Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags

<p>Abstract</p> <p>Background</p> <p>Nematodes are the dominant soil animals in Antarctic Dry Valleys and are capable of surviving desiccation and freezing in an anhydrobiotic state. Genes induced by desiccation stress have been successfully enumerated in nematodes; however we have little knowledge of gene regulation by Antarctic nematodes which can survive multiple environmental stresses. To address this problem we investigated the genetic responses of a nematode species, <it>Plectus murrayi</it>, that is capable of tolerating Antarctic environmental extremes, in particular desiccation and freezing. In this study, we provide the first insight into the desiccation induced transcriptome of an Antarctic nematode through cDNA library construction and suppressive subtractive hybridization.</p> <p>Results</p> <p>We obtained 2,486 expressed sequence tags (ESTs) from 2,586 clones derived from the cDNA library of desiccated <it>P. murrayi</it>. The 2,486 ESTs formed 1,387 putative unique transcripts of which 523 (38%) had matches in the model-nematode <it>Caenorhabditis elegans</it>, 107 (7%) in nematodes other than <it>C. elegans</it>, 153 (11%) in non-nematode organisms and 605 (44%) had no significant match to any sequences in the current databases. The 1,387 unique transcripts were functionally classified by using Gene Ontology (GO) hierarchy and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results indicate that the transcriptome contains a group of transcripts from diverse functional areas. The subtractive library of desiccated nematodes showed 80 transcripts differentially expressed during desiccation stress, of which 28% were metabolism related, 19% were involved in environmental information processing, 28% involved in genetic information processing and 21% were novel transcripts. Expression profiling of 14 selected genes by quantitative Real-time PCR showed 9 genes significantly up-regulated, 3 down-regulated and 2 continuously expressed in response to desiccation.</p> <p>Conclusion</p> <p>The establishment of a desiccation EST collection for <it>Plectus murrayi</it>, a useful model in assessing the structural, physiological, biochemical and genetic aspects of multiple stress tolerance, is an important step in understanding the genome level response of this nematode to desiccation stress. The type of transcript analysis performed in this study sets the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in nematodes.</p

Invertebrate Diversity in Taylor Valley Soils and Sediments

Explaining how ecosystems function across variable landscapes will require knowledge of biodiversity patterns. In particular, biodiversity studies of soils and sediments will help in understanding the linkages between ecosystem processes in both of these habitats (Freckman et al. 1997). Soils and sediments are domains for ecosystem processes such as decomposition and trace gas exchange. There are few studies, however, that have compared abundance and diversity of organisms in adjacent soils and sediments (Freckman et al. 1997). The goal of this study was to increase understanding of how the biotic communities involved in ecosystem processes are organized within an important feature of the Antarctic dry valley landscape—a stream channel and the soils and sediments surrounding it

Co- variation in soil biodiversity and biogeochemistry in northern and southern Victoria Land, Antarctica

Data from six sites in Victoria Land (72–77°S) investigating co-variation in soil communities (microbial and invertebrate) with biogeochemical properties showthe influence of soil properties on habitat suitability varied among local landscapes as well as across climate gradients. Species richness of metazoan invertebrates (Nematoda, Tardigrada and Rotifera) was similar to previous descriptions in this region, though identification of three cryptic nematode species of Eudorylaimus through DNA analysis contributed to the understanding of controls over habitat preferences for individual species. Denaturing Gradient Gel Electrophoresis profiles revealed unexpectedly high diversity of bacteria. Distribution of distinct bacterial communities was associated with specific sites in northern and southern Victoria Land, as was the distribution of nematode and tardigrade species. Variation in soil metazoan communities was related to differences in soil organic matter, while bacterial diversity and community structure were not strongly correlated with any single soil property. There were no apparent correlations between metazoan and bacterial diversity, suggesting that controls over distribution and habitat suitability are different for bacterial and metazoan communities. Our results imply that top-down controls over bacterial diversity mediated by their metazoan consumers are not significant determinants of bacterial community structure and biomass in these ecosystems

Tree Species Traits Influence Soil Physical, Chemical, and Biological Properties in High Elevation Forests

BACKGROUND: Previous studies have shown that plants often have species-specific effects on soil properties. In high elevation forests in the Southern Rocky Mountains, North America, areas that are dominated by a single tree species are often adjacent to areas dominated by another tree species. Here, we assessed soil properties beneath adjacent stands of trembling aspen, lodgepole pine, and Engelmann spruce, which are dominant tree species in this region and are distributed widely in North America. We hypothesized that soil properties would differ among stands dominated by different tree species and expected that aspen stands would have higher soil temperatures due to their open structure, which, combined with higher quality litter, would result in increased soil respiration rates, nitrogen availability, and microbial biomass, and differences in soil faunal community composition. METHODOLOGY/PRINCIPAL FINDINGS: We assessed soil physical, chemical, and biological properties at four sites where stands of aspen, pine, and spruce occurred in close proximity to one-another in the San Juan Mountains, Colorado. Leaf litter quality differed among the tree species, with the highest nitrogen (N) concentration and lowest lignin:N in aspen litter. Nitrogen concentration was similar in pine and spruce litter, but lignin:N was highest in pine litter. Soil temperature and moisture were highest in aspen stands, which, in combination with higher litter quality, probably contributed to faster soil respiration rates from stands of aspen. Soil carbon and N content, ammonium concentration, and microbial biomass did not differ among tree species, but nitrate concentration was highest in aspen soil and lowest in spruce soil. In addition, soil fungal, bacterial, and nematode community composition and rotifer, collembolan, and mesostigmatid mite abundance differed among the tree species, while the total abundance of nematodes, tardigrades, oribatid mites, and prostigmatid mites did not. CONCLUSIONS/SIGNIFICANCE: Although some soil characteristics were unaffected by tree species identity, our results clearly demonstrate that these dominant tree species are associated with soils that differ in several physical, chemical, and biotic properties. Ongoing environmental changes in this region, e.g. changes in fire regime, frequency of insect outbreaks, changes in precipitation patterns and snowpack, and land-use change, may alter the relative abundance of these tree species over coming decades, which in turn will likely alter the soils

Prey Nutritional Quality Interacts With Chemical Defenses to Affect Consumer Feeding and Fitness

Numerous studies have assessed the individual effects of prey nutritional quality or chemical defenses on consumer feeding behavior. However, little is known about how these traits interact to affect consumer feeding and performance. We tested the separate and interactive effects of prey chemical defenses and nutritional quality on the feeding behavior and fitness of six sympatric crustacean mesograzers. Natural concentrations of diterpene alcohols (dictyols) from the brown alga Dictyota menstrualis were incorporated, or not incorporated, into lower quality and higher quality foods to create artificial diets mimicking prey of variable value and defense. Five amphipods (Ampithoe longimana, A. valida, Cymadusa compta, Gammarus mucronatus, and Elasmopus levis) and one isopod (Paracerceis caudata), representing a continuum of closely to distantly related organisms, were fed intact algae or lower and higher quality diets containing or lacking dictyols. All six mesograzers preferred the green alga Enteromorpha intestinalis to the dictyol producing alga Dictyota menstrualis. In assays allowing consumers to choose between simultaneously available foods, dictyols deterred feeding by all five amphipods, but not the isopod; this occurred for both lower and higher quality foods. In no-choice assays, where consumers were confined with only one of our four treatment diets, effects on feeding became more complex. Nutritional quality alone affected feeding by five of the six species. These grazers compensated for lower quality by increasing consumption. Dictyols suppressed feeding for four of the six species. More interestingly, there were significant dictyol X quality interactions for three species. Dictyols decreased feeding more when placed in lower quality foods than higher quality foods. Two amphipods deterred by dictyols in the choice assays readily consumed dictyol-containing foods in no-choice situations and suffered few negative effects of doing so. Although all amphipods were deterred by dictyols in choice assays, dictyols decreased fitness (survivorship, growth, or reproduction) for only four of the five species. These effects included large and immediate decreases in survivorship, dramatic effects on reproduction, and modest effects on female growth. Dictyols enhanced survivorship of the isopod. Thus, the effects of secondary metabolites on feeding in choice situations vs. fitness in long-term assays were inconsistent. For three amphipods, certain effects of food quality, dictyols, or their interaction were detected only for females. In general, negative effects of dictyols on fitness were greater in lower than in higher quality foods, suggesting that prey nutritional value may counteract the effects of defensive metabolites. For example, when G. mucronatus consumed dictyols in lower quality foods, mortality was \u3e80% by day 5; for dictyols in higher quality foods, 80% mortality took 28 days to develop. Lower quality foods alone significantly decreased growth for the isopod, three of the amphipods, and the females of a fourth amphipod, concomitantly reducing fecundity for four of the five amphipods studied. The effects of both chemical defenses and nutritional quality were unrelated to consumer phylogeny; responses of congeners varied as much, or more, than responses of more distantly related consumers. Understanding mechanisms and consequences of food selection requires that the interactive effects of both chemical defenses and prey nutritional characteristics be considered explicitly

Exploring the boundaries of microbial habitability in soil

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dragone, N. B., Diaz, M. A., Hogg, I., Lyons, W. B., Jackson, W. A., Wall, D. H., Adams, B. J., & Fierer, N. Exploring the boundaries of microbial habitability in soil. Journal of Geophysical Research: Biogeosciences, 126(6), (2021): e2020JG006052, https://doi.org/10.1029/2020JG006052.Microbes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84–85°S, 174–177°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils—results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results suggest that microbial life is severely restricted in the coldest, driest, and saltiest Antarctic soils. Constant exposure to these conditions for thousands of years has limited microbial communities so that their presence and activity is below detectable limits using a variety of standard methods. Such soils are unlikely to be unique to the studied region with this work supporting previous hypotheses that microbial habitability is constrained by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that limit microbial life in terrestrial surface soils.This work was supported by grants from the U.S. National Science Foundation (ANT 1341629 to B. J. Adams, N. Fierer, W. Berry Lyons, and D. H. Wall and OPP 1637708 to B. J. Adams) with additional support provided to N. B. Dragone from University Colorado Department of Ecology and Evolutionary Biology

Metabarcoding inventory of an arctic tundra soil ecosystem reveals highly heterogeneous communities at a small scale

Biodiversity surveys of Arctic soil ecosystems are limited. Here, we provide a sequence-based inventory of soil fauna from an Arctic tundra ecosystem near the Canadian High Arctic Research Station in Cambridge Bay, Nunavut. Invertebrate communities were extracted at a vegetated and non-vegetated site in three replicates and inventoried using 18S metabarcode sequencing. A total of 361 amplicon sequence variants (ASV) were identified and assigned to the closest matching taxonomic orders, most of which belonged to the Nematoda and Arthropoda. Vegetated soils showed no significantly higher ASV richness relative to non-vegetated soils although they contained a significantly higher diversity of arthropod taxa including insects, mites, and springtails. Most taxa were found only at a single location and even samples from the same site displayed distinct communities, suggesting that belowground species richness in Arctic tundra habitats is highly heterogeneous. Preserving soil biodiversity in a changing Arctic is essential for Inuit communities who rely on intact tundra ecosystems for their health and wellbeing

Getting to the Root of Selenium Hyperaccumulation—Localization and Speciation of Root Selenium and Its Effects on Nematodes

Elemental hyperaccumulation protects plants from many aboveground herbivores. Little is known about effects of hyperaccumulation on belowground herbivores or their ecological interactions. To examine effects of plant selenium (Se) hyperaccumulation on nematode root herbivory, we investigated spatial distribution and speciation of Se in hyperaccumulator roots using X-ray microprobe analysis, and effects of root Se concentration on root-associated nematode communities. Perennial hyperaccumulators Stanleya pinnata and Astragalus bisulcatus, collected from a natural seleniferous grassland contained 100–1500 mg Se kg−1 root dry weight (DW). Selenium was concentrated in the cortex and epidermis of hyperaccumulator roots, with lower levels in the stele. The accumulated Se consisted of organic (C-Se-C) compounds, indistinguishable from methyl-selenocysteine. The field-collected roots yielded 5–400 nematodes g−1 DW in Baermann funnel extraction, with no correlation between root Se concentration and nematode densities. Even roots containing \u3e 1000 mg Se kg−1 DW yielded herbivorous nematodes. However, greenhouse-grown S. pinnata plants treated with Se had fewer total nematodes than those without Se. Thus, while root Se hyperaccumulation may protect plants from non-specialist herbivorous nematodes, Se-resistant nematode taxa appear to associate with hyperaccumulators in seleniferous habitats, and may utilize high-Se hyperaccumulator roots as food source. These findings give new insight into the ecological implications of plant Se (hyper)accumulation