The purpose of this review is to highlight key developments in nematode ecology from its beginnings to where it stands today as a discipline within nematology. Emerging areas of research appear to be ...driven by crop production constraints, environmental health concerns, and advances in technology. In contrast to past ecological studies which mainly focused on management of plant-parasitic nematodes, current studies reflect differential sensitivity of nematode faunae. These differences, identified in both aquatic and terrestrial environments include response to stressors, environmental conditions, and management practices. Methodological advances will continue to influence the role nematodes have in addressing the nature of interactions between organisms, and of organisms with their environments. In particular, the C. elegans genetic model, nematode faunal analysis and nematode metagenetic analysis can be used by ecologists generally and not restricted to nematologists.
Nematodes are among the most abundant metazoans in soils, but their true diversity and distribution patterns remain poorly investigated, especially in polar environments. Here, we studied three high ...Arctic tundra sites at Kongsford, NW Svalbard (78°55′N) to understand: (1) Whether there is detectable small-scale habitat variation, (2) What the predictors of diversity and community variation are, and (3) Whether molecular methodology reveals greater diversity than morphological studies. DNA was extracted using the Baermann funnel method, and PCR amplified for the 18S rRNA gene, followed by 454-pyrosequencing. Our samples revealed no difference in nematode OTU α-diversity between different tundra habitats. Similarly, we found no correlation between nematode α-diversity in individual samples and soil properties or vegetation coverage. However, β-diversity was lower in the highly vegetated tundra than in the other tundra. There was no evidence of distinct nematode communities between individual 1 m
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quadrats of different vegetation cover and soil parameters. Overall, the community composition of highly vegetated tundra clustered separately from less vegetated tundra. The phylogenetic community assembly analysis indicated that the variation of nematode community was deterministic. This suggests that—despite the ‘extreme’ environment—nematodes in the high Arctic tundra are still to some extent habitat specialized. This study also revealed a much greater overall nematode diversity than has been previously detected in Svalbard. The nematode OTU diversity in our samples was considerably higher than the total species previously reported. This suggests the potential of DNA-based methods to rapidly reveal the true diversity of metazoans.
The island species-area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet ...the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of "island" size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.
Introduction Global change events (e.g., worsening drought) are increasing environmental stress in a variety of terrestrial and aquatic habitats. The degree to which communities in soils and ...sediments are driven by temporal environmental changes across multiple habitat types from the same region is not clear. Methods We used nematodes, a common bioindicator of soil and sediment health, to determine how community diversity and composition are altered by rising alkalinity across lakes, shorelines, and prairies in the western Nebraska Sandhills. We sampled these three habitats from five lake basins spanning an alkalinity gradient (pH 7–11) across three years (2019, 2020, 2021). During our sampling, the Sandhills experienced a range of drought intensities, with 2019 being a wet year, followed by severe drought in 2020, and abnormally dry/moderate drought in 2021. To determine if diversity and composition of nematodes responded to increased alkalinity and drought-induced stress we used different modelling approaches, including Random Forest and pairwise comparisons. Results and discussion Overall, nematode diversity in lakes was most affected by increasing alkalinity over time, whereas in shorelines and prairies diversity was most reliant on bacterial diversity and potential nematode-nematode interactions. In comparison to shorelines and prairies, community composition in lakes was the least variable and consistently driven by pH and lake water levels. In contrast, compositions in the shorelines and prairies were more variable and explained at varying degrees by pH, year, lake basin, and climate-associated variables. In addition, relative abundance and compositional nature of select copious taxa were highly unpredictable, indicating potential instability in these habitats. Future research is necessary to address the ecologic stability of the Sandhills and determine where conservation efforts are most needed.
Cryoconite holes are holes in a glacier's surface caused by sediment melting into the glacier. These holes are self-contained ecosystems that include abundant bacterial life within their sediment and ...liquid water, and have recently gained the attention of microbial ecologists looking to use cryoconite holes as “natural microcosms” to study microbial community assembly. Here, we explore the idea that cryoconite holes can be viewed as “islands,” in the same sense that an island in the ocean is an area of habitat surrounded by a barrier to entry. In the case of a classic oceanic island, the ocean is a barrier between islands, but in the case of cryoconite holes, the ocean is comprised of impermeable solid ice. We test two hypotheses, born out of island biogeographic theory, that can be readily applied to cryoconite hole bacteria. First, we ask to what extent the size of a cryoconite hole is related to the amount of bacterial diversity found within it. Second, we ask to what extent cryoconite holes exhibit distance decay of similarity, meaning that geographically close holes are expected to harbor similar bacterial communities, and distant holes are expected to harbor more different bacterial communities. To test the island size hypothesis, we measured the sizes of cryoconite holes on three glaciers in Antarctica's Taylor Valley and used DNA sequencing to measure diversity of bacterial communities within them. We found that for two of these glaciers, there is a strong relationship between hole size and bacterial phylogenetic diversity, supporting the idea that cryoconite holes on those glaciers are “islands.” The high biomass dispersing to the third glacier we measured could explain the lack of size-diversity relationship, remaining consistent with island biogeography. To test the distance decay of similarity hypothesis, we used DNA sequence data from several previous studies of cryoconite hole bacteria from across the world. Combined with our Taylor Valley data, those data showed that cryoconite holes have strong spatial structuring at scales of one to several hundred kilometers, also supporting the idea that these dirty holes on glaciers are really islands in the cryosphere.
Chemical, biological and mechanical control methods are helpful in restricting the progress of invasive plants, but they may lack the full potential for the long-term goal of habitat management and ...restoration. Interactions and feedbacks between plant and soil microbiota represent potentially important factors regulating and facilitating the invasion process.
The tree Melaleuca quinquenervia, a native of Australia, invades all types of habitats in South Florida. Thus far, the invasion has converted >200,000 ha of South Florida ecosystems to closed-canopy M. quinquenervia forests with 60–80% loss of native biodiversity. The shrub Baccharis halimifolia, a native to South Florida, is spreading in coastal Australia.
We examined the impact of plant–soil biota feedbacks set in motion by the exotic plants in 2 × 2 factorial (species × location) field and microcosm experiments both within the invasive as well as natural range of both plant species using a metagenetic nematocentric approach. The results were inconsistent and did not lend themselves to simple generalizations as responses of nematode community composition patterns were specific to plant species, locations, years, and even to experimental conditions. For instance, greater diversity of plant-parasitic nematodes was confirmed for both plant species in their native ranges, but only in the field surveys (not microcosms) and only in the first year of sampling (not the second). Equally importantly, the specificity was only observed at the “near species” level allowed by the metagenetic approach and as the identification of nematodes became less resolved, i.e., as identification moved from the “near species”-level to coarser levels of taxonomic resolution, the specific responses generally diminished.
•We report on soil biota of two exotic plants in their invasive and natural ranges.•Nematode species were investigated under field and microcosm conditions.•Responses were specific to plant species, locations, years, and type of the study.•Specific responses diminished with coarser levels of taxonomic resolution.•Plant–nematode relationships were too complex to allow for broad generalizations.
Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to ...improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens-known and unknown, indigenous, and experimentally added-were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.
Climate warming is a key factor driving species range shifts. While previous work has focused on shifts of aboveground plant communities, changes in climate and vegetation should affect soil ...communities and hence ecosystem-level nutrient cycling and ecosystem functioning. High alpine ecosystems are particularly sensitive to climate warming because snow is among the main drivers of ecosystem structure and function. Climate-warming snow cover changes at Niwot Ridge in the Colorado Rocky Mountains have resulted in a consistent plant colonization of previously unvegetated soils generating a natural gradient of soil habitats ranging from unvegetated to increasingly vegetated. We used this gradient of plant communities at different successional stages to determine if nematodes respond to climate-driven changes in this high-alpine landscape and if they play a role in changes in soil C and N. We hypothesized that: 1) there would be clear shifts in nematode communities along the gradient as a function of snow cover, plant richness and density, and water holding capacity but that these shifts would be dependent on nematode feeding habits and their positioning in the soil foodweb and 2) the shifts would be associated with accumulating soil C and N. To test these hypotheses, we measured nematodes, plants, and soil microbes, snow cover, pH, soil water holding capacity, and different forms of soil C and N in 98 plots across the plant successional gradient. As predicted, nematode communities exhibited extensive shifts from a few individuals of a single species in unvegetated soils to hundreds of individuals and tens of species within every feeding group under complex plant communities. Representatives of omnivorous and bacterivorous K-strategists preceded plants and plant parasites and root associates depended on plants most. Linear regression models indicated that plants, microbial communities and soil water holding capacity, but not snow cover, were the most predictive factors of nematode diversity and density across all trophic levels and that all nematode groups were positively related to all measures of soil C and N. Structural equation models confirmed these results, but also indicated that effects of climate warming on nematodes were indirect primarily through shifts in plant and microbial communities and changes of soil water holding capacity. Moreover, nematode trophic group densities, but not their diversity, played a potential role in the accumulation of soil N, and to a lesser degree of soil C. Because nematode communities at Niwot Ridge are largely at their early phases of assembly, with continuing climate warming, we predict their increasing abundance and diversity will likely continue, as will their impact on soil C and N processes.
•Climate warming is a key factor driving species range shifts.•High alpine ecosystems are particularly sensitive to climate warming.•Soil nematodes expand their range of distribution akin to plants.•As nematodes become a part of the high alpine they contribute to C and N sequestration.
Cryoconite is a mixture of mineral and organic material covering glacial ice, playing important roles in biogeochemical cycles and lowering the albedo of a glacier surface. Understanding the ...differences in structure of cryoconite across the globe can be important in recognizing past and future changes in supraglacial environments and ice-organisms-minerals interactions. Despite the worldwide distribution and over a century of studies, the basic characteristics of cryoconite, including its forms and geochemistry, remain poorly studied. The major purpose of our study is the presentation and description of morphological diversity, chemical and photoautotrophs composition, and organic matter content of cryoconite sampled from 33 polar and mountain glaciers around the globe. Observations revealed that cryoconite is represented by various morphologies including loose and granular forms. Granular cryoconite includes smooth, rounded, or irregularly shaped forms; with some having their surfaces covered by cyanobacteria filaments. The occurrence of granules increased with the organic matter content in cryoconite. Moreover, a major driver of cryoconite colouring was the concentration of organic matter and its interplay with minerals. The structure of cyanobacteria and algae communities in cryoconite differs between glaciers, but representatives of cyanobacteria families Pseudanabaenaceae and Phormidiaceae, and algae families Mesotaeniaceae and Ulotrichaceae were the most common. The most of detected cyanobacterial taxa are known to produce polymeric substances (EPS) that may cement granules. Organic matter content in cryoconite varied between glaciers, ranging from 1% to 38%. The geochemistry of all the investigated samples reflected local sediment sources, except of highly concentrated Pb and Hg in cryoconite collected from European glaciers near industrialized regions, corroborating cryoconite as element-specific collector and potential environmental indicator of anthropogenic activity. Our work supports a notion that cryoconite may be more than just simple sediment and instead exhibits complex structure with relevance for biodiversity and the functioning of glacial ecosystems.
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•The morphology of cryoconite varies greatly between regions.•Cryoconite consists of loose mineral material or various types of granules.•Colour of cryoconite depends on organic matter content and its interplay with minerals.•Cryoconite is a complex structure providing various ecological niches for glacial microbes.
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