Population-specific transcriptional differences associated with freeze tolerance in a terrestrial worm

Gain of thermal tolerance through acclimation is quicker than the loss by de-acclimation in the freeze-tolerant potworm, Enchytraeus albidus

Environmental temperature variation, naturally occurring or induced by climate change, leads organisms to evolve behavioural and physiological responses to handle thermal fluctuations. Among them, phenotypic plasticity is considered a fundamental response to natural thermal variations. Nevertheless, we know little about the rate of thermal acclimation responses and the physiological mechanisms underpinning phenotypic plasticity in freeze-tolerant invertebrates. We assessed the temporal dynamics of heat and cold tolerance plasticity in the freeze-tolerant potworm Enchytraeus albidus following thermal acclimation. Acclimation responses were investigated in worms cultured at 5 or 20°C and acclimated for varying duration (hours to weeks) at the same temperature or relocated to the opposite temperature. The rate of phenotypic responses of thermal tolerance was evaluated by assessing survival after exposure to high and low stressful temperatures. Worms cultured at 5°C were more cold tolerant and less heat tolerant than worms cultured at 20°C. The plasticity of thermal tolerance in E. albidus varied in scope and response time according to both culture and acclimation temperatures: acclimation at 20°C of worms cultured at 5°C increased heat survival within 1 day and reduced cold tolerance in 5 days, while acclimation at 5°C of worms cultured at 20°C did not affect heat survival but considerably and quickly, within 1 day, increased cold tolerance. Effects of acclimation were also assessed on membrane phospholipid fatty acid (PLFA) composition and glycogen content of worms, and showed that improved tolerance was linked to changes in membrane PLFA desaturation and chain length.

Discovery and characterization of the α-amylases cDNAs from Enchytraeus albidus shed light on the evolution of "Enchytraeus-Eisenia type" Amy homologs in Annelida

Although enchytraeids have gained popularity in scientific research, fundamental questions regarding their feeding ecology and biology remain largely unexplored. This study investigates α-amylases, major digestive enzymes responsible for hydrolyzing starch and similar polysaccharides into sugars, in Enchytraeus albidus. Genetic data related to α-amylases is currently lacking for the family Enchytraeidae but also for the entire Annelida. To detect and identify coding sequences of the expressed α-amylase genes in COI-monohaplotype culture (PL-A strain) of E. albidus, we used classical "gene fishing" and transcriptomic approaches. We also compared coding sequence variants of α-amylase retrieved from transcriptomic data related to freeze-tolerant strains. Our results reveal that E. albidus possesses two distinct α-amylase genes (Amy I and Amy II) that are homologs to earthworm Eisenia fetida Ef-Amy genes. Different strains of E. albidus possess distinctive alleles of α-amylases with unique SNP patterns specific to a particular strain. Unlike Amy II, Amy I seems to be a highly polymorphic and multicopy gene. The domain architecture of the putative Amy proteins was found the same as for classical animal α-amylases with ABC-domains. A characteristic feature of Amy II is the lack of GHGA motif in the flexible loop region, similarly to many insect amylases. We identified "Enchytraeus-Eisenia type" α-amylase homologs in other clitellates and polychaetes, indicating the ancestral origin of Amy I/II proteins in Annelida. This study provides the first insight into the endogenous non-proteolytic digestive enzyme genes in potworms, discusses the evolution of Amy α-amylases in Annelida, and explores phylogenetic implications.

Trophic Position of the White Worm (Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis

To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no significant differences in the morphology or anatomy of their alimentary tracts. However, it is crucial to distinguish between the contribution of microbial enzymes and the animal's digestive capacity. Here, we computationally analyzed the endogenous digestive enzyme genes in Enchytraeus albidus. The analysis was based on RNA-Seq of COI-monohaplotype culture (PL-A strain) specimens, utilizing transcriptome profiling to determine the trophic position of the species. We also corroborated the results obtained using transcriptomics data from genetically heterogeneous freeze-tolerant strains. Our results revealed that E. albidus expresses a wide range of glycosidases, including GH9 cellulases and a specific digestive SH3b-domain-containing i-type lysozyme, previously described in the earthworm Eisenia andrei. Therefore, E. albidus combines traits of both primary decomposers (primary saprophytophages) and secondary decomposers (sapro-microphytophages/microbivores) and can be defined as an intermediate decomposer. Based on assemblies of publicly available RNA-Seq reads, we found close homologs for these cellulases and i-type lysozymes in various clitellate taxa, including Crassiclitellata and Enchytraeidae.

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system

Enchytraeids (Annelida) are soil invertebrates with worldwide distribution that have served as ecotoxicology models for over 20 years. We present the first high-quality reference genome of Enchytraeus crypticus, assembled from a combination of Pacific Bioscience single-molecule real-time and Illumina sequencing platforms as a 525.2 Mbp genome (910 gapless scaffolds and 18,452 genes). We highlight isopenicillin, acquired by horizontal gene transfer and conferring antibiotic function. Significant gene family expansions associated with regeneration (long interspersed nuclear elements), the innate immune system (tripartite motif-containing protein) and response to stress (cytochrome P450) were identified. The ACE (Angiotensin-converting enzyme) - a homolog of ACE2, which is involved in the coronavirus SARS-CoV-2 cell entry - is also present in E. crypticus. There is an obvious potential of using E. crypticus as a model to study interactions between regeneration, the innate immune system and aging-dependent decline.

Thermal optimum for mass production of the live feed organism Enchytraeus albidus

Live feed organisms are essential for the larval stages of many fish species grown in aquaculture, and juvenile fish reared on live feeds often exhibit higher survival and growth than those reared on formulated feed. The terrestrial enchytraeid (white worm), Enchytraeus albidus, has potential as a sustainable source of live feed because it can easily be mass produced, feeds on a wide range of organic waste materials and has high contents of protein and long-chain poly-unsaturated fatty acids. In the present study, we observed the effect of temperature on population growth over five months using soil microcosms. At the outset, each microcosm was supplied with approximately the same number of cocoons. Hatched enchytraeids were given rolled oats ad libitum as feed. We followed the population growth at seven temperatures in the range of 4-25 °C and investigated body composition in order to find optimal temperature for mass production. Results showed that E. albidus has a broad thermal optimum range and displays almost similar biomass production in the range of 15-22 °C with specific growth rates between 6.5 and 6.8%. In this temperature range, protein contents were 40-45%, glycogen contents 20-25% and total fatty acid contents 15-20% of dry weight. The temperature had a highly significant effect on fatty acid composition. In particular, the abundance of omega-3 fatty acids (18:3ω3 and 20:5ω3) was largest at low temperature. For what concerns achievable density of worms in mass cultures, our results surpassed previous results and showed that densities close to 100 g L^-1 substrate are realistic. Maximum production of biomass can likely reach 80 g live worms L^-1 month^-1 at temperatures between 15 and 22 °C.

Hepatic transcriptome of the freeze-tolerant Cope's gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing

Background

Cope’s gray treefrog, Dryophytes chrysoscelis, withstands the physiological challenges of corporeal freezing, partly by accumulating cryoprotective compounds of hepatic origin, including glycerol, urea, and glucose. We hypothesized that expression of genes related to cryoprotectant mobilization and stress tolerance would be differentially regulated in response to cold. Using high-throughput RNA sequencing (RNA-Seq), a hepatic transcriptome was generated for D. chrysoscelis, and gene expression was compared among frogs that were warm-acclimated, cold-acclimated, and frozen.

Results

A total of 159,556 transcripts were generated; 39% showed homology with known transcripts, and 34% of all transcripts were annotated. Gene-level analyses identified 34,936 genes, 85% of which were annotated. Cold acclimation induced differential expression both of genes and non-coding transcripts; freezing induced few additional changes. Transcript-level analysis followed by gene-level aggregation revealed 3582 differentially expressed genes, whereas analysis at the gene level revealed 1324 differentially regulated genes. Approximately 3.6% of differentially expressed sequences were non-coding and of no identifiable homology. Expression of several genes associated with cryoprotectant accumulation was altered during cold acclimation. Of note, glycerol kinase expression decreased with cold exposure, possibly promoting accumulation of glycerol, whereas glucose export was transcriptionally promoted by upregulation of glucose-6-phosphatase and downregulation of genes of various glycolytic enzymes. Several genes related to heat shock protein response, DNA repair, and the ubiquitin proteasome pathway were upregulated in cold and frozen frogs, whereas genes involved in responses to oxidative stress and anoxia, both potential sources of cellular damage during freezing, were downregulated or unchanged.

Conclusion

Our study is the first to report transcriptomic responses to low temperature exposure in a freeze-tolerant vertebrate. The hepatic transcriptome of Dryophytes chrysoscelis is responsive to cold and freezing. Transcriptomic regulation of genes related to particular pathways, such as glycerol biosynthesis, were not all regulated in parallel. The physiological demands associated with cold and freezing, as well as the transcriptomic responses observed in this study, are shared with several organisms that face similar ecophysiological challenges, suggesting common regulatory mechanisms. The role of transcriptional regulation relative to other cellular processes, and of non-coding transcripts as elements of those responses, deserve further study.

Climate change effects on earthworms - a review

Climate change can have a plethora of effects on organisms above and below the ground in terrestrial ecosystems. Given the tremendous biodiversity in the soil and the many ecosystem functions governed by soil organisms, the drivers of soil biodiversity have received increasing attention. Various climatic factors like temperature, precipitation, soil moisture, as well as extreme climate events like drought and flood have been shown to alter the composition and functioning of communities in the soil. Earthworms are important ecosystem engineers in the soils of temperate and tropical climates and play crucial roles for many ecosystem services, including decomposition, nutrient cycling, and crop yield. Here, we review the published literature on climate change effects on earthworm communities and activity. In general, we find highly species- and ecological group-specific responses to climate change, which are likely to result in altered earthworm community composition in future ecosystems. Earthworm activity, abundance, and biomass tend to increase with increasing temperature at sufficiently high soil water content, while climate extremes like drought and flooding have deleterious effects. Changing climate conditions may facilitate the invasion of earthworms at higher latitudes and altitudes, while dryer and warmer conditions may limit earthworm performance in other regions of the world. The present summary of available information provides a first baseline for predictions of future earthworm distribution. It also reveals the shortage of studies on interacting effects of multiple global change effects on earthworms, such as potential context-dependent effects of climate change at different soil pollution levels and across ecosystem types.

Conservation Genomics in a Changing Arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Species-specific transcriptomic responses in Daphnia magna exposed to a bio-plastic production intermediate

Hydroxymethylfurfural (HMF) is a plant-based chemical building block that could potentially substitute petroleum-based equivalents, yet ecotoxicological data of this compound is currently limited. In this study, the effects of HMF on the reproduction and survival of Daphnia magna were assessed through validated ecotoxicological tests. The mechanism of toxicity was determined by analysis of transcriptomic responses induced by exposure to different concentrations of HMF using RNA sequencing. HMF exerted toxicity to D. magna with an EC₅₀ for effects on reproduction of 17.2 mg/l. HMF exposure affected molecular pathways including sugar and polysaccharide metabolism, lipid metabolism, general stress metabolism and red blood cell metabolism, although most molecular pathways affected by HMF exposure were dose specific. Hemoglobin genes, however, responded in a sensitive and dose-related manner. No induction of genes involved in the xenobiotic metabolism or oxidative stress metabolism pathway could be observed, which contrasted earlier observations on transcriptional responses of the terrestrial model Folsomia candida exposed to the same compound in a similar dose. We found 4189 orthologue genes between D. magna and F. candida, yet only twenty-one genes of those orthologues were co-regulated in both species. The contrasting transcriptional responses to the same compound exposed at a similar dose between D. magna and F. candida indicates limited overlap in stress responses among soil and aquatic invertebrates. The dose-related expression of hemoglobin provides further support for using hemoglobin expression as a biomarker for general stress responses in daphnids.

Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.