03078nas a2200241 4500008004100000022001300041245011000054210006900164260001200233300001100245490000800256520229200264653002502556653002602581653002802607653002502635653002702660653001802687100001302705700002502718700002102743856007202764 2024 eng d a0929139300aAn Antarctic worm and its soil ecosystem: A review of an emerging research program in ecological genomics0 aAntarctic worm and its soil ecosystem A review of an emerging re c01/2024 a1051100 v1933 a

Relationships between the evolution of species and their ecosystems can be difficult to accurately assess due to the high number of confounding biological variables (e.g., biotic interactions among community members and the resulting complex relationships between genetic pathways and organism phenotypes). Thus, progress in ecological genomics by making inferences about fundamental ecological patterns and processes is hampered by high biodiversity and subsequent complex biotic interactions. Study systems that are naturally low in biological and ecological complexity, and strongly structured by abiotic drivers, can serve as models for bridging the gap between controlled mesocosm experiments and natural ecosystems. The terrestrial ecosystems of the Antarctic dry valleys have low biodiversity and constrained ecological complexity, primarily because ecological communities are so strongly shaped by physical, rather than biological, factors. The harsh constraints of the physical environment on organismal evolution and the structure of ecological communities make this an optimal natural system for disentangling the influence of specific environmental parameters on genotype/phenotype and gene by environment interactions. This work reviews the biology, evolution, and ecology of an emerging model organism, the free-living nematode Plectus murrayi, in a model ecosystem, the McMurdo Dry Valleys (MDVs) of Antarctica. In the MDVs, habitat suitability, including nutrient availability, has been shown to drive organismal (nematode) life history evolution, including growth and reproduction, primarily by way of changes in the expression of developmental genes. Changes in growth rates and reproductive schedules are accomplished primarily through alterations of nuclear rRNA gene copy number. The predicted and observed responses to natural experiments have been replicated in the laboratory, providing a synthesis of field observations and experimental evolution. Studying such natural model systems as this could fill several persistent knowledge gaps in our understanding of how genetic variation, genomic architecture, and gene regulation drive the genotype-phenotype paradigm, and the consequent effects of these drivers on ecosystem structure and functioning.

10aecological amplitude10aecological succession10aelemental stoichiometry10aextreme environments10alife history evolution10amodel systems1 aXue, Xia1 aThompson, Andrew, R.1 aAdams, Byron, J. uhttps://www.sciencedirect.com/science/article/pii/S092913932300308602076nas a2200313 4500008004100000245008700041210006900128260001200197300001100209490000800220520114900228653002801377653002701405653002401432653002401456653001301480653000901493100001301502700002501515700001601540700002201556700001701578700001801595700001601613700002401629700002001653700001701673856007201690 2023 eng d00aEcological stoichiometry drives the evolution of soil nematode life history traits0 aEcological stoichiometry drives the evolution of soil nematode l c02/2023 a1088910 v1773 a

Ecological stoichiometry is a useful theoretical framework for understanding the sources and controls on nutrient availability that structure the composition and diversity of biotic communities. One such relationship is that organismal development rate is positively linked to cellular Phosphorus (P). We hypothesized that P availability, relative to other nutrients, e.g., nitrogen and carbon, would drive the evolution of traits associated with organismal growth and development. We examined the effects of P availability both in situ and in vitro, on free-living soil nematodes. We found that P-deficient environments produce predictable changes in the ecology and evolution of important life history traits. Our results identify altered rRNA gene copy number and subsequent changes in gene expression and protein synthesis as mechanisms by which P-deficiency influences these traits. These findings have important implications for explaining soil ecological and evolutionary patterns across multiple levels of organization, including the structure and functioning of organisms, populations, communities, and ecosystems.

10aelemental stoichiometry10agrowth rate hypothesis10alife history theory10amolecular evolution10anematoda10arRNA1 aXue, Xia1 aAdhikari, Bishwo, N.1 aBall, Becky1 aBarrett, John, E.1 aMiao, Jinxin1 aPerkes, Ammon1 aMartin, Mac1 aSimmons, Breana, L.1 aWall, Diana, H.1 aAdams, Byron uhttps://www.sciencedirect.com/science/article/pii/S003807172200348002770nas a2200241 4500008004100000245007200041210006900113260001200182300000800194490000700202520208300209653001502292653001902307653001902326653001302345653002202358653002102380100002902401700002002430700001302450700002102463856004402484 2023 eng d00aTemperature response of metabolic activity of an Antarctic nematode0 aTemperature response of metabolic activity of an Antarctic nemat c01/2023 a1090 v123 a

Because of climate change, the McMurdo Dry Valleys of Antarctica (MCM) have experienced an increase in the frequency and magnitude of summer pulse warming and surface ice and snow melting events. In response to these environmental changes, some nematode species in the MCM have experienced steady population declines over the last three decades, but Plectus murrayi, a mesophilic nematode species, has responded with a steady increase in range and abundance. To determine how P. murrayi responds to increasing temperatures, we measured metabolic heat and CO2 production rates and calculated O2 consumption rates as a function of temperature at 5 °C intervals from 5 to 50 °C. Heat, CO2 production, and O2 consumption rates increase approximately exponentially up to 40 °C, a temperature never experienced in their polar habitat. Metabolic rates decline rapidly above 40 °C and are irreversibly lost at 50 °C due to thermal stress and mortality. Caenorhabditis elegans, a much more widespread nematode that is found in more temperate environments reaches peak metabolic heat rate at just 27 °C, above which it experiences high mortality due to thermal stress. At temperatures from 10 to 40 °C, P. murrayi produces about 6 times more CO2 than the O2 it consumes, a respiratory quotient indicative of either acetogenesis or de novo lipogenesis. No potential acetogenic microbes were identified in the P. murrayi microbiome, suggesting that P. murrayi is producing increased CO2 as a byproduct of de novo lipogenesis. This phenomenon, in conjunction with increased summer temperatures in their polar habitat, will likely lead to increased demand for carbon and subsequent increases in CO2 production, population abundance, and range expansion. If such changes are not concomitant with increased carbon inputs, we predict the MCM soil ecosystems will experience dramatic declines in functional and taxonomic diversity.

10aAntarctica10acarbon cycling10aclimate change10anematode10arespiration rates10asoil temperature1 aRobinson, Colin, Michael1 aHansen, Lee, D.1 aXue, Xia1 aAdams, Byron, J. uhttps://www.mdpi.com/2079-7737/12/1/10900974nas a2200217 4500008004100000245004900041210004200090260001200132490000700144520034200151653001500493653001700508653001300525653002500538653001000563653001400573100001300587700002100600700002200621856011300643 2022 eng d00aA draft mitogenome of Plectus murrayi0 adraft mitogenome of iPlectus murrayii c02/20220 v543 a

Plectus murrayi is a free-living microbivorous nematode endemic to Antarctic soils. Our draft assembly of its mitogenome was 15,656 bp long, containing 12 protein-coding, eight transfer RNA (tRNA), and two ribosomal RNA (rRNA) genes. Mitophylogenomic analyses extend our understanding of mitochondrial evolution in Nematoda

10aAntarctica10agenome decay10agenomics10amitochondrial genome10aMitoZ10aphylogeny1 aXue, Xia1 aAdams, Byron, J.1 aDilman, Adler, R. uhttps://www.sciendo.com/article/10.2478/jofnem-2022-0035https://www.sciendo.com/pdf/10.2478/jofnem-2022-003502256nas a2200217 4500008004100000245008600041210006900127260001200196520154900208653001401757653002401771653002001795653001701815653002001832100001301852700001901865700002201884700002201906700001701928856009301945 2021 eng d00aGenome analysis of Plectus murrayi, a nematode from continental Antarctica0 aGenome analysis of IPlectus murrayiI a nematode from continental c01/20213 a

Plectus murrayi is one of the most common and locally abundant invertebrates of continental Antarctic ecosystems. Because it is readily cultured on artificial medium in the laboratory and highly tolerant to an extremely harsh environment, Plectus murrayi is emerging as a model organism for understanding the evolutionary origin and maintenance of adaptive responses to multiple environmental stressors, including freezing and desiccation. The de novo assembled genome of Plectus murrayi contains 225.741 million base pairs and a total of 14,689 predicted genes. Compared to Caenorhabditis elegans, the architectural components of Plectus murrayi are characterized by a lower number of protein-coding genes, fewer transposable elements, but more exons, than closely related taxa from less harsh environments. We compared the transcriptomes of lab-reared Plectus murrayi with wild-caught Plectus murrayi and found genes involved in growth and cellular processing were up-regulated in lab-cultured Plectus murrayi, while a few genes associated with cellular metabolism and freeze tolerance were expressed at relatively lower levels. Preliminary comparative genomic and transcriptomic analyses suggest that the observed constraints on P. murrayi genome architecture and functional gene expression, including genome decay and intron retention, may be an adaptive response to persisting in a biotically simplified, yet consistently physically harsh environment.

10agene loss10agenome architecture10agenome assembly10agenome decay10aPlectus murrayi1 aXue, Xia1 aSuvorov, Anton1 aFujimoto, Stanley1 aDilman, Adler, R.1 aAdams, Byron uhttps://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkaa045/604418904018nas a2200217 4500008004100000245011800041210006900159260004000228490001000268520328000278653002403558653002703582653002103609653002703630653002003657653002403677653001803701100001303719700001703732856005103749 2018 eng d00aGenomics and transcriptomics of Antarctic nematodes reveal drivers of life history evolution and genome evolution0 aGenomics and transcriptomics of Antarctic nematodes reveal drive aProvo, UTbBrigham Young University0 vPh.D.3 a

Elemental stoichiometry defines a critical understanding of the relationship between nutrient availability and usage throughout different levels of the biological community. We found there is a link between available phosphorus (P), cellular phosphorus, and nematode development as postulated by the growth rate hypothesis (GRH). I predicted that in a P-poor environment, cellular RNA concentrations would be lower than they are in P-rich environment, and thus the 18srRNA expression level will have reduced. To most efficiently regulate the uptake of limited P, I predicted that nematodes in P-poor environments would decrease the number of copies of the 18s rRNA gene in their genome. I measured life history traits as well as rRNA gene expression and gene copy number. We found that elemental stoichiometry predicts evolutionary changes consistent with the Growth Rate Hypothesis. We sequenced and assembled a draft genome of P. murrayi. Although we expected to find genes responsible for stress tolerance, we hypothesized that in response to strong selection pressure associated with living in a simplified ecosystem, over time the genome of P. murrayi should have undergone significant decay (gene loss) relative to species in ecosystems structured more strongly by biotic interactions. We found significantly fewer genes in P. murrayi. To compare patterns of gene expression between two highly divergent Antarctic nematode species, we sequenced and assembled the transcriptomes of S. lindsayae and P. murrayi. Under laboratory conditions at 4  ̊C, S. lindsayae had significantly lower rates of gene expression but expressed a significantly larger number of genes. We speculate that the differences in gene expression are correlated with life history traits (developmental rates) while the differences in the number of genes expressed can be explained by their different genetic systems (S. lindsayae is amphimictic, P. murrayi is parthenogenic) and the soil environments to which they are adapted. Since we previously showed that differences in available P content can influence the evolution of gene expression via gene copy number, and that this ultimately influences growth rate, we wondered how much of this response is driven by genetics versus how strongly these patterns are driven by temperature. To better understand this, we maintained wild type populations of P. murrayi in P-rich and P-poor conditions at 5  ̊C, 10  ̊C and 15 ̊C in the laboratory for over 40 generations and sequenced the transcriptomes prepared from each treatment group. We found that nutrient levels played an important role in gene expression when the temperature is optimal for P. murrayi culturing and that temperature is more important in gene expression when the available P is limited. This work underscores the utility of using principles of elemental stoichiometry coupled with genomic and transcriptomics research tools to make and test predictions about life history evolution. The results of my work also inform inferences about the ways in which nutrient availability also drives the organization of trophic interactions and ultimately ecosystems.

10aAntarctic nematodes10aCaenorhabditis elegans10agenome evolution10agrowth rate hypothesis10aPlectus murrayi10aScottnema lindsayae10atranscriptome1 aXue, Xia1 aAdams, Byron uhttps://search.proquest.com/docview/2081899003