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As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/ M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013- 43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849).

In the polar desert ecosystem of the McMurdo Dry Valleys of Antarctica, biology is constrained by available liquid water, low temperatures, as well as the availability of organic matter and nutrient elements. These soil ecosystems are climate-sensitive, where projected future warming may have profound effects on biological communities and biogeochemical cycling. Warmer temperatures will mobilize meltwater from permafrost and glaciers, may increase precipitation and may be accompanied by pulses of nutrient availability. Enhanced water and nutrient availability have the potential to greatly influence desert soil biology and ecosystem processes. The objectives of this 5-year study were to determine which nutrient elements (C, N, P) are most limiting to dry valley soil communities and whether landscape history (i.e., in situ soil type and stoichiometry) influences soil community response to nutrient additions. After 3 years of no noticeable response, soil CO2 flux was significantly higher under addition of C+ N than the other treatments, regardless of in situ soil stoichiometry, but microbial biomass and invertebrate abundance were variable and not influenced in the same manner. A stable isotope incubation suggests that fertilization increases C and N mineralization from organic matter via stimulating microbial activity, with loss of both the applied treatments as well in situ C and N. However, these responses are relatively short-lived, suggesting long-term impacts on C and N cycling would only occur if meltwater and nutrient pulses are sustained over time, a scenario that is increasingly likely for the dry valleys.

Microbial biofilms are biological hotspots in many alpine and polar ecosystems, but the controls on and functional significance of their fauna are little known. We studied cyanobacterial mats and the underlying sediment in a glacial meltwater stream in the McMurdo Dry valleys, Antarctica. We investigated mat biomass (total and phototrophic), diatoms, and micro-meiofauna (nematodes, rotifers, and tardigrades) at nine sites along a 1670 m stream reach in a cold, low-flow growing season, and in a warmer growing season in which peak flows (above 100 L s−1) scoured the mats. Diatom and invertebrate communities were not related, but mat biomass in the low-flow year was negatively related to nematode abundance, including that of the omnivore Eudorylaimus. In the high flow year that followed, invertebrate abundance was reduced in the mats, diatom community structure was altered, and mat biomass was higher. The difference in invertebrate abundance between years was greater in mats in upstream reaches, where the greatest increases in flow velocity may have occurred, and was negligible in mats in downstream reaches as well as in the sediment beneath the mats. Integrating our results with previous findings, we generate two predictive hypotheses to be tested in glacial meltwater streams: (1) under peak flows invertebrates decline in the microbial mats, while (2) the sediment beneath the mats is a refuge from the flow disturbance. Our results also suggest that, under stable flow conditions, microinvertebrate grazers could exert top-down control on microbial mat biomass.

Soil food webs of the McMurdo Dry Valleys, Antarctica are simple. These include primary trophic levels of mosses, algae, cyanobacteria, bacteria, archaea, and fungi, and their protozoan and metazoan consumers (including relatively few species of nematodes, tardigrades, rotifers, and microarthropods). These biota are patchily distributed across the landscape, with greatest faunal biodiversity associated with wet soil. Understanding trophic structure is critical to studies of biotic interactions and distribution; yet, McMurdo Dry Valley soil food web structure has been inferred from limited laboratory culturing and microscopic observations. To address this, we measured stable isotope natural abundance ratios of C (13C/12C) and N (15N/14N) for different metazoan taxa (using whole body biomass) to determine soil food web structure in Taylor Valley, Antarctica. Nitrogen isotopes were most useful in differentiating trophic levels because they fractionated predictably at higher trophic levels. Using 15N/14N, we found that three trophic levels were present in wet soil habitats. While cyanobacterial mats were the primary trophic level, the nematode Plectus murrayi, tardigrade Acutuncus antarcticus, and rotifers composed a secondary trophic level of grazers. Eudorylaimus antarcticus had a 15N/14N ratio that was 2–4‰ higher than that of grazers, indicating that this species is the sole member of a tertiary trophic level. Understanding the trophic positions of soil fauna is critical to predictions of current and future species interactions and their distributions for the McMurdo Dry Valleys, Antarctica.

Long-term observations of ecological communities are necessary for generating and testing predictions of ecosystem responses to climate change. We investigated temporal trends and spatial patterns of soil fauna along similar environmental gradients in three sites of the McMurdo Dry Valleys, Antarctica, spanning two distinct climatic phases: a decadal cooling trend from the early 1990s through the austral summer of February 2001, followed by a shift to the current trend of warming summers and more frequent discrete warming events. After February 2001, we observed a decline in the dominant species (the nematode Scottnema lindsayae) and increased abundance and expanded distribution of less common taxa (rotifers, tardigrades, and other nematode species). Such diverging responses have resulted in slightly greater evenness and spatial homogeneity of taxa. However, total abundance of soil fauna appears to be declining, as positive trends of the less common species so far have not compensated for the declining numbers of the dominant species. Interannual variation in the proportion of juveniles in the dominant species was consistent across sites, whereas trends in abundance varied more. Structural equation modeling supports the hypothesis that the observed biological trends arose from dissimilar responses by dominant and less common species to pulses of water availability resulting from enhanced ice melt. No direct effects of mean summer temperature were found, but there is evidence of indirect effects via its weak but significant positive relationship with soil moisture. Our findings show that combining an understanding of species responses to environmental change with long-term observations in the field can provide a context for validating and refining predictions of ecological trends in the abundance and diversity of soil fauna.

Altered temperature profiles resulting in increased warming and freeze-thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals. FTCs reduced both bacterial and nematode abundance, but bacterial cell numbers also declined under warming, demonstrating decoupled consumer-prey responses. We predict that higher occurrence of FTCs in cold ecosystems will select for large body size within soil microinvertebrates and overall reduce their abundance. In contrast, warm temperatures without FTCs could lead to divergent responses in soil bacteria and their microinvertebrate consumers, potentially affecting energy and nutrient transfer rates in soil food webs of cold ecosystems.

Despite the importance of tree-thinking and evolutionary trees to biology, no appropriately developed concept inventory exists to measure student understanding of these important concepts. To address this need, we developed a multiple-choice concept inventory consisting of 24 pairs of items, and we provide evidence to support its use among undergraduate students. A set of learning outcomes was developed to guide the creation of the concept inventory. The learning outcomes, student interviews, and student responses were used to develop and revise inventory items. Supporting evidence was gathered from traditional item analysis, exploratory factor analysis, confirmatory factor analysis, traditional reliability analyses, and comparisons to alternative assessments. Appropriate implementation and utility of the concept inventory are discussed.

Climate changes are likely to have major influences on the distribution and abundance of Antarctic terrestrial biota. To assess arthropod distribution and diversity within the Ross Sea region, we examined mitochondrial DNA (COI) sequences for three currently recognized species of springtail (Collembola) collected from sites in the vicinity, and to the north of, the Mackay Glacier (77°S). This area acts as a transition between two biogeographic regions (northern and southern Victoria Land). We found populations of highly divergent individuals (5%–11.3% intraspecific sequence divergence) for each of the three putative springtail species, suggesting the possibility of cryptic diversity. Based on molecular clock estimates, these divergent lineages are likely to have been isolated for 3–5 million years. It was during this time that the Western Antarctic Ice Sheet (WAIS) was likely to have completely collapsed, potentially facilitating springtail dispersal via rafting on running waters and open seaways. The reformation of the WAIS would have isolated newly established populations, with subsequent dispersal restricted by glaciers and ice-covered areas. Given the currently limited distributions for these genetically divergent populations, any future changes in species’ distributions can be easily tracked through the DNA barcoding of springtails from within the Mackay Glacier ecotone.

Biological control agents including a wide range of organisms such as predators, parasitoids, and entomopathogens (bacteria, fungi, nematodes, and viruses) are frequently used to control insect pests. Despite commercial availability of these biocontrol agents their widespread use is limited due to biological and economic difficulties. Efficient mass-production relies heavily on the environment in which the agent is grown. Nutrition can play a significant role in important biocontrol traits such as colonization and survival, tolerance to environmental stress, reproduction, and longevity. Therefore, to increase biocontrol potential nutritional aspects should be considered prior to commercial production. This review aims to explore the role nutrition plays in the production and efficacy of biocontrol agents by summarizing the effect nutrition has on important biocontrol traits, specifically traits in organisms that target insect pests including predators, parasitoids, and microbial agents.

We examined levels of genetic variability within and among populations of three Antarctic springtail species (Arthropoda: Collembola) and tested the hypothesis that genetic divergences occur among glacially-isolated habitats. The study was conducted in southern Victoria Land, Ross Dependency, Antarctica, and samples were collected from locations in the vicinity of the Mackay Glacier. We analyzed mtDNA (cytochrome c oxidase subunit I; COI) sequence variability for 97 individuals representing three species (Gomphiocephalus hodgsoni, N = 67; Cryptopygus nivicolus, N = 20; and Antarcticinella monoculata, N = 8). Haplotype diversity and genetic divergences were calculated and used to indicate population variability and also to infer divergence times of isolated populations using molecular clock estimates. Two of the three species showed high levels of genetic divergence. Gomphiocephalus hodgsoni, a widespread and common species, showed 7.6% sequence divergence on opposite sides of the Mackay Glacier. The more range restricted C. nivicolus showed 4.0% divergence among populations. The third species, A. monoculata, was found in only one location. Molecular clock estimates based on sequence divergences suggest that populations separated within the last 4 Mya. We conclude that habitat fragmentation resulting from Pliocene (5 Mya) and Pleistocene (2 Mya to 10 Kya) glaciations has promoted and maintained high levels of diversity among isolated springtail populations on relatively small spatial scales. The region surrounding the Mackay Glacier is likely to have provided refugia for springtail populations during glacial maxima and remains an area of high genetic and species diversity for Collembola within the Ross Sea region.

Biological control agents have become increasingly important in integrated pest management programs. However, certain traits of these agents that are needed for efficient biocontrol often decrease or are lost during in vitro rearing. Entomopathogenic nematodes (EPNs) often exhibit trait deterioration when reared under laboratory conditions. EPN trait deterioration has been attributed (at least in part) to genetic causes; however, the underlying causes of trait deterioration in its bacterial endosymbiont have not been explored. In this study the EPN symbiont Photorhabdus luminescens was monitored for the deterioration of three traits; inclusion body production, reproductive potential, and virulence, in three different nutritional environments; lipid liquid medium (LLM), nutrient broth (NB), and tryptic soy broth + yeast extract (TSY). Significant trait deterioration did not occur for any of the traits in any environment. There was an increase in inclusion body production in TSY. Additionally, there was variation in growth within NB and TSY sub-cultured population lines and one TSY sub-population line was less virulent than the other two. However, returning bacteria to LLM restored all traits to wild-type levels. We infer the observed trait deterioration in Photorhabdus was minimal and appeared to be driven by environmental conditions as opposed to stable genetic changes. Our data suggest that variation among traits of in vitro cultures of Photorhabdus is more likely due to environmental variation than inadvertent laboratory selection or other genetic processes.

Photorhabdusis a bacterium that forms a mutualistic relationship with nematodes (Heterorhabditidae) and is responsible for insect mortality during nematode infection. The purpose of this study was to investigate virulence modulation (vmo) inPhotorhabdusspp. where individual colonies exhibit different levels of virulence. Despite in-depth studies on culturingPhotorhabdusspp. and its nematode partner, little is known about ideal growth conditions prior to virulence assays. Accordingly, eightPhotorhabdusstrains with representatives from each species were grown in four media types. All strains grew best in either Luria-Bertani broth + 0.1% pyruvate or tryptic soy broth + 0.5% yeast extract. However, on agar the only media on which all strains grew well were agar plates supplemented with pyruvate. To investigate vmo, virulence of individual colonies from three species was examined. Vmo was exhibited in two out of the three tested strains. Results may aid in the design ofPhotorhabdusvirulence assays.

In the Southern Hemisphere, the major sources of dust and other aeolian materials are from Patagonia, South Africa, Australia, and New Zealand. Dust from Patagonia and New Zealand has been identified in ice cores throughout Antarctica, suggesting that during arid and windy periods, such as glacial periods, dust can be entrained and transported onto the continent. However, little information exists on modern Antarctic dust sources, transport, and its role in the Southern Hemisphere dust cycle. We present the first geochemical characterization of aeolian materials collected at five heights (between 5 cm and 100 cm) above the surface in four valleys within the McMurdo Dry Valleys, the largest ice-free area in Antarctica. Our mineralogy data indicate that these materials are primarily derived from local rocks of the McMurdo Volcanics, Ferrar Dolerite, Beacon Sandstone and Granite Harbor Intrusives, with varying contributions of each rock type dependent on the valley location. While major oxide, trace element and rare earth element data show that low elevation and coastal locations (with respect to the Ross Sea) are dominated by local sources, high elevation and inland locations have accumulated both local materials and dust from other distant Southern Hemisphere sources. This far-traveled material may not be accumulating today, but represents a paleo source that is resuspended from the soils. By geochemically “fingerprinting” aeolian materials from the MDV, we can better inform future studies on the transport of materials within Antarctica and between Southern Hemisphere land masses.

Coynema poeyi (Coy, García & Álvarez, 1993) (Oxyuridomorpha: Hystrignathidae) is redescribed and illustrated with the aid of SEM. New features of the cephalic end of both sexes and copulatory papillae pattern of the males were observed and the generic diagnosis is emended in order to include such features. New locality records are given. The phylogenetic position of the species is inferred on the basis of the D2-D3 segment of the LSU rDNA. C. poeyi is located basal in a monophyletic clade formed by other hystrignathids: two species of Longior Travassos & Kloss, 1958 and Hystrignathus sp.

Imbalances in C:N:P supply ratios may cause bacterial resource limitations and constrain biogeochemical processes, but the importance of shifts in soil stoichiometry are complicated by the nearly limitless interactions between an immensely rich species pool and a multiple chemical resource forms. To more clearly identify the impact of soil C:N:P on bacteria, we evaluated the cumulative effects of single and coupled long-term nutrient additions (i.e., C as mannitol, N as equal concentrations NH4+ and NO3-, and P as Na3PO4) and water on communities in an Antarctic polar desert, Taylor Valley. Untreated soils possessed relatively low bacterial diversity, simplified organic C sources due to the absence of plants, limited inorganic N, and excess soil P potentially attenuating links between C:N:P. After six years of adding resources, an alleviation of C and N colimitation allowed one rare Micrococcaceae, an Arthrobacter species, to dominate, comprising 47% of the total community abundance and elevating soil respiration by 136% relative to untreated soils. The addition of N alone reduced C:N ratios, elevated bacterial richness and diversity, and allowed rare taxa relying on ammonium and nitrite for metabolism to become more abundant (e.g., nitrite oxidizing Nitrospira species (Nitrosomonadaceae), denitrifiers utilizing nitrite (Gemmatimonadaceae) and members of Rhodobacteraceae with a high affinity for ammonium). Based on community co-occurrence networks, lower C:P ratios in soils following P and CP additions created more diffuse and less connected communities by disrupting 73% of species interactions and selecting for taxa potentially exploiting abundant P. Unlike amended nutrients, water additions alone elicited no lasting impact on communities. Our results suggest that as soils become nutrient rich a wide array of outcomes are possible from species dominance and the deconstruction of species interconnectedness to the maintenance of biodiversity.

The status of Longior alius García & Coy, 1994 (Nematoda: Thelastomatoidea: Hystrignathidae) is discussed on the basis of new material obtained from its type host Antillanax pertyi (Kaup, 1869) (Coleoptera: Passalidae) from Limonar, Guantánamo province, Cuba, near the type locality. Based on morphological and molecular studies L. alius is considered synonymous with L. longior Morffe & García, 2011. L. longior and L. similis Morffe, García & Ventosa, 2009 are redescribed and illustrated with the aid of SEM. New locality records for both species are given. The conspecificity of females and males of both species is supported by comparison of the D2-D3 segment of the 28S LSU rDNA. The inter-specific differences and phylogenetic position of L. longior and L. similis are discussed.

Informationon the biology, distribution, host-parasite relationship and economic impact of plant-parasitic nematodes reported in Utah and Nevada during the past 100 years is reviewed. Special emphasis is given to problems caused by nematode parasites of above ground plant parts (Anguina agrostis, A. tritici, Mesoanguina balsamophila and Ditylenchus dipsaci) and roots (Heterodera avenae, H. schachtii, Meloidogyne chitwoodi, M. hapla, Pratylenchus neglectus, P. thornei, P. vulnus and Xiphinema americanum). Biological and morphological information about three nematode parasites of some trees and shrubs found in the natural environment in Utah (Bellodera utahensis, Nacobbus aberrans and Sphaeronema rumicis) is also included. Appropriate management practices of the species that damage cereals, forage legumes, grasses, potatoes and sugar beet are discussed.

Global climate change scenarios predict not only higher temperatures, but also increased climatic variability. In cold regions, these changes may bring about a shift in the frequency of soil freeze–thaw cycles (FTCs), which represent a significant physiological challenge, especially for small, poikilothermic animals with limited mobility. To assess the impact of FTCs on cold-adapted soil biota, we evaluated freeze–thaw dynamics (i.e., 0 °C crossings) and demographics of the dominant nematode Scottnema lindsayae (proportion of adults, population size) over 20 years in soils at two locations in Taylor Valley, Antarctica. Based on hourly soil temperature data, we demonstrate that FTCs are a frequent feature in Taylor Valley, but with high inter-annual and spatial variability. Valley topography and soil moisture were found to impact FTC frequency, suggesting that basins within Taylor Valley have different susceptibilities to environmental variability. Increased FTC frequency in 1999–2001 coincided with a shift in S. lindsayae populations, with fewer juveniles reaching maturity. In the years following decreased adult proportions, overall S. lindsayae numbers were reduced, implying a strong negative effect of FTCs on in situ recruitment. Our results suggest that increased FTC frequency in the Dry Valleys slows S. lindsayae development, reducing reproductive success, and may take years to impact population size, which demonstrates the importance of long-term research to accurately predict the consequences of climate change on soil biota and biogeochemical cycling in the cold regions.

This study reports part of a long-term program to help students improve scientific reasoning using higher-order cognitive tasks set in the discipline of cell biology. This skill was assessed using problems requiring the construction of valid conclusions drawn from authentic research data. We report here efforts to confirm the hypothesis that data interpretation is a complex, multifaceted exercise. Confirmation was obtained using a statistical treatment showing that various such problems rank students differently—each contains a unique set of cognitive challenges. Additional analyses of performance results have allowed us to demonstrate that individuals differ in their capacity to navigate five independent generic elements that constitute successful data interpretation: biological context, connection to course concepts, experimental protocols, data inference, and integration of isolated experimental observations into a coherent model. We offer these aspects of scientific thinking as a “data analysis skills inventory,” along with usable sample problems that illustrate each element. Additionally, we show that this kind of reasoning is rigorous in that it is difficult for most novice students, who are unable to intuitively implement strategies for improving these skills. Instructors armed with knowledge of the specific challenges presented by different types of problems can provide specific helpful feedback during formative practice. The use of this instructional model is most likely to require changes in traditional classroom instruction.

Tardigrade diversity is measured by the richness of species in a given area. Little is known about the diversity of marine tardigrades and only nine of 38 North American marine species have been documented along the Pacific coast. Recently, six species or subspecies were collected and identified from Santa Cruz Island. Only one, Echiniscoides sigismundi sigismundi, was previously known from the area. Echiniscoides sigismndi groenlandicus, Echiiscoides hoepneri, Antechiniscus marci, Batillipes dicrocercus, and Wingstrandarctus intermedius are new records for the Pacific coast of North America. This increases the known marine tardigrade diversity from 9 to 14 species. With these new finds, the statistical estimate of species richness along the California coast has grown to about 24, leading to the conclusion that many additional species will be found.

Although most models suggest continental Antarctica was covered by ice during the Last Glacial Maximum (LGM) it has been speculated that endemic species of soil invertebrates could have survived the Pleistocene at high elevation habitats protruding above the ice sheets. We analyzed a series of soil samples from different elevations at three locations along the Beardmore Glacier in the Transantarctic Mountains (in order of increasing elevation): Ebony Ridge (ER), Cloudmaker (CM), and Meyer Desert (MD). Geochemical analyses show the MD soils, which were exposed during the LGM, were the least weathered compared to lower elevations, and also had the highest total dissolved solids (TDS). MD soils are dominated by nitrate salts (NO3/Cl ratios >10) that can be observed in SEM images. High δ17O and δ18O values of the nitrate indicate that its source is solely of atmospheric origin. It is suggested that nitrate concentrations in the soil may be utilized to determine a relative “wetting age” to better assess invertebrate habitat suitability. The highest elevation sites at MD have been exposed and accumulating salts for the longest times, and because of the salt accumulations, they were not suitable as invertebrate refugia during the LGM.

Amplified climate change in polar regions is significantly altering regional ecosystems, yet there are few long-term records documenting these responses. The McMurdo Dry Valleys (MDV) cold desert ecosystem is the largest ice-free area of Antarctica, comprising soils, glaciers, meltwater streams and permanently ice-covered lakes. Multi-decadal records indicate that the MDV exhibited a distinct ecosystem response to an uncharacteristic austral summer and ensuing climatic shift. A decadal summer cooling phase ended in 2002 with intense glacial melt (‘flood year’)—a step-change in water availability triggering distinct changes in the ecosystem. Before 2002, the ecosystem exhibited synchronous behaviour: declining stream flow, decreasing lake levels, thickening lake ice cover, decreasing primary production in lakes and streams, and diminishing soil secondary production. Since 2002, summer air temperatures and solar flux have been relatively consistent, leading to lake level rise, lake ice thinning and elevated stream flow. Biological responses varied; one stream cyanobacterial mat type immediately increased production, but another stream mat type, soil invertebrates and lake primary productivity responded asynchronously a few years after 2002. This ecosystem response to a climatic anomaly demonstrates differential biological community responses to substantial perturbations, and the mediation of biological responses to climate change by changes in physical ecosystem properties. The McMurdo Dry Valleys is the largest ice-free ecosystem in Antarctica. Here, the varied community responses to an anomalous melt season are documented.

Artículo escrito por un elevado número de autores, sólo se referencian el primero, los autores que firman como Universidad Autónoma de Madrid y el grupo de colaboración en el caso de que aparezca en el artículo, The role of aerial dispersal in shaping patterns of biodiversity remains poorly understood, mainly due to a lack of coordinated efforts in gathering data at appropriate temporal and spatial scales. It has been long known that the rate of dispersal to an ecosystem can significantly influence ecosystem dynamics, and that aerial transport has been identified as an important source of biological input to remote locations. With the considerable effort devoted in recent decades to understanding atmospheric circulation in the south-polar region, a unique opportunity has emerged to investigate the atmospheric ecology of Antarctica, from regional to continental scales. This concept note identifies key questions in Antarctic microbial biogeography and the need for standardized sampling and analysis protocols to address such questions. A consortium of polar aerobiologists is established to bring together researchers with a common interest in the airborne dispersion of microbes and other propagules in the Antarctic, with opportunities for comparative studies in the Arctic, The SCAR ANTECO Programme for hosting the workshop. Special thanks to Maria L. Ávila-Jiménez who produced the Figures. AD thanks ANR-15-CE01 INHALE and IPEV (GMOstral 1028)

Spatial distribution of soil nematode populations in Antarctic terrestrial ecosystems is tightly controlled by environmental factors and thus highly sensitive to changes in soil properties. Increases in the magnitude and frequency of episodic warming events as well as eventual warming trends are likely to result in increased water availability due to glacial melting and permafrost thaw, and may also incite changes in soil physical and chemical characteristics that determine nematode habitat suitability. We hypothesized that climate warming would result in new suitable soil habitats leading to heightened diversity and activity in nematode communities. In order to test this hypothesis, we compared nematode populations in patches of soil wetted by naturally enhanced permafrost thaw versus adjacent soils unaffected by thaw. We found that thaw sites had significantly lower nematode abundances and living to dead ratios, contradicting our hypothesis. We also observed significantly altered soil texture (finer particle size), lower pH and higher salinity in permafrost seeps. These observations suggest that current and future changes in climate may alter soil properties and result in significant changes in nematode population structure, distribution and function.

Mutualistic association between entomopathogenic Photorhabdus bacteria and Heterorhabditis nematodes represents one of the emerging model systems in symbiosis studies, yet little is known about this partnership from a coevolutionary perspective. Herein, we investigated phylogenetic and cophylogenetic relationships of Heterorhabditis and Photorhabdus strains using molecular markers Internal Transcribed Spacer and gyrase B gene sequences, respectively. The phylogenies presented consistent, well supported, monophyletic groups in the parsimonious and likelihood analyses for both the nematode and bacterial strains and supported the placement of currently recognized taxa, from which a potentially new Heterorhabditis species represented by a Thailand strain MP68 was identified. While the nematode strains with distant geographic distributions showed no detectable phylogenetic divergence within H. bacteriophora or H. georgiana monophyletic groups, their respective symbiotic bacteria speciated into two Photorhabdus species: P. luminescens and P. temperata, indicating the occurrence of duplication. Although such evolutionary process reduces the phylogenetic congruence between Heterorhabditis nematodes and Photorhabdus bacteria, global cophylogenetic tests using ParaFit detected a highly significant correlation between the two phylogenies (ParaFitGlobal = 0.001). Further, the associations between H. zealandica, H. indica and H. megidis strains and their symbiotic bacteria exhibited significant contribution to the overall cophylogenetic structure. Overall, this study reveals evidence of coevolution between Photorhabdus bacteria and Heterorhabditis nematodes and provides a framework for further examination of the evolution of these associations.

The rapidly changing climate in Antarctica is impacting the ecosystems. Since records began, climate changes have varied considerably throughout Antarctica with both positive and negative trends in temperatures and precipitation observed locally. However, over the course of this century a more directional increase in both temperature and precipitation is expected to occur throughout Antarctica. The soil communities of Antarctica are considered simple with most organisms existing at the edge of their physiological capabilities. Therefore, Antarctic soil communities are expected to be particularly sensitive to climate changes. However, a review of the current literature reveals that studies investigating the impact of climate change on soil communities, and in particular nematode communities, in Antarctica are very limited. Of the few studies focusing on Antarctic nematode communities, long-term monitoring has shown that nematode communities respond to changes in local climate trends as well as extreme (or pulse) events. These results are supported by in situ experiments, which show that nematode communities respond to both temperature and soil moisture manipulations. We conclude that the predicted climate changes are likely to exert a strong influence on nematode communities throughout Antarctica and will generally lead to increasing abundance, species richness, and food web complexity, although the opposite may occur locally. The degree to which local communities respond will depend on current conditions, i.e., average temperatures, soil moisture availability, vegetation or more importantly the lack thereof, and the local species pool in combination with the potential for new species to colonize.

The nematode communities of Antarctica are considered simple. The few species present are well adapted to the harsh conditions and often endemic to Antarctica. Knowledge of Antarctic terrestrial ecosystems is increasing rapidly, but nematode communities remain to be explored in large parts of Antarctica. In soil samples collected at Byers Peninsula (Antarctic Specially Protected Area No. 126), Livingston Island we recorded 37 nematode taxa but samples showed great variation in richness and abundance. Nematode richness decreased with increasing soil pH, whereas total abundances, and the abundance of several trophic groups, were greatest at intermediate pH (around 6.5–7). Moreover, the community composition was mainly related to pH and less so to soil moisture. Trophic group, and total nematode, rotifer and tardigrade, abundances were generally positively correlated. Byers Peninsula is thus, by maritime Antarctic standards, a nematode biodiversity hotspot, and the presence of several previously unrecorded genera indicates that nematode species richness in maritime Antarctica is probably underestimated. Our results indicate that abiotic factors influence nematode communities with little evidence for biotic interactions. The unexplained heterogeneity in community composition is probably related to variation in microclimate, vegetation, topography and unmeasured soil properties, but may also be contributed to by biological processes.

We examined mitochondrial DNA (COI) variability and distribution of Stereotydeus spp. in Victoria Land and the Transantarctic Mountains, and constructed Neighbour Joining (NJ) and Maximum Likelihood (ML) phylogenetic trees using all publicly available COI sequences for the three Stereotydeus species present (S. belli, S. mollis and S. shoupi). We also included new COI sequences from Miers, Marshall and Garwood valleys in southern Victoria Land (78°S), as well as from the Darwin (79°S) and Beardmore Glacier (83°S) regions. Both NJ and ML methods produced trees which were similar in topology differing only in the placement of the single available S. belli sequence from Cape Hallett (72°S) and a S. mollis haplotype from Miers Valley. Pairwise sequence divergences among species ranged from 9.5–18.1%. NJ and ML grouped S. shoupi from the Beardmore Glacier region as sister to those from the Darwin with pairwise divergences of 8%. These individuals formed a monophyletic clade with high bootstrap support basal to S. mollis and S. belli. Based on these new data, we suggest that the distributional range of S. shoupi extends northward to Darwin Glacier and that a barrier to dispersal for Stereotydeus, and possibly other arthropods, exists immediately to the north of this area.

SUMMARY Nematodes are the dominant soil animals of the 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, little is known about gene regulation by Antarctic nematodes that can survive multiple types and incidences of environmental stress. In order to reveal the molecular response of anhydrobiotic survival, we investigated the genetic response of an Antarctic nematode, Plectus murrayi, which can survive desiccation and freezing. Using molecular approaches, we provide insight into the regulation of desiccation-induced transcripts during different stages of stress survival under conditions characteristic of the Antarctic Dry Valley environment. Our study revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress, metabolism and signal transduction-related genes and improves desiccation and freezing survival compared with nematodes exposed to fast desiccation and freezing. Temporal analyses of gene expression showed that pre-exposure to mild stress promotes survival of harsher stress. Our results further show that exposure to slow dehydration not only improves extreme desiccation survival but also promotes enhanced cold tolerance. We also provide evidence that slow dehydration can enhance freeze tolerance in an Antarctic nematode. Expression profiling of P. murrayi transcripts is an important step in understanding the genome-level response of this nematode to different environmental stressors.

Snow accumulation can influence soil properties in arctic and alpine tundra, boreal and temperate forests, and temperate grasslands. However, snow may be even more influential in arid ecosystems, which by definition are water limited, such as the hyper-arid polar desert of the McMurdo Dry Valleys, Antarctica. Moreover, snow accumulation may be altered by climate change in the future. In order to investigate the impact of changes in snow accumulation on soils in the McMurdo Dry Valleys we experimentally manipulated the quantity of snow at two locations and monitored soil properties over 5 years in relation to a snow depth gradient created by snow fences. We predicted that increased snow depth would be associated with increased soil moisture and a shift in soil animal community structure. While we did not observe changes in soil biochemistry or community structure along the snow depth gradient at either site, increased snow accumulation caused by the snow fence altered soil properties across the entire length of the transects at one site (Fryxell), which collected substantially more snow than the other site. At Fryxell, the presence of the snow fence increased gravimetric soil moisture from 1 to 5–9%. This was associated with a decline in abundance of the dominant animal, Scottnema lindsayae, a nematode typically found in dry soil, and an increase in Eudorylaimus sp. a nematode associated with moist soil. We also observed changes in soil pH, salinity, and concentrations of inorganic nitrogen and chlorophyll a over the course of the experiment, but it was difficult to determine if these were caused by snow accumulation or simply represented temporal variation related to other factors.

Molecular techniques have had a profound impact in biology. Major disciplines, including evolutionary biology, now consistently utilize molecular tools. In contrast, molecular techniques have had a more limited impact in ecology. This discrepancy is surprising. Here, we describe the unexpected paucity of ecological research in the field colloquially referred to as ‘molecular ecology.’ Publications over the past 15 years from the journals Ecology, Evolution and Molecular Ecology reveal that much of the research published under the molecular ecology banner is in fact evolutionary in nature, and that comparatively little ecological research incorporates molecular tools. This failure to more broadly utilize molecular techniques in ecology is alarming because several promising lines of ecological inquiry could benefit from molecular approaches. Here we summarize the use of molecular tools in ecology and evolution, and suggest several ways to renew the ecological focus in ‘molecular ecology’.

Climate models predict significant future warming in polar regions. In the McMurdo Dry Valleys, Antarctica, projected summer climate warming is expected to increase snow and glacial melt, resulting in higher stream discharge, rising lake levels, and an increase in areas of moist soil, but the potential influence of warming and associated changes in hydrology on the soil ecosystem is poorly understood. To examine the effects of soil warming and changes in the availability of liquid water on populations of soil invertebrates and their habitat, we established a full-factorial warming and water addition experiment at one experimental site in each of the three hydrologic basins of Taylor Valley, Antarctica, and measured responses over 8 years. We hypothesized that an increase in temperature and moisture together would enhance habitat suitability for soil invertebrates thereby increasing abundance, biomass and diversity of the soil animal communities. Instead, warming treatments had an overall negative effect on density and body size of the microbial-feeding nematode Scottnema lindsayae, the dominant animal in the dry valleys, which decreased by 42% in warmed plots. While experimental moisture additions as a single annual pulse had no effect on nematodes, the surface flooding of one site from rapid melting of upslope subsurface ice (the result of an unusual natural warming event) drastically altered soil moisture, salinity, and animal communities; mortality of S. lindsayae increased and densities decreased. This extreme soil wetting event also resulted in an increase in chlorophyll a and populations of Eudorylaimus spp, a nematode species that prefers moist to wet habitats and feeds on soil micro-algae. Our results suggest that warming in the dry valleys could significantly affect soil nematode populations and species composition both directly and indirectly by altering species-specific habitat suitability for soil biota.

Several groups of people are essential for effectively teaching the theory of evolution in public schools. Teachers of course are at the leading edge of educating students. However, school district administrators, school boards, state education officers, and university professors all play critical roles in this endeavor. Whereas scientific discoveries and teacher training typically occur at the university level, it is school district leaders and teachers who actually disseminate this information in a way that creates an educated population of students. In this study, we introduce a partnership focused on strengthening evolution education in Utah’s public schools. Our program centers on the importance of evolution as an applied science and one that can be readily integrated throughout the biology curriculum. Our 2-day workshop—conducted in each Utah school district—brings together elected school board members, school district administrators, public school science teachers, and university professors to overcome barriers that can arise when teaching the theory of evolution as part of the 7–12 public school curriculum.

In the McMurdo Dry Valleys region of Antarctica, above-ground production is often limited to mosses and algae that occur near seasonally available liquid water such as ephemeral streams and ice-covered lakes. Compared to surrounding dry soils these critical transition zones are highly productive and harbor a more diverse assemblage of soil animals, including rotifers, tardigrades, nematodes and microarthropods. Current cooling trends punctuated by warming events, and predicted future climate warming are expected to affect the hydrology of this region and thereby biodiversity and ecosystem functioning. Above-ground communities are exposed to more variable temperature, relative humidity and greater UV radiation, and may be more vulnerable to climate change than sediments beneath, which are buffered from short-term changes. In this study, we compared above- and below-ground communities associated with either moss or cyanobacterial mats along glacial-fed streams and lakes differing in biological complexity (diversity, productivity and habitat suitability). All groups of soil fauna were more abundant in the above-ground material compared to the sediment beneath. Common indicators of habitat suitability (chlorophyll a, soil pH, soil salinity, and soil nitrogen) did not differ between vegetation types but were significantly different among sites. Variables most correlated with invertebrate abundances were sediment salinity, chlorophyll a content and nitrogen concentration. The McMurdo Dry Valleys are expected to become warmer and wetter as a result of climate change. This will likely increase the area of suitable habitat for most soil animals as areas of liquid water potentially increase and become available for longer periods of time.

Antarctic ecosystems are often considered nearly pristine because levels of anthropogenic disturbance are extremely low there. Nevertheless, over recent decades there has been a rapid increase in the number of people, researchers and tourists, visiting Antarctica. We evaluated, over 10 years, the direct impact of foot traffic on the abundance of soil animals and soil properties in Taylor Valley within the McMurdo Dry Valleys region of Antarctica. We compared soils from minimally disturbed areas with soils from nearby paths that received intermediate and high levels of human foot traffic (i.e., up to approximately 80 passes per year). The nematodes Scottnema lindsayae and Eudorylaimus sp. were the most commonly found animal species, whereas rotifers and tardigrades were found only occasionally. On the highly trampled footpaths, abundance of S. lindsayae and Eudorylaimus sp. was up to 52 and 76% lower, respectively, than in untrampled areas. Moreover, reduction in S. lindsayae abundance was more pronounced after 10 years than 2 years and in the surface soil than in the deeper soil, presumably because of the longer period of disturbance and the greater level of physical disturbance experienced by the surface soil. The ratio of living to dead Eudorylaimus sp. also declined with increased trampling intensity, which is indicative of increased mortality or reduced fecundity. At one site there was evidence that high levels of trampling reduced soil CO2 fluxes, which is related to total biological activity in the soil. Our results show that even low levels of human traffic can significantly affect soil biota in this ecosystem and may alter ecosystem processes, such as carbon cycling. Consequently, management and conservation plans for Antarctic soils should consider the high sensitivity of soil fauna to physical disturbance as human presence in this ecosystem increases. Resumen: Los ecosistemas de la Antartida a menudo son considerados casi pristinos porque los niveles de perturbacion antropogenica son extremadamente bajos. Sin embargo, en las decadas recientes ha habido un rapido incremento en el numero de personas, investigadores y turistas, que visitan la Antartida. Evaluamos, durante 10 anos, el impacto directo del trafico peatonal sobre la abundancia de animales del suelo y las propiedades del suelo en el Valle Taylor dentro de la region de los Valles Secos McMurdy de la Antartida. Comparamos suelos de las areas con minima perturbacion con suelos de veredas cercana que tenian niveles intermedios y altos de trafico peatonal (i.e., hasta ∼80 pases por ano). Los nematodos Scottnema lindsayae y Eudorylaimus sp. fueron las especies animales mas comunes, mientras que solo encontramos rotiferos y tardigrados ocasionalmente. En las veredas con trafico peatonal intenso, la abundancia de S. lindsayae y de Eudorylaimus sp. fue hasta 52% y 76% menor, respectivamente, que en las areas sin trafico. Mas aun, la reduccion en la abundancia de S. lindsayae fue mas pronunciada despues de 10 anos que dos anos y en el suelo superficial que en el suelo profundo, presumiblemente debido a un periodo de perturbacion mas largo y al mayor nivel de perturbacion fisica en el suelo superficial. La proporcion vivos – muertos de Eudorylaimus sp. tambien declino con el incremento de la intensidad del trafico peatonal, lo cual es un indicador de incremento de la mortalidad o reduccion de la fecundidad. En un sitio, hubo evidencia de que los niveles altos de trafico peatonal reducian los flujos de CO2 del suelo, que esta relacionado con una actividad biologica total en el suelo. Nuestros resultados muestran que aun niveles bajos de trafico humano pueden afectar significativamente a la biota en este ecosistema y pueden alterar procesos del ecosistema, como el ciclo del carbono. Consecuentemente, los planes de manejo y de conservacion de los suelos de la Antartida deberian considerar la alta sensibilidad del la fauna del suelo a la perturbacion fisica a medida que incrementa la presencia humana en este ecosistema.

In this study, we used a recently developed supertrees method to test for shared phylogeographical signal in partially overlapping geographical ranges of lizards of the genus Liolaemus from the Andean Range in south-central Chile. We reconstruct mtDNA gene trees for three partially codistributed species (Liolaemus tenuis, L. lemniscatus and L. pictus), and our sampling effort is sufficient to allow statistical tests of shared signal between the combinations L. tenuis–L. pictus, and L. tenuis–L. lemniscatus. For both combinations, standardized maximum agreement subtrees scores showed statistically significant signal for shared pattern in regions of overlap, as evaluated by randomization tests ( P< 0.001 and < 0.05, respectively). The matrix representation with parsimony tree obtained from the combination of the three different gene trees revealed concordant phylogeographical associations of all species, and was consistent with the geographical association of intraspecific haploclades with three Chilean bioclimatic zones. A multidimensional scaling analysis of several climate variables showed highly significant differences among these zones, which further suggests that they may have contributed to similar patterns of intraspecific divergence across all three species. In the mesomorphic zone in Central Chile, the species L. tenuis and L. lemniscatus may have codiverged in response to shared orogenic vicariant events, which likely predominated over climatic events associated with cycles of glacial advance and retreat. In the hygromorphic zone in southern Chile, however, glacial cycles likely predominated in structuring the phylogeographical histories of L. tenuis and L. pictus, although important ecological differences between these two caution against broad generalizations at this point.

Low-diversity ecosystems cover large portions of the Earth's land surface, yet studies of climate change on ecosystem functioning typically focus on temperate ecosystems, where diversity is high and the effects of individual species on ecosystem functioning are difficult to determine. We show that a climate-induced decline of an invertebrate species in a low-diversity ecosystem could contribute to significant changes in carbon (C) cycling. Recent climate variability in the McMurdo Dry Valleys of Antarctica is associated with changes in hydrology, biological productivity, and community composition of terrestrial and aquatic ecosystems. One of the greatest changes documented in the dry valleys is a 65% decrease in the abundance of the dominant soil invertebrate (Scottnema lindsayae, Nematoda) between 1993 and 2005, illustrating sensitivity of biota in this ecosystem to small changes in temperature. Globally, such declines are expected to have significant influences over ecosystem processes such as C cycling. To determine the implications of this climate-induced decline in nematode abundance on soil C cycling we followed the fate of a 13C tracer added to soils in Taylor Valley, Antarctica. Carbon assimilation by the dry valley nematode community contributed significantly to soil C cycling (2–7% of the heterotrophic C flux). Thus, the influence of a climate-induced decline in abundance of a dominant species may have a significant effect on ecosystem functioning in a low-diversity ecosystem.

Critical transition zones, such as aquatic–terrestrial interfaces, have been recognized as important features in landscape ecology. Yet changes in the community structure of soil and sediment biota across aquatic–terrestrial boundaries remain relatively unstudied. We investigated the community structure of the dominant fauna, namely nematodes, rotifers and tardigrades, across lake sediment–soil transects in three basins in a species-poor, polar desert ecosystem (McMurdo Dry Valleys, Antarctica). We also examined substrate (that is, soil and sediment) properties, including moisture, salinity, carbon, nitrogen and phosphate concentration, across these transects. Differences in faunal community structure and biochemical properties were typically explained by hydrologic basin and the sediment–soil gradient, but not by transects within each basin. Bonney Basin contained the least organic carbon, chlorophyll a, nematodes and taxa, whereas there was little difference in many of these measures between Fryxell and Hoare Basins. Nematode (Scottnema lindsayae and Plectus sp.) and rotifer abundance varied along sediment–soil transects. Scottnema lindsayae, the most abundant and widely distributed soil animal in this ecosystem, increased in abundance from sediments to soils, whereas Plectus sp. and rotifer abundance, and taxa richness (that is, nematodes, rotifers and/or tardigrades), decreased; Eudorylaimus sp. and tardigrade abundance did not differ significantly along the transects. Previous studies of soil biodiversity and faunal abundance in this ecosystem have revealed a positive association between these measures and biogeochemistry, if this holds true for lake sediments, our findings suggest sediments in Lake Bonney experience lower rates of nutrient cycling than either Lakes Fryxell or Hoare. Despite differences in faunal abundances along the sediment–soil transects, taxa occurrence was surprisingly similar in soil and sediment, only S. lindsayae was restricted to soil or the lake shore. In contrast, in other ecosystems, soil community composition differs greatly from lake sediments, suggesting that the observed similarity in species occurrence in both soils and sediments may be unique to Antarctica. This finding might result from the extreme low diversity of this ecosystem, presumably limiting competition among fauna, and thus promoting broad ecological niches. Alternatively, environmental conditions in Antarctica may select for species with broad ecological niches.

Two different molecular tools for the diagnosis of the cereal and legume root-lesion nematode Pratylenchus thornei were developed. A randomly amplified DNA (RAPD) fragment specific to P. thornei was identified. After sequencing the fragment, longer primers were designed that complement the terminal sequences of the RAPD fragment, and this pair of specific primers was used to amplify the sequence-characterized amplified region (SCAR). Using the developed pair of SCAR primers, the SCAR fragment specific to P. thornei was easily amplified with DNA extracts obtained from different life stages of the nematode. The described SCARPCR- based assay has the potential to be optimized for routine practical diagnostic tests. In addition, the use of a species-specific satellite DNA sequence to distinguish P. thornei from other Pratylenchus spp. is discussed., This research was supported by grant AGF98-0878 from Comisión Interministerial de Ciencia y Tecnología (CICYT) of Spain

Photorhabdus is a genus of Gram-negative bacteria belonging to the Enterobacteriaceae family. In addition to forming a mutualistic relationship with the Heterorhabditidae family of nematodes, these bacteria are the causal agent of insect mortality during nematode infection, and are commonly used as biocontrol agents against pest insects in managed ecosystems. There are three described species of Photorhabdus; Photorhabdus luminescens and Photorhabdus temperata, which are strictly entomopathogens, and Photorhabdus asymbiotica, which has been isolated from wound infections in humans. While there has been extensive research on its virulence mechanisms, the evolution of virulence in Photorhabdus has not previously been investigated within a phylogenetic context. To investigate how virulence has evolved in this genus, we first reconstructed the phylogenetic relationships among 18 strains representing each of the main taxonomic lineages in the genus. Bacterial cells were injected into Galleria mellonella and Tenebrio molitor larvae, and the LT50 was calculated for each strain. These values were mapped onto the phylogeny using ancestral character reconstruction methods. With few exceptions, we found that the general trend of Photorhabdus evolution is one of increasing virulence. We also explored the relationship between virulence and Photorhabdus cell types and growth rates. Although we found no correlation between cell type and virulence, there was a strong correlation between virulence and growth rates in T. molitor. A better understanding of the origin and maintenance of virulence in this bacterium will aid in unraveling the mechanisms of the Heterorhabditis-Photorhabdus complex, resulting in the selection of more effective nematode-bacterium complexes for biocontrol.

Background Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri). Results We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis. Conclusions We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein–DNA relationships shared between these two genera. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0746-6) contains supplementary material, which is available to authorized users.

Francisella tularensis has been the focus of much research over the last two decades mainly because of its potential use as an agent of bioterrorism. F. tularensis is the causative agent of zoonotic tularemia and has a worldwide distribution. The different subspecies of F. tularensis vary in their biogeography and virulence, making early detection and diagnosis important in both the biodefense and public health sectors. Recent genome sequencing efforts reveal aspects of genetic diversity, evolution and phylogeography previously unknown for this relatively small organism, and highlight a role for detection by various PCR assays. This review explores the advances made in understanding the evolution and genetic diversity of F. tularensis and how these advances have led to better PCR assays for detection and identification of the subspecies.