Nematode community structure as a bioindicator in environmental monitoring

Dissection of the synthesis of polyunsaturated fatty acids in nematodes and Collembola of the soil fauna

It is becoming increasingly clear that not only unicellular, photoautotrophic eukaryotes, plants, and fungi, but also invertebrates are capable of synthesizing ω3 long-chain polyunsaturated fatty acids (LC-PUFA) de novo. However, the distribution of this anabolic capacity among different invertebrate groups and its implementation at the gene and protein level are often still unknown. This study investigated the PUFA pathways in common soil fauna, i.e. two nematode and two Collembola species. Of these, one species each (Panagrellus redivivus, Folsomia candida) was assumed to produce ω3 LC-PUFA de novo, while the others (Acrobeloides bodenheimeri, Isotoma caerulea) were supposed to be unable to do so. A highly labeled oleic acid (99 % 13C) was supplemented and the isotopic signal was used to trace its metabolic path. All species followed the main pathway of lipid biosynthesis. However, in A. bodenheimeri this terminated at arachidonic acid (ω6 PUFA), whereas the other three species continued the pathway to eicosapentaenoic acid (ω3 PUFA), including I. caerulea. For the nematode P. redivivus the identification and functional characterization of four new fatty acid desaturase (FAD) genes was performed. These genes encode the FAD activities Δ9, Δ6, and Δ5, respectively. Additionally, the Δ12 desaturase was analyzed, yet the observed activity of an ω3 FAD could not be attributed to a coding gene. In the Collembola F. candida, 11 potential first desaturases (Δ9) and 13 front-end desaturases (Δ6 or Δ5 FADs) have been found. Further sequence analysis indicates the presence of omega FADs, specifically Δ12, which are likely derived from Δ9 FADs.

Root traits drive the recovery of soil nematodes during restoration of open mines in a tropical rainforest

Mining is a major threat to vegetation and soil in the tropical forests. Reforestation of degraded surface mines is critically dependent on the recovery of soil health, where the nematodes play an important role. However, the key determinants of community assembly of soil nematodes during mine-restoration remain unknown in the tropical rainforests. Here, the recovery of taxonomic diversity of nematode communities and their trophic groups during reforestation of an extremely degraded tropical open-mining area is studied. The factors that may impact their recovery, such as root traits (length, area and tissue density), soil properties (pH and soil organic matter content (SOM)), and taxonomic diversities of soil bacterial and fungal communities are investigated. Differences in these parameters were evaluated in the three soil types: (i) mined soil - the erstwhile soil that was removed during mining and stock-piled for 10 years at the foot of an extremely degraded open-mining area; (ii) reforested soil, sampled from a 10-year successful restoration, which used the mined soil for reforestation; and (iii) undisturbed soil, collected from an adjacent undisturbed/not-mined tropical rainforest. A total of 11, 34 and 29 nematode-genera were identified in mined-, undisturbed-, and reforested soils, respectively. The taxonomic diversities of the 5 nematode groups in the mined soil were 1.5-5.2 times lower than in the undisturbed soil, but were similar in the restored and undisturbed soils. Taxonomic diversities of phytophagous and predator nematodes were correlated to restored root traits; whereas of bacterivores, fungivores, and omnivores were correlated to pH, SOM, soil bacterial and fungal communities. Consequently, complete loss of roots during mining likely severely reduced the nematodes, but their recovery after reforestation led to the restoration of taxonomic diversity of nematode communities. The mix-planting fast-growing tree species may be appropriate for recovering soil health, including nematode diversity, during reforestation of open tropical mines.

Post-fire recovery of nematode communities along a slope gradient in a pine forest

We investigated the enduring consequences of a wildfire on nematode diversity and abundance in a pine forest, employing a slope gradient approach. Our primary objective was to determine the extent of post-fire alterations in the nematode community 3 years after the incident, to understand if the ecosystem has returned to its pre-fire state or has transitioned to a distinctive ecological environment. Three distinct burned pine forest sites at varying elevations were sampled to capture short-scale soil property variations due to slope gradients, while unburned forest sites served as controls. A consistent pattern emerged where the lowest altitude sites exhibited the highest nematode abundances, although still lower than unburned sites. Fire-induced changes were profound, shifting from fungivore dominance in unburned sites to bacterivore and herbivore dominance in burned sites. Alterations in soil properties post-fire, particularly reduced organic matter and nitrogen content, were closely associated with nematode community shifts. Water availability played a crucial role with lower moisture levels at higher elevations impacting nematode populations. Structural differences in the nematode community primarily resulted from fire disturbance rather than altitude. This study emphasizes the persistent and transformative impact of wildfire on nematode communities, highlighting the intricate interplay between ecological disturbances, soil properties, and nematode trophic dynamics.

The Life-History Traits of Soil-Dwelling Nematode (Acrobeloides sp.) Exhibit More Resilience to Water Restriction Than Caenorhabditis elegans

In the context of climate warming, the intensity and frequency of drought occurrences are progressively increasing. However, current research on the impacts of drought on the life-history traits and physiological activities of animals rarely encompasses soil animals that play crucial roles within soil ecosystems. Therefore, this study focused on a soil nematode species (Acrobeloides sp.) and a model nematode (Caenorhabditis elegans) to investigate whether nematodes adjust the trade-off of their life-history traits to confront arid environments, utilizing a Petri dish experiment. Subsequently, we assessed the resilience of the two nematode species to moisture variations by comparing the extent of changes in various indicators (i.e., life-history traits, physiological traits, and oxidative stress) of nematodes before and after drought and rehydration. The results revealed that both nematode species are capable of adapting to arid environments by altering the trade-off between life-history traits. Specifically, they reduce reproductive investment and body mass while maintaining life span, thus responding to drought conditions. Follow-up rehydration experiments post-drought stress highlighted that the soil-dwelling nematode exhibits a superior recovery capacity in response to moisture fluctuations in comparison to the model nematode. To the best of our knowledge, this is the first investigation into life history of drought adaptation within soil-dwelling nematodes. Moreover, the findings hold significant implications for the exploration of drought adaptation and its mechanisms in soil-dwelling animals.

Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms

Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.

Integrative taxonomic study of mononchid nematodes from riparian habitats in Bulgaria. I. Genera Mononchus Bastian, 1865 and Coomansus Jairajpuri & Khan, 1977 with the description of Mononchuspseudoaquaticus sp. nov. and a key to the species of Mononchus

The species diversity of the genera Mononchus Bastian, 1865 and Coomansus Jairajpuri & Khan, 1977 was assessed in a study of the mononchid nematodes from a wide range of riparian habitats in Bulgaria. Four species were identified based on morphological and morphometric data: Coomansusparvus (de Man, 1880), Mononchustruncatus Bastian, 1865, Mononchuspseudoaquaticus sp. nov., and Mononchus sp. The first three species were characterised both morphologically and molecularly (18S and 28S rRNA gene sequences) and the integration of these data and phylogenetic analyses provided support for their distinct species status. This paper provides detailed descriptions, morphometric data for multiple species populations, drawings and photomicrographs, and the first taxonomically verified sequences for C.parvus (n = 6), M.truncatus (sensu stricto) (n = 4) and M.pseudoaquaticus sp. nov. (n = 3). Comparative sequence and phylogenetic analyses suggested that the utility of the 18S rRNA gene for species delimitation is rather limited at least for some species complexes within the genus Mononchus. At the generic and suprageneric level, the 18S and 28S rDNA phylogenies both recovered the three genera represented by two or more species (Mononchus, Mylonchulus, and Parkellus) as monophyletic with strong support, the Mononchidae as paraphyletic, the Anatonchidae as monophyletic, and there was no support for a sister-group relationship between Mylonchulus and Mononchus. A key to the species of Mononchus is provided to facilitate the identification of the currently recognised 31 species.

Linking nematodes and ecosystem function: a trait-based framework

Trait-based approaches are being increasingly adopted to understand species' ecological strategies and how organisms influence ecosystem function. Trait-based research on soil organisms, however, remains poorly developed compared with that for plants. The abundant and diverse soil nematodes are prime candidates to advance trait-based approaches belowground, but a unified trait framework to describe nematode ecological strategies and assess their linkages with ecosystem function is lacking. We categorized nematode traits as morphological, physiological, life history, and community clusters, and proposed the nematode economics spectrum (NES) to better understand nematode ecological strategies and their association with ecosystem function. We argue that bridging the NES and the plant economics spectrum will facilitate a more holistic understanding of ecosystem carbon and nutrient cycling under global change.

Flooding soil with biogas slurry suppresses root-knot nematodes and alters soil nematode communities

Root-knot nematodes (RKNs) pose a serious threat to crop production. Flooding soil with biogas slurry, combined with soil heating before crop planting, has the potential for RKN disease suppression. However, the actual effect of this method has not been verified under field conditions. Here, we present the results of a two-year field experiment in a greenhouse demonstrating the control effect on RKN disease and plant growth using this method, as well as its influence on the soil nematode community. Four treatments were set: untreated control (CK), local control method for RKN (CC), soil flooded with 70 % biogas slurry (BS70), and soil flooded with undiluted biogas slurry (BS100). In the first year, all three RKN control treatments significantly reduced the root-knot index (p < 0.05). In the next year, only BS70 and BS100 still presented significantly suppressed effects (p < 0.05), and it was more obvious under BS70 with a relative control effect of 74.6 %. In the first year, BS70 and BS100 significantly inhibited the plant height of watermelon (p < 0.05). In the next year, however, all three RKN control treatments promoted the growth of watermelon, and their stem diameter was significantly greater than that of CK. The application of biogas slurry (BS70 and BS100) significantly increased nematode richness and the Shannon index in the second year (p < 0.05). However, the structure index showed no significant difference among treatments (p > 0.05), indicating that biogas slurry application did not increase the soil food web complex. Principal component analysis showed that the application of biogas slurry changed the nematode community, especially under BS70, which presented a more lasting influence. The high-level input of biogas slurry also caused soil NH4+-N and heavy-metal and arsenic accumulation in the first year, but these soil-pollution risks disappeared in the second year.

Experimental study of organic enrichment on meiofaunal diversity

The organic enrichment effects on the meiofauna and nematofauna were assessed for field sediment and other experimental ones enriched with organic matters conducted in the laboratory for 4 weeks. Also, dissolved oxygen (DO) and pH were monitored for each one. The abundance and diversity of meiofaunal groups and nematofauna varied. Strong significant correlations were found between DO and the studied items. Nematoda was the most abundant group in the field sediment and other experimental ones; their counts increased with the increase in organic enrichments and were dominated by deposit feeders. Amphipoda, Ostracoda and predator/omnivore nematodes disappeared in highly organic-enriched sediments. Changes in DO and organic enrichments might be the more attributable reasons for the alteration of the meiobenthic assemblages. The generic compositions of Nematoda provide a good indicator for environmental alterations.

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.

Comparative analysis of soil nematode biodiversity from five different fruit orchards in Osmaneli district, Bilecik, Türkiye

Nematode population densities were determined in 60 soil and root samples collected from 6 fruit orchards in the Bilecik province (western Turkey), between April 2022 and June 2022. The total number of identified nematodes have reached up to 2418 individuals (number of female: 1036; male: 154; and juvenile: 1228). They belong to 54 species, 54 genera, 33 families and 11 orders. Plant parasitic nematodes that were detected mostly are listed as follows: Helicotylenchus (6,12 %), Pratylenchus (5,74 %), Paratylenchus (4.83 %), Xiphinema (3,06 %), Tylenchorhynchus (2,19 %), Malenchus (1.94 %) and Tylenchus (1.19 %). According to the maturity index analysis, mean values showed the highest maturity level at peach trees (MI value: 3,52), followed by; walnut trees (MI value: 2.49), cherry trees (MI value: 2.15), nectarine trees (MI value: 1.86), plum trees (MI value: 1.57), and olive trees (MI value: 1.42). Mostly the diverse group in terms of species richness was within the order Dorylaimida. The nematodes associated with peach and walnut trees here showed the most stable environments in terms of soil nematode community structure.

Livestock grazing modifies soil nematode body size structure in mosaic grassland habitats

Body size is closely related to the trophic level and abundance of soil fauna, particularly nematodes. Therefore, size-based analyses are increasingly prominent in unveiling soil food web structure and its responses to anthropogenic disturbances, such as livestock grazing. Yet, little is known about the effects of different livestock on the body size structure of soil nematodes, especially in grasslands characterized by local habitat heterogeneity. A four-year field grazing experiment from 2017 to 2020 was conducted in a meadow steppe characterized by typical mosaics of degraded hypersaline patches and undegraded hyposaline patches to assess the impacts of cattle and sheep grazing on the body size structure of soil nematodes within and across trophic groups. Without grazing, the hypersaline patches harbored higher abundance of large-bodied nematodes in the community compared to the hyposaline patches. Livestock grazing decreased large-bodied nematodes within and across trophic groups mainly by reducing soil microbial biomass in the hypersaline patches, with sheep grazing resulting in more substantial reductions compared to cattle grazing. The reduction in large-bodied nematode individuals correspondingly resulted in decreases in nematode community-weighted mean (CWM) body size, nematode biomass, and size spectra slopes. However, both cattle and sheep grazing had minimal impacts on the CWM body size and size spectra of total nematodes in the hyposaline patches. Our findings suggest that livestock grazing, especially sheep grazing, has the potential to simplify soil food webs by reducing large-bodied nematodes in degraded habitats, which may aggravate soil degradation by weakening the bioturbation activities of soil fauna. In light of the widespread land use of grasslands by herbivores of various species and the ongoing global grassland degradation of mosaic patches, the recognition of the trends revealed by our findings is critical for developing appropriate strategies for grassland grazing management.

Environmental heterogeneity of cold seep by biological trait analysis of marine nematodes at Site F cold seep in South China Sea

Cold seeps provide high environmental heterogeneity for marine benthos. Site F is one of the active cold seeps in the South China Sea. In this study, free-living marine nematode communities were investigated at Site F and the adjacent deep-sea area. A total of 67 genera and 32 families were identified. The mean density at cold seep sites ranged from 13.6 to 181.8 ind./10 cm2, and that at the adjacent deep-sea sites ranged from 36.9 to 301.4 ind./10 cm2. At cold seep sites, the most dominant nematode genera were Desmoscolex, Pierrickia, Sabatieria, Halalaimus, and Dorylaimopsis while at deep-sea sites, the most dominant genera were Retrotheristus, Thalassomonhystera, Desmoscolex, Cobbia, and Halalaimus. Deposit feeders of nematodes were dominant at all sites. Results of biological trait analysis showed that there was high environmental heterogeneity for nematodes at Site F. Water depth, sediment organic matter content, and sand proportion had important influences on nematode communities.

Examining the Shift in the Decomposition Channel Structure of the Soil Decomposer Food Web: A Methods Comparison

Selecting the appropriate indicators and measuring time point numbers is important for accurately examining the shift in soil gross decomposition channel structure. Through a selected case study on a natural forest vs. rainfed arable system over a two-month-long experiment, the utility of three commonly employed indicators (fungi to bacteria ratio (F:B), fungivore to bacterivore ratio (FF:BF), and glucosamine to muramic acid ratio (GlcN:MurN)) were compared to reflect the shift in soil gross decomposition channel structure. The requirement of measuring the time point numbers for the three indicators was also assessed, and we suggest a potential methodology. Our results revealed that the GlcN:MurN ratio was more reliable for assessing the shifts in gross decomposition channel structure for long-term land use changes, while it was less sensitive to short-term drought compared with the other two indicators. The F:B ratio was more applicable than the FF:BF ratio for reflecting both long- and short-term changes. Furthermore, the reliability of the GlcN:MurN ratio was the least dependent on measuring time point numbers. We suggest the use of multiple indicators and the adoption of multiple measuring time points for the overall methodology.

Evaluation of the Effect of Organic Matter from Invasive Plants on Soil Nematode Communities

Invasive plants can cause loss of biodiversity and degradation of ecosystems with varying degrees of impact on soil communities. Little is known about how the organic matter of these invaders in the soil affects soil properties and nematode communities. We performed a pot experiment with non-invaded grassland soil and organic matter from two invasive plants, Fallopia japonica and Solidago gigantea, to assess and compare the composition and function of the nematode communities and soil properties. We tested five treatments: (1) non-invaded grassland soil (S), (2) 100% decayed organic matter from F. japonica (OMF), (3) 100% decayed organic matter from S. gigantea (OMS), (4) 50% soil plus 50% organic matter from F. japonica (S/OMF), and (5) 50% soil plus 50% organic matter from S. gigantea (S/OMS). Analysis of nematode composition was conducted over five months from May to September. The number of identified genera and diversity index was highest in the S treatment. The soil moisture content was highest, pH and the diversity index were lowest and herbivorous nematodes were absent in OMF and OMS treatments. The addition of OMF and OMS to soil decreased the soil pH and moisture content and increased the contents of organic carbon and total nitrogen. In S/OMF, the abundance of herbivores was lower than in S and the abundances of bacterivores and fungivores decreased during the study period. In the S/OMS, a significantly high diversity index was observed, similar to that in the S treatment. The selected ecological and functional indices differed between S/OMF, S/OMS and S, but not significantly. Our findings indicated that the organic matter from the two invasive plants could differentially contribute to interactions with nematode communities. A decrease in productivity and the slowing of nutrient cycling demonstrated by the decrease in the abundances of bacterivores and fungivorous nematodes may be common adding organic matter of invasive plants to soil. A decrease in the abundance of herbivores after the application of organic matter of F. japonica could potentially be used as an ecologically friendly management strategy against plant parasitic nematodes.

Nematodes Degrade Extracellular Antibiotic Resistance Genes by Secreting DNase II Encoded by the nuc-1 Gene

This study investigated the degradation performance and mechanism of extracellular antibiotic resistance genes (eARGs) by nematodes using batch degradation experiments, mutant strain validation, and phylogenetic tree construction. Caenorhabditis elegans, a representative nematode, effectively degraded approximately 99.999% of eARGs (tetM and kan) in 84 h and completely deactivated them within a few hours. Deoxyribonuclease (DNase) II encoded by nuc-1 in the excretory and secretory products of nematodes was the primary mechanism. A neighbor-joining phylogenetic tree indicated the widespread presence of homologs of the NUC-1 protein in other nematodes, such as Caenorhabditis remanei and Caenorhabditis brenneri, whose capabilities of degrading eARGs were then experimentally confirmed. C. elegans remained effective in degrading eARGs under the effects of natural organic matter (5, 10, and 20 mg/L, 5.26-6.22 log degradation), cation (2.0 mM Mg2+ and 2.5 mM Ca2+, 5.02-5.04 log degradation), temperature conditions (1, 20, and 30 °C, 1.21-5.26 log degradation), and in surface water and wastewater samples (4.78 and 3.23 log degradation, respectively). These findings highlight the pervasive but neglected role of nematodes in the natural decay of eARGs and provide novel approaches for antimicrobial resistance mitigation biotechnology by introducing nematodes to wastewater, sludge, and biosolids.

Nematode community structures in the presence of wastewater treatment plant discharge

Wastewater treatment plants (WWTPs) represent major point sources of pollution in coastal systems, affecting benthic ecosystems. In the present study, we assessed the potential role that WWTPs have in shaping nematode communities and established baseline knowledge of free-living nematode community structures in St. Andrew Bay, Florida. Sediment samples were collected from four sites representing areas of WWTP outflow and areas with no apparent outflow, during the winter and summer. Nematode communities across sites were significantly different, and the differences were strongly associated with the distance to the nearest WWTP. While the communities were not different along transects at each site, nor across seasons, community dissimilarity across sites was high, implying strong contrasts throughout the bay system. Dominance of tolerant, opportunistic genera and Ecological Quality Status assessments suggest that the system is stressed by organic enrichment, possibly linked to the WWTPs. Our results suggest that knowledge on the life-history of dominant genera is imperative to assess the ecological quality of a benthic system, in addition to taxonomic and functional metrics. Considering the value of marine nematodes as bioindicators, more work should be done to monitor temporal variability in nematode communities in this system as future infrastructure changes alter its dynamics.

The Invasion of Alien Populations of Solanum elaeagnifolium in Two Mediterranean Habitats Modifies the Soil Communities in Different Ways

We aimed to explore how the invasion of the alien plant Solanum elaeagnifolium affects soil microbial and nematode communities in Mediterranean pines (Pinus brutia) and maquis (Quercus coccifera). In each habitat, we studied soil communities from the undisturbed core of both formations and from their disturbed peripheral areas that were either invaded or not by S. elaeagnifolium. Most studied variables were affected by habitat type, while the effect of S. elaeagnifolium was different in each habitat. Compared to maquis, the soil in pines had higher silt content and lower sand content and higher water content and organic content, supporting a much larger microbial biomass (PLFA) and an abundance of microbivorous nematodes. The invasion of S. elaeagnifolium in pines had a negative effect on organic content and microbial biomass, which was reflected in most bacterivorous and fungivorous nematode genera. Herbivores were not affected. In contrast, in maquis, organic content and microbial biomass responded positively to invasion, raising the few genera of enrichment opportunists and the Enrichment Index. Most microbivores were not affected, while herbivores, mostly Paratylenchus, increased. The plants colonizing the peripheral areas in maquis probably offered a qualitative food source to microbes and root herbivores, which in pines was not sufficient to affect the much larger microbial biomass.

Effects of fertilization on soil nematode communities in an alpine meadow of Qinghai-Tibet plateau

Nitrogen and phosphorus are important nutrient elements for plants and underground organisms. The nematode is an important part of the soil food web. Although many studies have explored the effects of fertilization on soil nematode community structure, little is known about the response mechanism of the nematode community to fertilization. In this study, we investigated the diversity and functional diversity of soil nematode communities, as well as soil physicochemical properties, root functional traits, and plant richness. We explored the response mechanism of soil nematode communities to nitrogen and phosphorus fertilizer. Nitrogen fertilizer increased the abundance and richness of bacterivorous nematodes, while phosphorus fertilizer decreased the total abundance of bacterivorous nematodes. Meanwhile, the diversity of the nematode community was significantly affected by soil physicochemical properties and plant root functional traits. Therefore, our study revealed the effects of nitrogen and phosphorus fertilizer on soil nematode community diversity and functional diversity. Exploring the response mechanism of soil nematode communities to fertilization interference provides further evidence for the role of nematodes in maintaining the function of subsurface ecosystems.

Legionella pneumophila and Free-Living Nematodes: Environmental Co-Occurrence and Trophic Link

Free-living nematodes harbor and disseminate various soil-borne bacterial pathogens. Whether they function as vectors or environmental reservoirs for the aquatic L. pneumophila, the causative agent of Legionnaires’ disease, is unknown. A survey screening of biofilms of natural (swimming lakes) and technical (cooling towers) water habitats in Germany revealed that nematodes can act as potential reservoirs, vectors or grazers of L. pneumophila in cooling towers. Consequently, the nematode species Plectus similis and L. pneumophila were isolated from the same cooling tower biofilm and taken into a monoxenic culture. Using pharyngeal pumping assays, potential feeding relationships between P. similis and different L. pneumophila strains and mutants were examined and compared with Plectus sp., a species isolated from a L. pneumophila-positive thermal source biofilm. The assays showed that bacterial suspensions and supernatants of the L. pneumophila cooling tower isolate KV02 decreased pumping rate and feeding activity in nematodes. However, assays investigating the hypothesized negative impact of Legionella’s major secretory protein ProA on pumping rate revealed opposite effects on nematodes, which points to a species-specific response to ProA. To extend the food chain by a further trophic level, Acanthamoebae castellanii infected with L. pneumphila KV02 were offered to nematodes. The pumping rates of P. similis increased when fed with L. pneumophila-infected A. castellanii, while Plectus sp. pumping rates were similar when fed either infected or non-infected A. castellanii. This study revealed that cooling towers are the main water bodies where L. pneumophila and free-living nematodes coexist and is the first step in elucidating the trophic links between coexisting taxa from that habitat. Investigating the Legionella–nematode–amoebae interactions underlined the importance of amoebae as reservoirs and transmission vehicles of the pathogen for nematode predators.

Drivers of nematode diversity in forest soils across climatic zones

Nematodes are the most abundant multi-cellular animals in soil, influencing key processes and functions in terrestrial ecosystems. Yet, little is known about the drivers of nematode abundance and diversity in forest soils across climatic zones. This is despite forests covering approximately 30% of the Earth's land surface, providing many crucial ecosystem services but strongly varying in climatic conditions and associated ecosystem properties across biogeographic zones. Here, we collected nematode samples from 13 forests across a latitudinal gradient. We divided this gradient into temperate, warm-temperate and tropical climatic zones and found that, across the gradient, nematode abundance and diversity were mainly influenced by soil organic carbon content. However, mean annual temperature and total soil phosphorus content in temperate zones, soil pH in warm-temperate zones, and mean annual precipitation in tropical zones were more important in driving nematode alpha-diversity, biomass and abundance. Additionally, nematode beta-diversity was higher in temperate than in warm-temperate and tropical zones. Together, our findings demonstrate that the drivers of nematode diversity in forested ecosystems are affected by the spatial scale and climatic conditions considered. This implies that high resolution studies are needed to accurately predict how soil functions respond if climate conditions move beyond the coping range of soil organisms.

Hydrogen cyanide, a key plant defense, as a potential driver of root-associated nematode communities along urbanization gradients

Introduction

Plant chemical defenses can influence the distribution, community composition, and abundance of soil biota. Urbanization plays a key role in shaping soil biotic communities either directly through changes in soil properties or indirectly via changes in plant characteristics such as defense traits. The effects of urbanization and plant defenses on the abundance and structure of aboveground plant-associated communities have been studied, yet their effects on belowground root-associated communities are poorly understood.

Methods

Here we sampled white clover (Trifolium repens L.) leaves and roots along urban–rural gradients in the cities of Antwerp and Ghent, Belgium. We measured production of hydrogen cyanide (HCN) in leaves, a known defense trait against herbivores, and abundances of different feeding guilds of nematodes associated with the roots.

Results

We found that HCN production decreased with increasing levels of urbanization in both cities. Urbanization was significantly correlated with shifts in root-associated nematode community structure in Antwerp but not in Ghent. Responses of nematode feeding guilds and trophic groups to urbanization were highly dependent on the clovers’ HCN production, especially in Ghent. Changes in nematode channel ratio in Antwerp indicated that urban root-associated nematode communities of white clover were more strongly dominated by fungivorous nematodes.

Discussion

Our results demonstrate that urbanization is driving changes in a plant phenotypic trait and in the community structure of root-associated nematodes, as well as that both changes interact. Plant defense mechanisms could thus help elucidate the effects of urbanization on root-associated biota communities. As strong differences existed between the two studied cities, the particular properties of cities should be taken into account to better understand the direction and strength of phenotypic trait changes driven by urbanization.

Nematode mitochondrial metagenomics: A new tool for biodiversity analysis

DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.

Nematodes and their bacterial prey improve phosphorus acquisition by wheat

Plant growth is greatly influenced by the rhizosphere microbiome, which has been traditionally investigated from a bottom-up perspective assessing how resources such as root exudates stimulate microbial growth and drive microbiome assembly. However, the importance of predation as top-down force on the soil microbiome remains largely underestimated. Here, we planted wheat both in natural and in sterilized soils inoculated with the key microbiome predators - bacterivorous nematodes - to assess how plant performance responds to top-down predation of the soil microbiome and specific plant growth-promoting bacteria, namely phosphate-solubilizing bacteria. We found that nematodes enriched certain groups (e.g. Actinobacteria, Chloroflexi, and Firmicutes) and strengthened microbial connectance (e.g. Actinobacteria and Proteobacteria). These changes in microbiome structure were associated with phosphate-solubilizing bacteria that facilitated phosphorus (P) cycling, leading to greater P uptake and biomass of wheat in both soils. However, the enhancement varied between nematode species, which may be attributed to the divergence of feeding behavior, as nematodes with weaker grazing intensity supported greater abundance of phosphate-solubilizing bacteria and better plant performance compared with nematodes with greater grazing intensity. These results confirmed the ecological importance of soil nematodes for ecosystem functions via microbial co-occurrence networks and suggested that the predation strength of nematodes determines the soil bacteria contribution to P biogeochemical cycling and plant growth.

Contrasting influences of two dominant plants, Dasiphora fruticosa and Ligularia virguarea, on aboveground and belowground communities in an alpine meadow

Soil organisms are abundant, phylogenetically and functionally diverse, and interact to catalyse and regulate critical soil processes. Understanding what structures belowground communities is therefore fundamental to gaining insight into ecosystem functioning. Dominant plants have been shown to influence belowground communities both directly and indirectly through changes in abiotic and biotic factors. In a field study, we used piecewise structural equation modelling to disentangle and compare the effects of a dominant allelopathic plant, Ligularia virgaurea, and a dominant facilitative plant, Dasiphora fruticosa, on understory plant, soil microbial and nematode community composition in an alpine meadow on the Tibetan plateau. Dasiphora fruticosa was associated with changes in edaphic variables (total nitrogen, soil organic carbon, pH and ammonium), understory plant and soil bacterial communities, whereas Ligularia virguarea was associated with increased soil ammonium content and soil fungal richness relative to dominant plant-free control plots. Moreover, nematode richness was significantly greater under D. fruticosa, with no change in nematode community composition. By contrast, nematode richness under Ligularia virgaurea was similar to that of dominant plant-free control plots, but nematode community composition differed from the control. The effects of both plants were predominantly direct rather than mediated by indirect pathways despite the observed effects on understory plant communities, soil properties and microbial assemblages. Our results highlight the importance of plants in determining soil communities and provide new insight to disentangle the complex above- and belowground linkages.

Post-Fire Recovery of Soil Nematode Communities Depends on Fire Severity

Following the creation of a new organic layer after a forest fire, there is an initial build-up phase of overall biota. We studied soil nematode community development in a chronosequence of post-fire coniferous forest sites in relation to different fire severity. The taxonomic and functional composition of the soil nematode community was analyzed to detect immediate changes and levels of post-fire recovery in soil food web structures, i.e., 0, 1, 4, 8, 14, 20, 45, and 110 years after the event. Unburned forest sites served as controls. With small exceptions recorded immediately after the burn (mean nematode abundance, total biomass), the low severe wildfires had no impacts on the structures of nematode communities. The structures of nematode communities were found to be stable on sites affected by low severe wildfires, without considerable fluctuations in comparison to the unburned sites during chronosequence. On the contrary, nematode communities responded considerably to fires of high severity. The significant changes, i.e., a decrease of mean nematode abundance, plant parasites, omnivores and predators, species number, and nematode diversity, the values of CI, SI, MI, but an increase in the number of bacterivores and EI were recorded immediately after the fire. Such status, one year after a fire of high severity, has been observed. Full recovery of nematode communities 14 years after the disruption was found. Overall, our results showed that fire severity was a considerable element affecting soil nematode communities immediately after events, as well as the time needed to recover communities’ structure during post-fire chronosequence.

Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic

Estuarine environments are suggested to be the final receivers of human pollution and are impacted by surrounding urbanization and compounds carried by the river waters that flow from the continent. Polycyclic aromatic hydrocarbons (PAHs) are among the contaminants that can reach estuaries and can directly affect marine conservation, being considered highly deleterious to organisms living in these environments. This research investigated the meiofauna of three estuaries exposed to different levels of urbanization and consequently different levels of PAH concentrations, in order to assess how these compounds and environmental factors affect the distribution, structure and diversity of these interstitial invertebrates. A total of 15 major meiofauna groups were identified, with Nematoda being the dominant taxon (74.64%), followed by Copepoda (9.55%) and Polychaeta (8.56%). It was possible to observe significant differences in all diversity indices studied in the estuaries. With the exception of average density, the diversity indices (richness, Shannon index and evenness) were higher in the reference estuary, Goiana estuarine system (GES). On the other hand, the Timbó estuarine system (TES) had the lowest Shannon index value and richness, while the Capibaribe estuarine system (CES) had the lowest evenness value. The latter two estuaries (TES and CES) presented intermediate and high levels of urbanization, respectively. The ecological quality assessment (EcoQ) in the studied estuaries was classified from Poor to Moderate and the estuary with the lowest demographic density in its surroundings, GES, showed a better ecological quality (Moderate EcoQ). A significant distance-based multivariate linear modelling regression (DistLM) was observed between the environmental variables and the density of the meiobenthic community, where PAHs and pH were the main contributors to organism variation. The sediments were characterized by predominance of very fine sand and silt-clay in the most polluted environments, while the control site environment (GES) was dominated by medium grains. The highest concentrations of PAHs were found in the most urbanized estuaries, and directly affected the structure of the interstitial benthic community. The metrics used in the present study proved to be adequate for assessing the environmental quality of the investigated estuaries.

Responses of soil nematode community within soil aggregates to tea plantation age

It is increasingly believed that soil nematodes play an important role in the soil community and have a pronounced influence on the evaluation of soil health and the monitoring of soil food web changes. Soil aggregates provide habitable pore space and resource availability for soil organisms. The distribution of soil nematodes, which are relatively small soil fauna, may be related to the degree of soil aggregates. Soil nematode communities were studied with different soil components: large macro-aggregates (> 2 mm), medium macro-aggregates (2-1 mm), small macro-aggregates (1-0.25 mm), and micro-aggregates (< 0.25 mm) extracted from the same crop variety plantings (Sichuan tea) of different ages (19 years, 26 years, 34 years, and 56 years) in Sichuan province, southwestern China, in 2018. The results showed that the tea plantation with 26 years of cultivation was more suitable for the propagation of nematode communities, and the numbers of total nematodes were highest in the > 2 mm fractions. Compared with other tea plantations, the Margalef index (SR) of 26-year-old tea plantation was significantly higher than that within the large and medium macro-aggregates, and the maturity index (MI) was higher in the large and small macro-aggregates in the 26-year-old tea plantation. In the large macro-aggregates, the value of functional metabolic footprints decreased with the tea plantation age. In addition, the functional metabolic footprints increased with the increase in soil aggregate size. Our finding suggests that nematode communities are limited by resource availability and resource quality played an important role in determining nematode communities. Moreover, the soil food web was degenerated with the age of tea cultivation. Therefore, in the study area, it is necessary to pay attention to the rational allocation and application of organic fertilizer in the late stage of tea planting, so as to maintain the soil fertility and soil food web structure of the tea garden.

Ecological impact assessment of irrigation dam in the Mekong Delta using intertidal nematode communities as bioindicators

The ecological response of nematode communities to dam construction has limited attention. In this study, the response of intertidal nematode communities in the Ba Lai River (Mekong Delta, Vietnam) to the construction of an irrigation dam was investigated. Nematode communities and environmental parameters were investigated during the rainy season of 2015. The obtained results showed that the Ba Lai dam had caused negative impacts on the local environment by disrupting longitudinal connectivity, the accumulation of nutrients (total organic carbon, total nitrogen, total phosphorus), and heavy metals (copper, iron, arsenic, lead) in the upstream and the lateral sides of the dam, consequently leading to changes in the nematode communities. The response of nematode communities to the dam's presence was clear based on their abundance, diversity, dominant genera, and community composition. Furthermore, changes in the abundance and diversity of nematodes in the Ba Lai River appeared to be controlled primarily by acidity (pH), total suspended solids (TSS), iron (Fe), clay, and salinity most responsible for changes to nematode communities. Because the nematode communities are well adapted to the physicochemical disturbances caused by dam construction, they are a potential tool for ecological monitoring and understanding the influence of dams on aquatic ecosystems.

Life in a Contaminated Environment: How Soil Nematodes Can Indicate Long-Term Heavy-Metal Pollution

We investigated the genera, trophic groups, and functional guilds of soil nematodes at five alluvial meadows along the Litavka River in the Czech Republic to assess their usefulness as indicators of heavy metal pollution in soils. The Litavka River flows around the waste-sedimentation pond of a smelter in the city of Příbram in the Central Bohemian Region. Lead, zinc, and arsenic are the main pollutants in the soils in the vicinity of the smelter. The alluvial meadows closest to the pond and mine waste were the most heavily polluted sites, and contamination decreased downstream along the river with increasing distance from the sources of pollution. The nematode communities were sensitive to pollution, with the most contaminated sites having considerably fewer nematode individuals, fewer genera, and a less diverse and more degraded food web with less nematode biomass. Arsenic, lead, and zinc contents were significantly negatively correlated with the numbers of bacterivores, predators, omnivores, plant parasites, and fungivores, which were significantly less abundant at highly polluted sites. This correlation suggests that nematode groups with higher c-p values, and those with c-p 1 and 2 designations, can be useful indicators of high heavy-metal contamination in areas polluted for a long time. In contrast, the abundance of c-p 3 plant parasitic nematodes was positively correlated with copper, nickel, and zinc contents and with soil-moisture content in the alluvial meadows. Maturity index (MI) and MI2-5 were the most sensitive indices of the degree of disturbance of the soil ecosystem, with enrichment index, structure index, and basal index indicating the altered decomposition channels and diminished structure of the food web.

Effects of Grass-Based Crop Rotation, Nematicide, and Irrigation on the Nematode Community in Cotton

Plant-parasitic and free-living nematodes – bacterivores, fungivores, omnivores, predators – comprise the nematode community. Nematicide application and crop rotation are important tools to manage plant-parasitic nematodes, but effects on free-living nematodes and nematode ecological indices need further study. The nematicide fluopyram was recently introduced in cotton (Gossypium hirsutum) production and its effects on the nematode community need assessment. This research was conducted in 2017 and 2018 at a long-term field site in Quincy, FL where perennial grass/sod-based (bahiagrass, Paspalum notatum) and conventional cotton rotations were established in 2000. The objective of this research was to evaluate the effects of fluopyram nematicide, crop rotation phase, and irrigation on free-living nematodes and nematode ecological indices based on three soil sampling dates each season. We did not observe consistent effects of crop rotation phase on free-living nematodes or nematode ecological indices. Only omnivores were consistently negatively impacted by fluopyram. Nematode ecological indices reflected this negative effect by exhibiting a degraded/ stressed environmental condition relative to untreated plots. Free-living nematodes were not negatively impacted by nematicide when sod-based rotation was used.

Identification and characterization of epicuticular proteins of nematodes sharing motifs with cuticular proteins of arthropods

Specific collagens and insoluble proteins called cuticlins are major constituents of the nematode cuticles. The epicuticle, which forms the outermost electron-dense layer of the cuticle, is composed of another category of insoluble proteins called epicuticlins. It is distinct from the insoluble cuticlins localized in the cortical layer and the fibrous ribbon underneath lateral alae. Our objective was to identify and characterize genes and their encoded proteins forming the epicuticle. The combination between previously obtained laboratory results and recently made available data through the whole-genome shotgun contigs (WGS) and the transcriptome Shotgun Assembly (TSA) sequencing projects of Ascaris suum allowed us to identify the first epicuticlin gene, Asu-epic-1, on the chromosome VI. This gene is formed of exon1 (55 bp) and exon2 (1067 bp), separated by an intron of 1593 bp. Exon 2 is formed of tandem repeats (TR) whose number varies in different cDNA and genomic clones of Asu-epic-1. These variations could be due to slippage of the polymerases during DNA replication and RNA transcription leading to insertions and deletions (Indels). The deduced protein, Asu-EPIC-1, consists of a signal peptide of 20 amino acids followed by 353 amino acids composed of seven TR of 49 or 51 amino acids each. Three highly conserved tyrosine motifs characterize each repeat. The GYR motif is the Pfam motif PF02756 present in several cuticular proteins of arthropods. Asu-EPIC-1 is an intrinsically disordered protein (IDP) containing seven predicted molecular recognition features (MoRFs). This type of protein undergoes a disorder-to-order transition upon binding protein partners. Three epicuticular sequences have been identified in A. suum, Ascaris lumbricoides, and Toxocara canis. Homologous epicuticular proteins were identified in over 50 other nematode species. The potential of this new category of proteins in forming the nematode cuticle through covalent interactions with other cuticular components, particularly with collagens, is discussed. Their localization in the outermost layer of the nematode body and their unique structure render them crucial candidates for biochemical and molecular interaction studies and targets for new biotechnological and biomedical applications.

Nematode Community of a Natural Grassland Responds Sensitively to the Broad-Spectrum Fungicide Mancozeb in Soil Microcosms

Fungicides make up the largest part of total pesticide use, with the dithiocarbamate mancozeb being widely applied as a nonsystemic contact pesticide to protect a wide range of field crops against fungal diseases. Although nematodes are key drivers of soil functioning, data on effects of fungicides, and especially mancozeb, on these nontarget organisms are scarce. Therefore, the effects of mancozeb on a soil nematode community from a natural grassland were assessed in small-scale soil microcosms. Nematodes were exposed to mancozeb-spiked soil in six nominal concentrations (7-133 mg/kg dry soil) and analyzed after 14, 56, and 84 days in terms of densities, genus composition, and functional traits. Because this fungicide is known to quickly degrade in soils (50% degradation time <1 day), mancozeb concentrations were analyzed for all sampling occasions. Chemical analysis revealed considerably lower measured concentrations compared with the aimed nominal soil concentrations at the beginning of the exposure (1-18 mg/kg dry soil), suggesting fast degradation during the spiking process. Nevertheless, the native nematode community responded sensitively to the fungicide mancozeb, revealing lower no-observed-effect concentration and 10% effect concentration (EC10) values than reported for other soil invertebrates such as springtails and earthworms. Using the EC10 for the most sensitive nematode community endpoint (percentage of predators and omnivores: 1.2 mg/kg dry soil), the risk assessment exhibited a toxicity exposure ratio of 0.66 and, thus, a high risk of mancozeb for soil nematodes. Keeping in mind their abundance and their central roles in soil food-web functioning, the demonstrated sensitivity to a widely applied fungicide underscores the relevance of the inclusion of nematodes into routine risk-assessment programs for pesticides. Environ Toxicol Chem 2022;41:2420-2430. © 2022 SETAC.

Effects of source sample amount on biodiversity surveys of bacteria, fungi, and nematodes in soil ecosystems

Bacteria, fungi, and nematodes are major components of soil ecosystems, playing pivotal roles in belowground material cycles and biological community processes. A number of studies have recently uncovered the diversity and community structure of those organisms in various types of soil ecosystems based on DNA metabarcoding (amplicon sequencing). However, because most previous studies examined only one or two of the three organismal groups, it remains an important challenge to reveal the entire picture of soil community structure. We examined how we could standardize DNA extraction protocols for simultaneous DNA metabarcoding of bacteria, fungi, and nematodes. Specifically, in an Illumina sequencing analysis of forest and farmland soil samples, we performed DNA extraction at five levels of soil-amount (0.5, 2, 5, 10, and 20 g). We then found that DNA extraction with the 0.5 g soil setting, which had been applied as default in many commercial DNA extraction kits, could lead to underestimation of α-diversity in nematode community. We also found that dissimilarity (β-diversity) estimates of community structure among replicate samples could be affected by soil sample amount. Based on the assays, we conclude that DNA extraction from at least 20 g of soil is a standard for comparing biodiversity patterns among bacteria, fungi and nematodes.

Responses of bryosphere fauna to drought across a boreal forest chronosequence

Projected changes in precipitation regimes can greatly impact soil biota, which in turn alters key ecosystem functions. In moss-dominated ecosystems, the bryosphere (i.e., the ground moss layer including live and senesced moss) plays a key role in carbon and nutrient cycling, and it hosts high abundances of microfauna (i.e., nematodes and tardigrades) and mesofauna (i.e., mites and springtails). However, we know very little about how bryosphere fauna responds to precipitation, and whether this response changes across environmental gradients. Here, we used a mesocosm experiment to study the effect of volume and frequency of precipitation on the abundance and community composition of functional groups of bryosphere fauna. Hylocomium splendens bryospheres were sampled from a long-term post-fire boreal forest chronosequence in northern Sweden which varies greatly in environmental conditions. We found that reduced precipitation promoted the abundance of total microfauna and of total mesofauna, but impaired predaceous/omnivorous nematodes, and springtails. Generally, bryosphere fauna responded more strongly to precipitation volume than to precipitation frequency. For some faunal functional groups, the effects of precipitation frequency were stronger at reduced precipitation volumes. Context-dependency effects were found for microfauna only: microfauna was more sensitive to precipitation in late-successional forests (i.e., those with lower productivity and soil nutrient availability) than in earlier-successional forests. Our results also suggest that drought-induced changes in trophic interactions and food resources in the bryosphere may increase faunal abundance. Consequently, drier bryospheres that may result from climate change could promote carbon and nutrient turnover from fauna activity, especially in older, less productive forests.

Sunflower Seed Husk as Promising By-Product for Soil Biodisinfestation Treatments and Fertility Improvement in Protected Lettuce Crop

One of the major challenges in biodisinfestation treatments against soilborne pathogens is the selection of the proper organic amendments and mixture features. The use of agro-industrial by-products is a sustainable alternative with proven efficacy, but the availability has to be considered in terms of location and quantity. Sunflower seed is one of the five major oil crops widely cultivated and the husk constitutes a significant part that is discarded. This by-product brings together the features to be considered an interesting organic amendment in agricultural soils because of its lignocellulose content, but no references have been found in this field. In this study, sunflower seed husk was used with fresh cow manure in biodisinfestation treatments, alone or combined with other by-products (rapeseed cake, beer bagasse and wheat bran). The assay was performed in summer in a commercial greenhouse with significant yield losses in lettuce crops caused by the root-knot nematode Meloidogyne incognita. Four different amendment mixtures were applied which included 3kg/m2 cow manure, as common waste, and 1 kg/m2 of by-products (dry weight), considering 6mgC/g soil in all treatments but different C/N ratio (23, 29, 31, 34) and by-products. Data was collected in three moments: (i) before and (ii) after biodisinfestation treatments and (iii) after harvesting the first crop after biodisinfestations. Crop damage was assessed through root galling index and the number of eggs in roots. The effects on the pathogen population and the whole soil nematode community were assessed along with some physicochemical and soil microbiological variables (respiration rate, microbial organic C, water-soluble organic C and physiological profile of heterotrophic bacteria through Biolog Ecoplates™). All treatments reported effectiveness in disease control without significant differences among them, but among times. However, soil temperatures during biodisinfestations were higher at higher C/N ratios and fertility variables also increased in these cases, mainly in the treatment with husk as the only by-product. Sunflower seed husk proved to be an interesting source of organic C to improve both biodisinfestation treatments and soil fertility in humid temperate climate zones.

The Life Cycle of the Bacterial-Feeding Nematode Diplolaimella stagnosa and Its Population Growth in Response to Temperature and Food Availability

Diplolaimella is a ubiquitous cosmopolitan genus, but information on the life cycles of its species is limited. Here, we describe the life cycle of a free-living bacterivorous nematode, Diplolaimella stagnosa, and report the effects of temperature and food availability on its population dynamics. Specimens were primarily collected from the intertidal zone of Hangzhou Bay Wetland, China and culture experiments were conducted in nutrient agar media with habitat water at 20°C. The nematode primarily fed on an unidentified bacterium that it carried. Under these conditions, both males and females matured in 16 days. Reproduction was by gamogenesis and gravid females normally carried 7–8 eggs. Embryogenesis was completed in 58 h, and the entire life cycle (egg to adult) was completed in 16–18 days. During juvenile development, body lengths of worms increased linearly up to the 16th day, and then remained constant. Body lengths of males and females were 898.1 ± 6.0 μm and 1039.7 ± 14.7 μm, respectively. Nematodes kept at 25°C had a greater population increase than those at 20°C, and the population growth of nematodes was substantially higher in microcosms with abundant bacteria supplied by leaves of Phragmites australis than in microcosms without plant litter. Based on its life strategy and the influence of food availability and temperature on population growth, D. stagnosa was allocated to group c-p 2, suggesting its potential use as a model organism in toxicological studies.

Changes in the Abundance and Community Complexity of Soil Nematodes in Two Rice Cultivars Under Elevated Ozone

The atmospheric ozone concentrations have substantially increased in the surface layer over the past decades, and consequently exhibited a strong influence on soil microbial communities and functions. However, the effect of elevated ozone (eO₃) on the abundance, diversity, and structural complexity of soil nematode communities are elusive under different rice (Oryza sativa L.) cultivars. Here, the soil nematode community was investigated in two rice cultivars (Hybrid, Shanyou 63 vs. Japonica, Wuyujing 3) under open-top chambers (OTC) with control and eO₃ conditions. The results showed that the abundance of soil nematode community was altered by eO₃, but the responses were dependent on crop cultivars. The eO₃ decreased the total abundance and simplified the network complexity of the soil nematode community for both cultivars. However, eO₃ increased the abundance of c-p 4 in Shanyou 63, rather than Wuyujing 3, indicating that the hybrid rice cultivar could tradeoff the adverse impacts of eO₃ on the functional group of soil nematodes. Similarly, bacterivores belonging to K-strategy (c-p 4) increased under eO₃ in Shanyou 63, suggesting that the soil food web formed a bacteria-dominated channel under eO₃ for the hybrid rice cultivar. This study shed new light on the critical importance of rice cultivars in shaping the impacts of eO₃ on the soil micro-food web. Therefore, breeding and biotechnological approaches may become valuable pathways to improve soil health by shaping the community structures of the soil micro-food web in response to climate change in the future.

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.

Free-living marine nematodes community structure in the conservation area (Chaojing Park) and its adjacent area of Keelung, Taiwan

Studies conducted in the same seas or even study sites nearby each other, showed very different community structure, implying the patchiness of free-living marine nematodes which may be related to the sedimentary environment such as sediment type and food availability of the study area. This study was motivated by the concerns about the impacts of high level of anthropogenic activities on Chaojing Park (gazetted as Wanghaixiang’s Chao-Jing Bay Resource Conservation Area (WCJBRA) in 2016). The present study provides baseline knowledge of free-living marine nematode community structure in WCJBRA and identify potential marine nematodes as bioindicators to indicate possible impacts of the anthropogenic activities to the Chaojing Park. A total of 15 stations were selected in the subtidal zones of WCJBRA and its adjacent area. Marine nematode sample collection was carried out on the 13th and 14th of September 2019 using SCUBA diving technique. Results showed positive correlation between nematode density and medium sand (500μm-1.0mm). Presence of certain species such as Daptonema sp., Pomponema sp. and Innocuonema sp. indicates presence of disturbances in S12 and S13. Several species also showed potential to be introduced as indicator for healthy environment subjected to further studies on nematode-pollutants relationship, particularly on autecology as per se. Higher species diversity, H’ index of S1-S8 and S11 was categorised as Good Condition; followed by station with moderate species diversity index (S9, S10, S14 –Moderate Condition) zone; and lastly S12, S13 and S15 (Poor Condition).

Soil Nematodes as the Silent Sufferers of Climate-Induced Toxicity: Analysing the Outcomes of Their Interactions with Climatic Stress Factors on Land Cover and Agricultural Production

Unsustainable anthropogenic activities over the last few decades have resulted in alterations of the global climate. It can be perceived through changes in the rainfall patterns and rise in mean annual temperatures. Climatic stress factors exert their effects on soil health mainly by modifying the soil microenvironments where the soil fauna reside. Among the members of soil fauna, the soil nematodes have been found to be sensitive to these stress factors primarily because of their low tolerance limits. Additionally, because of their higher and diverse trophic positions in the soil food web they can integrate the effects of many stress factors acting together. This is important because under natural conditions the climatic stress factors do not exert their effect individually. Rather, they interact amongst themselves and other abiotic stress factors in the soil to generate their impacts. Some of these interactions may be synergistic while others may be antagonistic. As such, it becomes very difficult to assess their impacts on soil health by simply analysing the physicochemical properties of soil. This makes soil nematodes outstanding candidates for studying the effects of climatic stress factors on soil biology. The knowledge obtained therefrom can be used to design sustainable agricultural practices because most of the conventional techniques aim at short-term benefits with complete disregard of soil biology. This can partly ensure food security in the coming decades for the expanding population. Moreover, understanding soil biology can help to preserve landscapes that have developed over long periods of climatic stability and belowground soil biota interactions.

Management effects on soil nematode abundance differ among functional groups and land-use types at a global scale

Anthropogenic land use is threatening global biodiversity. As one of the most abundant animals on Earth, nematodes occupy several key positions in belowground food webs and contribute to many ecosystem functions and services. However, the effects of land use on nematode abundance and its determinants remain poorly understood at a global scale. To characterize nematodes' responses to land use across trophic groups, we used a dataset of 6,825 soil samples globally to assess how nematode abundance varies among regional land-use types (i.e., primary vegetation, secondary vegetation, pasture, cropland, and urban) and local land-use intensities (i.e., human-managed or not). We also quantified the interactive effects of land use and environmental predictors (i.e., mean annual temperature, annual precipitation, soil organic carbon, soil pH, global vegetation biomass, and global vegetation productivity) on nematode abundance. We found that total nematode abundance and the abundance of bacterivores, fungivores, herbivores, omnivores, and predators generally increased or were not affected under management across land-use types. Specifically, the most numerically abundant bacterivores were higher in managed than in unmanaged secondary vegetation habitats and urban areas, and herbivores were more abundant in managed than in unmanaged primary and secondary vegetation habitats. Furthermore, the numbers of significant environmental predictors of nematode abundance were reduced and the magnitude and the direction of the predictors were changed under management. We also found that nematode abundance was more variable and less determined by environmental factors in urban than in other land-use types. These findings challenge the view that human land use decreases animal abundance across trophic groups, but highlight that land use is altering the trophic composition of soil nematodes and its relationships with the environment at the global scale.

Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes

Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.

Selenium Effect Threshold for Soil Nematodes Under Rice Biofortification

Crop biofortification with inorganic selenium (Se) fertilizer is a feasible strategy to improve the health of residents in Se-deficient areas. For eco-friendly crop Se biofortification, a comprehensive understanding of the effects of Se on crop and soil nematodes is vital. In this study, a rice pot experiment was carried out to test how selenite supply (untreated control (0), 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100, or 200 mg Se kg^-1) in soil affected rice growth, rice Se accumulation, and soil nematode abundance and composition. The results showed that selenite supply (5-200 mg kg^-1) generally increased the number of rice tillers, rice yield, and Se concentrations in rice grains. In soil under 10 mg kg^-1 Se treatment, the genus composition of nematodes changed significantly compared with that in the control soil. With increased Se level (> 10 mg kg^-1), soil nematode abundance decreased significantly. Correlation analysis also demonstrated the positive relationships between soil Se concentrations (total Se and bioavailable Se) with rice plant parameters (number of rice tillers, rice yield, and grain Se concentration) and negative relationships between soil Se concentrations (total Se and bioavailable Se) with soil nematode indexes (nematode abundance and relative abundance of Tobrilus). This study provides insight into balancing Se biofortification of rice and soil nematode community protection and suggests the effective concentrations for total Se (1.45 mg kg^-1) and bioavailable Se (0.21 mg kg^-1) to soil nematode abundances at 20% level (EC20) as soil Se thresholds. At Se concentrations below these thresholds, rice plant growth and Se accumulation in the grain will still be promoted, but the disturbance of the soil nematodes would be negligible.

Environmental Factors Indirectly Impact the Nematode Carbon Budget of Subalpine Spruce Forests

Nematodes play a significant role in soil biogeochemical cycling. However, our understanding of their community carbon budget response for a shift in the environmental conditions of natural and planted forests is limited. Therefore, we investigated the nematode community composition, daily carbon used in production and daily carbon budget, environmental variables, and the interaction among trophic groups in the moss, litter and 0–5 cm soil layers of natural subalpine spruce forest and plantations in western Sichuan, China. The result revealed that plantations increased the total nematode daily carbon budget by approximately 52% through the herbivore channel in the 0–5 cm soil layer. The herbivorous nematodes’ daily carbon budget and production in the moss layer of plantations decreased by approximately 60% compared to natural forests. Nematode daily carbon used in production and carbon budget had a strong negative correlation with genus richness. The water content and total carbon was the most important environmental factor that affected the nematode carbon budget and production, respectively. However, the environmental factors indirectly affect the daily carbon budget of herbivore nematodes through omnivore top-down control in subalpine forest ecosystems. Our findings highlight that the planted ecosystems have a certain capacity to maintain abundance, richness, and carbon budget of soil nematode but increase the risk of herbivorous pests.

The Impact of Bio-Based Fertilizer Integration Into Conventional Grassland Fertilization Programmes on Soil Bacterial, Fungal, and Nematode Communities

Phosphorus (P) is an essential plant macro-nutrient applied to soil in agriculture, mainly sourced from non-renewable mined phosphate-rock, of which readily accessible reserves are currently under pressure, while global food demand continues to grow. Meanwhile, an abundance of P is lost in waste-streams. Hence, bio-based fertilizers are increasingly produced using nutrient-recovery technologies and evaluated as a sustainable fertilizer alternative. However, there is little knowledge of how these products affect soil microorganisms. In this study, four new phosphate bio-based fertilizers (two struvite and two incinerator ashes) were assessed in permanent grassland-plots to understand their impact on soil bacterial, fungal, and nematode community responses. The experiment consisted of 40 plots (each 6 × 2 m2) of 8 treatments (2 struvite, 2 ash, cattle slurry, 100% mineral fertilizer, zero P fertilizer, and a control without fertilization) with 5 replications arranged in a randomized complete block design. Community data were obtained by amplicon sequencing of DNA extracted from soil samples and subsequent analysis of community composition, diversity, structure and influencing environmental variables. Diversity of the soil microorganisms was maintained by all bio-based fertilizer treatments. Results showed that soil bacterial, fungal, and nematode communities of the struvite-treatments were similar to those in 100% mineral treatment. Communities in ash-treatments were more disturbed in their compositions, abundances and structures, possibly due to their high pH and heavy metal content. From canonical correspondence analysis, available P, K, and Mg, as well as plant P uptake and biomass yield, were identified as factors significantly influencing bacterial and nematode communities across different treatment groups. In particular, the abundance of environmental disturbance sensitive nematodes (e.g., Dorylaimida) was significantly reduced by one of the ash products. Overall, results indicate that both struvites are benign to soil bacterial, fungal, and nematode communities and can be safely applied as a source of renewable P to meet crop nutrition requirement. The ash products require further investigations before recommending their regular application as fertilizer. As the application of novel bio-based fertilizers will increase in the foreseeable future, the findings of this study would be valuable to feed into developing environmental risk assessment protocols.

Diversity of plant parasitic nematodes characterized from fields of the French national monitoring programme for the Columbia root-knot nematode

Plant parasitic nematodes are highly abundant in all agrosystems and some species can have a major impact on crop yields. To avoid the use of chemical agents and to find alternative methods to manage these pests, research studies have mainly focused on plant resistance genes and biocontrol methods involving host plants or natural enemies. A specific alternative method may consist in supporting non-damaging indigenous species that could compete with damaging introduced species to decrease and keep their abundance at low level. For this purpose, knowledge about the biodiversity, structure and functioning of these indigenous communities is needed in order to carry out better risk assessments and to develop possible future management strategies. Here, we investigated 35 root crop fields in eight regions over two consecutive years. The aims were to describe plant parasitic nematode diversity and to assess the potential effects of cultivation practices and environmental variables on communities. Community biodiversity included 10 taxa of plant parasitic nematodes. Despite no significant abundance variations between the two sampling years, structures of communities varied among the different regions. Metadata collected for the past six years, characterizing the cultural practices and soils properties, made it possible to evaluate the impact of these variables both on the whole community and on each taxon separately. Our results suggest that, at a large scale, many variables drive the structuration of the communities. Soil variables, but also rainfall, explain the population density variations among the geographical areas. The effect of the variables differed among the taxa, but fields with few herbicide applications and being pH neutral with low heavy metal and nitrogen concentrations had the highest plant parasitic nematode densities. We discuss how these variables can affect nematode communities either directly or indirectly. These types of studies can help to better understand the variables driving the nematode communities structuration in order to support the abundance of indigenous non-damaging communities that could compete with the invasive species.

Biodiversity of Nematode Communities Associated with Wheat (Triticum aestivum L.) in Southern Morocco and Their Contribution as Soil Health Bioindicators

Soil nematodes are major soil organisms known to reduce wheat production worldwide. However, they are a crucial part of soil biodiversity. Due to the limited data available regarding nematode biodiversity associated with cereal crops in Morocco, a survey was conducted in 2019 across 80 wheat fields. Thirty-three nematode taxa were obtained with different trophic groups: 11 bacterivores (i.e., Rhabditis and Cephalobus spp.), 11 herbivores (i.e., Pratylenchus and Heterodera spp.), 6 fungivores (i.e., Ditylenchus and Aphelenchoides spp.), 4 omnivores (i.e., Dorylaimus and Aporcelaimus spp.) and one predator (Mononchus spp.). For each locality, the diversity of nematode communities was assessed through multiple diversity indices. Three areas (Ait Melloul, Oulad Dahou, and Sidi Boushab) were more diversified and had pronounced nematode occurrence. Moreover, few localities (e.g., Ait Amira and Lqliaa) were shown to be disturbed. Our study underlined that several nematode taxa were significantly correlated with edaphic and climatic/geographic properties. On the other hand, the spatial and parsimony analyses revealed that plant feeders were most associated with bacterial feeders in disturbed soils. This work revealed that the soil nematodes associated with wheat crops are diverse and can serve as an important tool for soil biomonitoring at a large scale.