body surface area affects desiccation resistance only indirectly via changes in water loss rate. Our results also show that soil moisture determines isopod species distributions by filtering them according to traits underpinning desiccation resistance. These findings reveal that it is possible to use functional traits measured under standard conditions to predict soil biota responses to water availability in the field over broad spatial scales. Taken together, our results demonstrate an increasing need to generate mechanistic models to predict the effect of global changes on functionally important organisms.

Summary 1.The relationship between thermal resistance and expression of inducible heat shock proteins, especially Hsp70, depends on the species and temperature treatments. The induction of Hsp70 has been shown to be essential for heat stress survival in a number of species, yet the maximum protein expression levels do not coincide with peak survival after heat hardening in Drosophila . 2.Here we study the functional relationship between heat-induced expression of the heat shock protein Hsp70, and thermal resistance in adult Orchesella cincta by comparing thermal resistance (survival of 37·4 ° C for 60 min) with Hsp70 gene and protein expression levels, all three measured at time points 2, 4, 6, 23, 27, 49 h after a heat hardening treatment (35·4 ° C for 60 min). 3. Thermotolerance increased over time after heat hardening until 49 h after exposure when the experiment ended. On the other hand the expression of hsp70 messenger RNA reached a peak within the first 2 h and then sharply decreased after 6 h. Within 23 h hsp70 expression was back to control levels. 4. Surprisingly, protein levels of Hsp70 followed thermotolerance and reached the highest levels 49 h after heat hardening. A significant positive association was found between thermotolerance and Hsp70 protein levels, but not with hsp70 mRNA levels. 5. Our results support a strong correlation between Hsp70 expression levels and thermal resistance following a heat hardening treatment. They also show that gene and protein expression follow different dynamics, a difference that may be important for our understanding of the role of candidate genes in functional studies.

Increasing concern about pollution of our environment calls for advanced and rapid methods to estimate ecological toxicity. The use of gene expression microarrays in environmental studies can potentially meet this challenge. We present a novel method to examine soil toxicity. We exposed the collembolan Folsomia candida to soil containing an ecologically relevant cadmium concentration, and found a cumulative total of 1586 differentially expressed transcripts across three exposure durations, including transcripts involved in stress response, detoxification, and hypoxia. Additional enrichment analysis of gene ontology (GO) terms revealed that antibiotic biosynthesis is important at all time points examined. Interestingly, genes involved in the "penicillin and cephalosporin biosynthesis pathway" have never been identified in animals before, but are expressed in F. candida's tissue. The synthesis of antibiotics can possibly be a response to increased cadmium-induced susceptibility to invading pathogens, which might be caused by repression of genes involved in the immune-system (C-type lectins and Toll receptor). This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil, and provides a mechanistic basis for the development of a gene expression soil quality test.