Tom Bongers

A framework for soil food web diagnostics : extension of the nematode faunal analysis concept

Nematodes, the earth’s most abundant metazoa, are ubiquitous in the soil environment. They are sufficiently large to be identifiable by light microscopy and sufficiently small to inhabit water films surrounding soil particles. They aggregate around and in food sources. They include component taxa of the soil food web at several trophic levels. They can be categorized into functional guilds whose members respond similarly to food web enrichment and to environmental perturbation and recovery. Indices derived through nematode faunal analysis provide bioindicators for disturbance of the soil environment and condition of the soil food web. We enhance the resolution of faunal analyses by providing a weighting system for the indicator importance of the presence and abundance of each functional guild in relation to enrichment and structure of the food web. Graphical representations of food web structure, based on nematode faunal analyses, allow diagnostic interpretation of its condition. Simple ratios of the weighted abundance of representatives of specific functional guilds provide useful indicators of food web structure, enrichment, and decomposition channels.

Functional diversity of nematodes

Abstract Nematodes are the most abundant metazoa. Their food specificity, the high number of species and high abundance in every habitat where decomposition takes place indicates that the structure of the nematode community has a high information content. Since nematodes respond rapidly to new resources, and the nematode fauna can be efficiently analyzed, the structure of the nematode community offers an instrument to assess (changes in) the conditions of soils. A functional grouping of nematodes is generally synonymous with allocation into feeding groups. However, soil quality assessment indices based on the presence of all feeding groups still provide insufficient information regarding the functioning of soil ecosystems and their threats. An alternative concept of functional groups is based on the life history of nematodes. In this paper we present the most recent colonizer–persister allocation and the application of this scaling in the Maturity Index, cp-triangles, MI(2–5) and PPI/MI-ratio. We propose to integrate the life strategy approach and trophic group classification to obtain a better understanding of nematode biodiversity and soil functioning. Attention is given to competitive exclusion and coexistence and we summarize present concepts regarding succession and degradation.

Nematode community structure as a bioindicator in environmental monitoring

Four of every five multicellular animals on the planet are nematodes. They occupy any niche that provides an available source of organic carbon in marine, freshwater and terrestrial environments. Nematodes vary in sensitivity to pollutants and environmental disturbance. Recent development of indices that integrate the responses of different taxa and trophic groups to perturbation provides a powerful basis for analysis of faunal assemblages in soil as in situ environmental assessment systems.

The Maturity Index, the evolution of nematode life history traits, adaptive radiation and cp-scaling

Nematodes are increasingly being used in environmental studies. One of the potential parameters to measure the impact of disturbances and to monitor changes in structure and functioning of the below-ground ecosystem is the nematode Maturity Index; an index based on the proportion of colonizers (r-strategists s.l.) and persisters (K-strategists s.l.) in samples. In this paper the original allocation of nematode taxa on the colonizer-persister scale, and the tolerance and sensitivity of colonizers and persisters are discussed from an evolutionary viewpoint. The phenomenon that neither relative egg size nor body length is an unequivocal character to scale nematodes suggests that the main selection for life history traits occurred independently in the major evolutionary branches.

Short-term effects of cadmium, copper, nickel and zinc on soil nematodes from different feeding and life-history strategy groups

Abstract The effects of cadmium, copper, nickel and zinc on a nematode community were examined with a ‘natural soil method’. Changes in the indigenous nematode community structure were studied 1–2 weeks after the addition of these metals (as sulphates) to soil collected from an agroecosystem. The soil was acid and only contained a moderate quantity of organic matter as the main metal-binding constituent. As a result, its metal-binding capacity was rather low. The nematode community was found to be affected by increasing concentrations of Cu, Ni and Zn up to 1600 mg kg−1, but not by Cd up to 160 mg kg−1. EC50 values for the reduction in population size of individual taxa showed a low intra-taxon variation for Cu, Ni and Zn. For these heavy metals, uptake and elimination processes as well as their final effect appear similar within the same taxon. Omnivorous and predatory nematodes, known to be K-strategists, were among the most sensitive taxa, and were already significantly affected by 100 mg kg−1 Cu, Ni or Zn added to the soil. The relative abundance of the different life-history groups and, to a lesser extent, the different feeding groups indicated pollution-induced changes in the soil community. However, neither classification predicts the acute effects of Cu, Ni and Zn on different nematode genera in an adequate way.

Inverse relationship between the nematode maturity index and plant parasite index under enriched nutrient conditions.

Abstract The maturity index, an ecological measure of the state of succession, is based on the composition of the nematode fauna. Nematodes that feed on higher plants were originally excluded; a separate plant parasite index was proposed for nematodes feeding on higher plants. In the present study it is shown that, under certain conditions, the maturity index and plant parasite index are inversely related. Therefore it is concluded that the inclusion of plant feeders into the maturity index, as recently suggested, leads to an index which is less sensitive to changes in the environment than the original maturity index. The divergence of maturity index and plant parasite index is confirmed by literature data and is assumed to be a nutrient enrichment effect. The ratio between maturity index and plant parasite index is proposed as a sensitive parameter for monitoring agro-ecosystems.

Nematode community structure as indicator of soil functioning in European grassland soils

This investigation analyses whether soil nematode diversity is correlated with soil functional parameters to serve as bioindicator of soil functioning. The analysis focuses on the interrelations of nematofauna, microflora, and soil nitrogen pools. The sites studied represent six major European grassland types: Northern tundra, atlantic heath, wet grassland, seminatural temperate grassland, East European steppe, and mediterranean garigue. Continental and local climate gradients were combined to a wide and continuous range of microclimate conditions. Nematode richness, as indicated by the number of genera, was highest under temperate conditions and declined towards the climatic extremes. Differences in richness affected all nematode feeding types proportionally. Nematode richness was the only parameter among a range of 15 alternatives tested that exhibited consistent correlations with mass and activity parameters of both nematofauna and microflora in the mineral grassland soils (garigue, wet grassland, seminatural grassland, steppe). In the same soils, the nematode Maturity Index was the best indicator of nitrogen status. We conclude that a high nematode richness can generally be seen as a good indicator of an active nematofauna and microflora in mineral grassland soils, and hence as an indicator of the decomposition function. The prospects of exploiting nematode diversity as an indicator of soil functioning are critically discussed.

Nematode community structure in relation to soil and vegetation characteristics

Abstract To test the hypothesis that nematodes can contribute to an ecological soil classification, the nematode fauna of several Dutch terrestrial habitats was studied. A total of 209 samples from 44 nature reserves or slightly managed sites ( n = 94) differing in vegetation (forest, shrubs, heathland, grassland) and soil type (clay, loam, sand) were studied. A selection of sites was studied over four seasons, and at one site variation in nematode fauna composition as a result of the selected sampling technique was studied. Nematodes extracted from bulk soil samples taken from the 0–10 cm depth mineral soil, and were identified to genus. Multivariate analysis techniques were used to classify the nematode samples into seven sample groups (SG) as described by soil characteristics in combination with the vegetation as follows: (1) SG A grasslands, dwarf-shrub vegetation and forest gaps on sandy soils; (2) SG B grasslands and forests on clayey soils; (3) SG C-D deciduous forests on sandy-loam soils; (4) SG E-F deciduous forests on sandy soils; (5) SG G coniferous forests on sandy soils. The nematode fauna of SG D-G were very similar, and were dominated by ten taxa: Acrobeloides, Aphelenchoides, Cephalenchus, Filenchus A, Filenchus B, Plectus A, Prismatolaimus, Rhabditidae, Tylolaimophorus and Wilsonema . Variation due to seasonal fluctuations and sampling technique, was small compared with differences in nematode fauna structure between different sites. The actual vegetation of some sites was not in agreement with the natural vegetation expected on ‘site characteristics’. Analyses of the nematode fauna supported the observed inconsistencies between actual and natural vegetation. It was shown that for a range of terrestrial habitats nematode communities could be defined, and that these communities could be related to soil characteristics and vegetation.

Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA

Abstract Consensus nematode 18S ribosomal DNA primers were designed by aligning available 18S sequences and identifying a variable region flanked by highly conserved regions. These primers were then used to amplify nematode 18S rDNA from whole soil community DNA extracted from a range of European grassland types. Cloning of the PCR amplicons (778 bp) followed by restriction digest analysis (RFLP) resulted in the recovery of 34 unique nematode sequences from the four grasslands studied. Comparison of these data with the limited number of 18S rDNA nematode sequences currently held in on-line databases revealed that all of the sequences could be assigned to known nematode taxa albeit tentatively in some cases. Two of the sequences recovered from the site in the Netherlands (wet, hay-grassland) were recovered in a clade that included a sequence of the genus Trichodorus whilst other sequences from this site showed similarity with 18S rDNA sequences of the genus Prismatolaimus (five sequences), Xiphinema (one sequence) and Enoplus (one sequence). Of the remaining sequences, two showed some affinity with Mylonchulus (UK, upland peat), four with Steinernema (UK) and one sequence with Mesorhabditis (Hungary, east European Steppe). Three sequences from the Netherlands and one from Hungary were recovered in a clade that included a sequence of the genus Pratylenchoides whilst three further sequences from the Netherlands and two from Hungary were recovered in a clade encompassing the genus Globodera. Of the remaining nine sequences, two (NL6, NL62) formed a distinct lineage within the Adenophorea with 90% bootstrap recovery in a paraphyletic clade that included sequences of Prismatolaimus and Trichodorus. Seven sequences (three from the Netherlands, three from the UK and one from Greece) were left unassigned though the tree topology suggested some relationship (58% bootstrap recovery) with the genus Cephalobus. To assess whether primers used to amplify 18S rDNA might be used to fingerprint genetic diversity in nematode communities in soil, the environmental sequence data were used to design a second set of primers carrying a GC-clamp. These primers amplified a 469 bp fragment internal to the region flanked by the primer set used to derive the nematode trees and were used to amplify 18S rDNA for subsequent analysis using denaturing gradient gel electrophoresis (DGGE). DGGE analysis of six major European grassland types revealed considerable genetic diversity between sites. However, the relationships seen with the DGGE data were inconsistent with previous studies where the same soils had been characterized with respect to functional and morphological diversity. To confirm that this second set of primers was amplifying nematode sequences, selected bands on the DGGE gels were extracted, PCR amplified and sequenced. The final alignment was 337 bases. These analyses revealed the presence of sequence signatures from the genera Paratrichodorus, Plectus, Steinernema, Globodera, Cephalobus and Pratylenchoides.

A ribosomal DNA‐based framework for the detection and quantification of stress‐sensitive nematode families in terrestrial habitats

Indigenous communities of soil‐resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under‐exploitation as soil health indicators, and a user‐friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress‐sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full‐length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA‐based systematics, Mononchida families (indicated here as M1–M5) are relatively well‐supported and, consequently, family‐specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (≈ 1000 bp from the 5′‐end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1–D9, PP1–PP3) that shows only distant similarity with ‘classical’ Dorylaimid systematics. Most subclades were trophically homogeneous, and — in most cases — specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real‐time polymerase chain reaction). Our results constitute proof‐of‐principle for the concept of DNA sequence signatures‐based monitoring of stress sensitive nematode families in environmental samples.