A novel molecular approach for rapid assessment of soil nematode assemblages - variation, validation and potential applications

Nematodes As Soil Stress Indicators for Polycyclic Aromatic Hydrocarbons: a Review

Polycyclic aromatic hydrocarbons (PAHs) are an important group of organic pollutants present in all parts of the environment, affecting ecosystems and human health. PAHs, which have a strong affinity for organic carbon, are found in large quantities in soil, which is one of the most important sinks for these contaminants. Their impact on the soil biotic compartments depends on a number of different factors in combination with PAH behaviour and can be assessed using soil monitoring. Soil fauna have already shown excellent properties for biomonitoring of contaminants with most promising indicator frameworks based on nematodes, which are involved in essential processes in this environment. Nematodes respond to PAHs at multiple levels, including molecular, individual and community levels. At the molecular level, this is associated with activation of metabolic pathways for xenobiotics and increased demand for energy and resources. At the individual level, this is reflected in the slowing down of various physiological processes, which has consequences at the individual and community level for sensitive taxa. In this review, the toxicity and the direct and indirect effects of PAHs on soil nematode communities are discussed. It also considers the perspectives and challenges in assessing the toxicity of PAHs and their indication using soil nematodes.

Impact of land use and management practices on soil nematode communities of Machair, a low-input calcareous ecosystem of conservation importance

Machair is a vulnerable low-lying coastal ecosystem with internationally recognised conservation importance. It is characterised by wind-blown calcareous shell-sand soils that support a patchwork of low-input land-use types including species rich grasslands and small-scale arable production. In contrast to numerous above-ground studies, few below-ground studies have been made on the Machair. Thus, a knowledge gap exists, and no baseline data is available to determine the impact, if any, of fundamental changes in Machair land management practices such as a move from traditional rotational to permanent grazing, and increased use of inorganic fertiliser. To address this knowledge deficit, we assessed the impact of different agronomic management practices (cropped, fallow and grasslands) on the structure of soil nematode communities over a two-year period along a geographically limited north-south gradient of coastal Machair of the Outer Hebrides archipelago. Land use followed by season were the main drivers of nematode communities from Machair soils. Functionally, nematode communities from grassland were typically distinct from cropped or fallow communities driven primarily by differential contributions to the overall nematode community by the dominant bacterial-feeding nematodes. Temporally, nematode communities sampled in spring and autumn were distinct.

On the identity of Eucephalobus oxyuroides (de Man, 1876) Steiner, 1936 (Rhabditida, Cephalobidae), with an updated taxonomy of the genus and notes about its phylogeny

The identity of Eucephalobus oxyuroides is discussed after studying two Iberian populations that fit the original description of the species. A new characterization is consequently provided as follows: 0.49 to 0.70 mm long body, lip region continuous with the adjoining body and bearing short probolae prongs, neck 132 to 158 µm long, spermatheca 23 to 47 µm long or 1.0 to 1.8 times the corresponding body diameter, post-vulval uterine sac 40 to 54 µm long or 2.0 to 2.5 times as long as the body diameter, V  =  58 to 64, female tail conical elongate with very acute terminus (60-79 µm, c = 7.1-10.0, c′ = 4.9-5.8), male tail conical (36-49 µm, c =10.9-14.3, c′ = 2.4-3.4) with an elongate acute mucro, and spicules 21 to 22 µm long. Previous records of the species are revised. An emended diagnosis of the genus is proposed, and its taxonomy is updated with a list of species, key to their identification and illustrations. The evolutionary relationships of Eucephalobus, as derived from the analyses of 18S and 28S rDNA fragments, reveals that it occupies a basal position within the subfamily Cephalobidae.

New live screening of plant-nematode interactions in the rhizosphere

Free living nematodes (FLN) are microscopic worms found in all soils. While many FLN species are beneficial to crops, some species cause significant damage by feeding on roots and vectoring viruses. With the planned legislative removal of traditionally used chemical treatments, identification of new ways to manage FLN populations has become a high priority. For this, more powerful screening systems are required to rapidly assess threats to crops and identify treatments efficiently. Here, we have developed new live assays for testing nematode responses to treatment by combining transparent soil microcosms, a new light sheet imaging technique termed Biospeckle Selective Plane Illumination Microscopy (BSPIM) for fast nematode detection, and Confocal Laser Scanning Microscopy for high resolution imaging. We show that BSPIM increased signal to noise ratios by up to 60 fold and allowed the automatic detection of FLN in transparent soil samples of 1.5 mL. Growing plant root systems were rapidly scanned for nematode abundance and activity, and FLN feeding behaviour and responses to chemical compounds observed in soil-like conditions. This approach could be used for direct monitoring of FLN activity either to develop new compounds that target economically damaging herbivorous nematodes or ensuring that beneficial species are not negatively impacted.

New data on two remarkable Antarctic species Amblydorylaimusisokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpusparadoxus (Loof, 1975), gen. n., comb. n. (Nematoda, Dorylaimida)

The taxonomic position of two antarctic dorylaimid species Amblydorylaimusisokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpusparadoxus (Loof, 1975), gen. n., comb. n. are discussed on the basis of morphological, including SEM study, morphometric, postembryonic and sequence data of 18S rDNA and the D2-D3 expansion fragments of large subunit rDNA. The evolutionary trees inferred from 18S sequences show insufficient resolution to determine the assignment of the two species to particular families, moreover Pararhyssocolpusparadoxus gen. n., comb. n. (=Rhyssocolpusparadoxus) previously regarded as a member of Nordiidae or Qudsianematidae, showed distant relationship both to Rhyssocolpusvinciguerrae and Eudorylaimus spp. The phylogram inferred from 28S sequences revealed that Amblydorylaimusisokaryon is a member of a well-supported group comprised of several Aporcelaimellus spp., while, no close relationships could be revealed for the Pararhyssocolpusparadoxus gen. n., comb. n. to any nematode genus. On the basis of molecular data and morphological characteristics, some taxonomic changes are proposed. Amblydorylaimusisokaryon is transferred from family Qudsianematidae to family Aporcelaimidae, and a new monotypic genus Pararhyssocolpus gen. n. is proposed, attributed to Pararhyssocolpidaefam. n. The diagnosis of the new family is provided together with emended diagnosis of the genera Amblydorylaimus and Pararhyssocolpus gen. n. Data concerning distribution of these endemic genera in the Antarctic region are also given.

Calcaridorylaimus castaneae sp. n. (Nematoda, Dorylaimidae) from Bulgaria with an identification key to the species of the genus

An unknown species belonging to the genusCalcaridorylaimus Andrássy, 1986 was collected from the litter of broadleaf forests dominated by Castanea sativa Mill. and mixed with Quercus daleshampii Ten. and Fagus sylvatica L. on Belasitsa Mountain, south-western Bulgaria. Calcaridorylaimus castaneae sp. n. is characterised by its long body (1.4-2.1 mm), lip region practically not offset, vulva transverse, short odontostyle (14.5-16 μm) and tail (75.5-110.5 μm, c=14.7-23.6; c'=2.9-4.4) in females and 38-46 μm long spicules with small spur before their distant end in males. It is most similar to C. andrassyi Ahmad & Shaheen, 2004, but differs in having transverse vs pore-like vulva and shorter spicules (38-46 μm vs 52-57 μm). An identification key to the species of the genus Calcaridorylaimus is proposed. Phylogenetic analyses were performed on 18S and D2-D3 expansion domains of 28S rRNA genes by Neighbor-Joining, Maximum Likelihood and Bayesian Inference methods. The phylograms inferred from 18S sequences showed closest relationships of the new species with some species belonging to the genus Mesodorylaimus. However, insufficient molecular data for members of both genera do not allow the phylogenetic relationships of Calcaridorylaimus and the new species described herein to be elucidated.

SSU ribosomal DNA-based monitoring of nematode assemblages reveals distinct seasonal fluctuations within evolutionary heterogeneous feeding guilds

Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked.