A global database of soil nematode abundance and functional group composition

Robustness and variability in Caenorhabditis elegans dauer gene expression

Both plasticity and robustness are pervasive features of developmental programs. The dauer in Caenorhabditis elegans is an arrested, hypometabolic alternative to the third larval stage of the nematode. Dauers undergo dramatic tissue remodeling and extensive physiological, metabolic, behavioral, and gene expression changes compared to conspecifics that continue development and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. Therefore, dauer induction is an example of phenotypic plasticity. However, whether gene expression in dauer larvae induced to arrest development by different genetic or environmental triggers is invariant or varies depending on their route into dauer has not been examined. By using RNA-sequencing to characterize gene expression in different types of dauer larvae and computing the variance and concordance within Gene Ontologies (GO) and gene expression networks, we find that the expression patterns within most pathways are strongly correlated between dauer larvae, suggestive of transcriptional robustness. However, gene expression within specific defense pathways, pathways regulating some morphological traits, and several metabolic pathways differ between the dauer larvae. We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in adaptation, allowing the dauers induced by different stimuli to survive in and exploit different niches.

Global contribution of invertebrates to forest litter decomposition

Forest litter decomposition is an essential component of global carbon and nutrient turnover. Invertebrates play important roles in litter decomposition, but the regional pattern of their effects is poorly understood. We examined 476 case studies across 93 sites and performed a meta-analysis to estimate regional effects of invertebrates on forest litter decomposition. We then assessed how invertebrate diversity, climate and soil pH drive regional variations in invertebrate-mediated decomposition. We found that (1) invertebrate contributions to litter decomposition are 1.4 times higher in tropical and subtropical forests than in forests elsewhere, with an overall contribution of 31% to global forest litter decomposition; and (2) termite diversity, together with warm, humid and acidic environments in the tropics and subtropics are positively associated with forest litter decomposition by invertebrates. Our results demonstrate the significant difference in invertebrate effects on mediating forest litter decomposition among regions. We demonstrate, also, the significance of termites in driving litter mass loss in the tropics and subtropics. These results are particularly pertinent in the tropics and subtropics where climate change and human disturbance threaten invertebrate biodiversity and the ecosystem services it provides.

Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate

Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.

Global fine-resolution data on springtail abundance and community structure

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil

Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.

Toxicity of Per- and Polyfluoroalkyl Substances to Nematodes

Per- and polyfluoroalkyl substances (PFASs) are a class of compounds that persist in the environment globally. Besides being transported to the soil and sediments, which act as their sinks, PFASs can be transferred to several species of higher organisms directly or via bacteria, eliciting a wide range of adverse effects. Caenorhabditis elegans has been widely used in toxicological studies and life science research owing to its numerous advantages over traditional vertebrate models; notably, C. elegans has 65% conserved human-disease-associated genes and does not require ethical approvals for experimental use. This review covers a range of topics, from reported accumulation characteristics and lethal concentrations of PFAS in C. elegans to the mechanisms underlying the toxicity of PFAS at different levels, including reproductive, developmental, cellular, neurologic, oxidative, metabolic, immune, and endocrine toxicities. Additionally, the toxicity levels of some PFAS substitutes are summarized. Lastly, we discuss the toxicological mechanisms of these PFAS substitutes and the importance and promising potential of nematodes as in vivo models for life science research, epidemiological studies (obesity, aging, and Alzheimer's disease research), and toxicological investigations of PFASs and other emerging pollutants compared with other soil animals or model organisms.

Studying root-environment interactions in structured microdevices

In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.

Nematode Pheromones: Structures and Functions

Pheromones are chemical signals secreted by one individual that can affect the behaviors of other individuals within the same species. Ascaroside is an evolutionarily conserved family of nematode pheromones that play an integral role in the development, lifespan, propagation, and stress response of nematodes. Their general structure comprises the dideoxysugar ascarylose and fatty-acid-like side chains. Ascarosides can vary structurally and functionally according to the lengths of their side chains and how they are derivatized with different moieties. In this review, we mainly describe the chemical structures of ascarosides and their different effects on the development, mating, and aggregation of nematodes, as well as how they are synthesized and regulated. In addition, we discuss their influences on other species in various aspects. This review provides a reference for the functions and structures of ascarosides and enables their better application.

Shepherd R, Slos D, O. Powers T, L. Porazinska D. 18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.

Fungivorous nematodes drive microbial diversity and carbon cycling in soil

Soil bacteria and fungi mediate terrestrial biogeochemical cycling, but we know relatively little about how trophic interactions influence their community composition, diversity, and function. Specifically, it is unclear how consumer populations affect the activity of microbial taxa they consume, and therefore the interaction of those taxa with other members of the microbial community. Due to its extreme diversity, studying trophic dynamics in soil is a complex feat. Seeking to address these challenges, we performed a microcosm-based consumer manipulation experiment to determine the impact of a common fungal-feeding nematode (Aphelenchus avenae) on soil microbial community composition, diversity, and activity (e.g., C cycling parameters). Fungivory decreased fungal and bacterial α-diversity and stimulated C and N cycling, possibly via cascading impacts of fungivory on bacterial communities. Our results present experimental evidence that soil trophic dynamics are intimately linked with microbial diversity and function, factors that are key in understanding global patterns in biogeochemical cycling.

Interactions between Soil Bacterial Diversity and Plant-Parasitic Nematodes in Soybean Plants

Plant-parasitic nematodes are an important group of pests causing economic losses in agriculture worldwide. Among the plant-parasitic nematodes, the root-knot (Meloidogyne spp.) and root-lesion nematodes (Pratylenchus spp.) are considered the two most important ones affecting soybeans. In general, they damage soybean roots, causing a reduction of about one-third in productivity. The soil microbial community can exert a suppressive effect on the parasitism of plant-parasitic nematodes. Here, we investigated the effects of soil bacterial diversity on Meloidogyne javanica (Meloidogyne-assay) and Pratylenchus brachyurus (Pratylenchus-assay) suppression by manipulating microbial diversity using the dilution-to-extinction approach in two independent experiments under controlled conditions. Furthermore, we recorded the changes in the soil microbial community induced by plant-parasitic nematode infection. In Meloidogyne-assay, microbial diversity reduced the population density of M. javanica and improved plant performance. In Pratylenchus-assay, microbial diversity sustained the performance of soybean plants even at high levels of P. brachyurus parasitism. Each nematode population affected the relative abundance of different bacterial genera and altered the core microbiome of key groups within the bacterial community. Our findings provide fundamental insights into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants. IMPORTANCE Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. Fortunately, the soil microbial community may suppress these pests, acting as an environmentally friendly alternative to control nematodes. However, the effects of soil microbial diversity on the parasitism of plant-parasitic nematodes still poorly understood. In this study, we provide fundamental insight into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants, which may be useful for the development of new strategies to control these phytopathogens.

Toxin-Producing Endosymbionts Shield Pathogenic Fungus against Micropredators

The fungus Rhizopus microsporus harbors a bacterial endosymbiont (Mycetohabitans rhizoxinica) for the production of the antimitotic toxin rhizoxin. Although rhizoxin is the causative agent of rice seedling blight, the toxinogenic bacterial-fungal alliance is, not restricted to the plant disease. It has been detected in numerous environmental isolates from geographically distinct sites covering all five continents, thus raising questions regarding the ecological role of rhizoxin beyond rice seedling blight. Here, we show that rhizoxin serves the fungal host in fending off protozoan and metazoan predators. Fluorescence microscopy and coculture experiments with the fungivorous amoeba Protostelium aurantium revealed that ingestion of R. microsporus spores is toxic to P. aurantium. This amoebicidal effect is caused by the dominant bacterial rhizoxin congener rhizoxin S2, which is also lethal toward the model nematode Caenorhabditis elegans. By combining stereomicroscopy, automated image analysis, and quantification of nematode movement, we show that the fungivorous nematode Aphelenchus avenae actively feeds on R. microsporus that is lacking endosymbionts, whereas worms coincubated with symbiotic R. microsporus are significantly less lively. This study uncovers an unexpected ecological role of rhizoxin as shield against micropredators. This finding suggests that predators may function as an evolutionary driving force to maintain toxin-producing endosymbionts in nonpathogenic fungi.

Whole-genome sequencing and analysis of Streptomyces strains producing multiple antinematode drugs

Background

Nematodes are parasitic animals that cause over 100 billion US dollars loss in agricultural business. The whole-genomes of two Streptomyces strains, Streptomyces spectabilis KCTC9218^T and Streptomyces sp. AN091965, were sequenced. Both strains produce spectinabilin, an antinematode drug. Its secondary metabolism was examined to aid the development of an efficient nematicidal drug-producing host strain.

Results

The whole-genome sequences of S. spectabilis KCTC9218^T and Streptomyces sp. AN091965 were analyzed using PacBio and Illumina sequencing platforms, and assembled using hybrid methodology. The total contig lengths for KCTC9218^T and AN091965 were 9.97 Mb and 9.84 Mb, respectively. A total of 8,374 and 8,054 protein-coding genes, as well as 39 and 45 secondary metabolite biosynthetic gene clusters were identified in KCTC9218^T and AN091965, respectively. 18.4 ± 6.45 mg/L and 213.89 ± 21.30 mg/L of spectinabilin were produced by S. spectabilis KCTC9218^T and Streptomyces sp. AN091965, respectively. Pine wilt disease caused by nematode was successfully prevented by lower concentration of spectinabilin injection than that of abamectin recommended by its manufacturer. Production of multiple antinematode drugs, including spectinabilin, streptorubin B, and undecylprodigiosin was observed in both strains using high-resolution liquid chromatography mass spectrometry (LC–MS) analysis.

Conclusions

Whole-genome sequencing of spectinabilin-producing strains, coupled with bioinformatics and mass spectrometry analyses, revealed the production of multiple nematicidal drugs in the KCTC9218^T and AN091965 strains. Especially, Streptomyces sp. AN091965 showed high production level of spectinabilin, and this study provides crucial information for the development of potential nematicidal drug producers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08847-4.

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.

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.

Protist Predation Influences the Temperature Response of Bacterial Communities

Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer-protists-influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species-Tetrahymena thermophila and Colpidium sp.-at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.

Increasing Levels of Physical Disturbance Affect Soil Nematode Community Composition in a Previously Undisturbed Ecosystem

Soil is essential for the sustenance of life. Diverse soil organisms support several biological processes such as organic matter decomposition, mineralization, nutrient cycling, and controlling pests and diseases. Among multicellular soil organisms, nematodes are ubiquitous, functionally diverse, and abundant. Notably, agricultural practices have diverse impacts on plants, soils, and soil organisms. Tillage affects nematodes directly by altering pore size and disrupting the continuity of water films and indirectly by affecting the lower trophic groups such as bacteria and fungi. The primary goal of this study was to examine the effect of increasing levels of physical disturbance on nematode communities in an undisturbed forest ecosystem. The experiment included four treatments: control with no disturbance, surface litter removed with no litter and no vegetation, tilling the soil with a rototiller every 2 mon, and every 2 wk. Tillage significantly reduced the overall abundance and overall richness of nematode communities over time. Among nematode trophic groups, tillage significantly reduced the abundance and richness of bacterial feeders, predators, and omnivores over time. The abundance and richness of c-p 2, c-p 4, and c-p 5 class nematodes were significantly decreased by tillage. Unlike tillage, minimal disturbance such as removal of surface litter resulted in a significant decrease in the abundance of only three genera: Acrobeles, Aporcelaimellus, and Boleodorus. Nonmetric multidimensional scaling analysis revealed that nematodes of higher c-p classes such as Dorylaimida, Aporcelaimellus, Alaimus, Clarkus, and Tripyla were sensitive to physical disturbances. Bacterial feeders belonging to the c-p 2 class such as Tylocephalus, Acrobeles, Ceratoplectus, Plectus, and Pseudacrobeles were significantly reduced by tillage. Moreover, tillage significantly reduced the functional metabolic footprint of nematodes, which indicates decreased metabolic activity, reduced C inflow, and poorly structured soil food webs. Previous studies conducted in agricultural ecosystems determined that Clarkus, Filenchus, and Plectus were tolerant to tillage; however, they were found sensitive to tillage in our study. Overall, our study suggests that increasing levels of physical disturbance are detrimental to nematode community abundance and diversity that could affect soil ecosystem stability and sustainability.

Phytoparasitic nematodes of organic vegetables in the Argan Biosphere of Souss-Massa (Southern Morocco)

Agroecological productivity of the Arganeraie Biosphere Reserve of Morocco is limited by the wide spread and dynamics of plant parasitic nematodes (PPN). Ecological studies of nematode communities are required to develop effective biological management of these bioagressors as conventional control methods of PPN are inadequate and have persistent harmful effects. Fifty-nine organic vegetable soils in Souss-Massa were nematologically sampled, and assessment of taxonomic proliferation was made in relation to host species, geographical origin, and climatic and microclimatic factors. Twenty-four nematode genera were identified as obligate and facultative plant feeders. Taxonomic diversity increased from Chtouka to Taroudant and Tiznit provinces. Soil texture, organic matter, pH, nitrogen, zinc, magnesium, copper, altitude, and humidity and temperature were seen to effect driving roles in the abundance, distribution, and community structures of nematodes. The most prevalent taxa posing a high risk to organic agriculture of Souss Massa were needle nematodes (Longidorus spp.) and root-knot nematodes (Meloidogyne spp.). Edaphic and climatic variables effected nematode populations greatly. A combination of biological treatments and appropriate agroecological practices restricting important economic PPN growth and enhancing soil quality are required to achieve sustainable management in the area.

Bacterial endosymbionts protect beneficial soil fungus from nematode attack

Soil is a complex and competitive environment, forcing its inhabitants to develop strategies against competitors, predators, and pathogens. Identifying and understanding the molecular mechanisms has translational value for medicine, ecology, and agriculture. In this study, we show that a member of important soil-dwelling fungi (Mortierella) forms a tight alliance with toxin-producing bacteria (Mycoavidus) that live within the fungal hyphae and protect their host from nematode attack. This discovery is relevant since Mortierella species correlate with healthy soils and are used as plant growth–promoting fungi in agriculture. Unraveling an ecological role for fungal endosymbionts in Mortierella, our results contribute to the understanding of a mainspring in fungal–endobacterial symbioses and open the possibility for the development of new biocontrol agents.

Fungi of the genus Mortierella occur ubiquitously in soils where they play pivotal roles in carbon cycling, xenobiont degradation, and promoting plant growth. These important fungi are, however, threatened by micropredators such as fungivorous nematodes, and yet little is known about their protective tactics. We report that Mortierella verticillata NRRL 6337 harbors a bacterial endosymbiont that efficiently shields its host from nematode attacks with anthelmintic metabolites. Microscopic investigation and 16S ribosomal DNA analysis revealed that a previously overlooked bacterial symbiont belonging to the genus Mycoavidus dwells in M. verticillata hyphae. Metabolic profiling of the wild-type fungus and a symbiont-free strain obtained by antibiotic treatment as well as genome analyses revealed that highly cytotoxic macrolactones (CJ-12,950 and CJ-13,357, syn. necroxime C and D), initially thought to be metabolites of the soil-inhabiting fungus, are actually biosynthesized by the endosymbiont. According to comparative genomics, the symbiont belongs to a new species (Candidatus Mycoavidus necroximicus) with 12% of its 2.2 Mb genome dedicated to natural product biosynthesis, including the modular polyketide-nonribosomal peptide synthetase for necroxime assembly. Using Caenorhabditis elegans and the fungivorous nematode Aphelenchus avenae as test strains, we show that necroximes exert highly potent anthelmintic activities. Effective host protection was demonstrated in cocultures of nematodes with symbiotic and chemically complemented aposymbiotic fungal strains. Image analysis and mathematical quantification of nematode movement enabled evaluation of the potency. Our work describes a relevant role for endofungal bacteria in protecting fungi against mycophagous nematodes.

Organic fertilization influences nematode diversity and maturity index in coffee tree plantations using an agroforestry system

In conventional coffee farming, soil fauna can be negatively affected by the intensive management practices adopted and the use of an agroforestry system (AFS) is an alternative to reduce these impacts. In coffee AFS, soil nutrition is provided mainly using organic fertilizers. This soil management favors the microbiota and can alter the population dynamics of some organisms. Our objective was to evaluate the effect of organic fertilizers on the nematode community in coffee AFS and to determine their impact on soil ecology. Soil samples were collected from three coffee AFS and a nearby Atlantic rainforest fragment. Nematodes were extracted from the samples and identified to the genus. The identified populations were compared using several community and diversity indices to determine the environmental conditions of the systems under evaluation. No differences in total abundance among nematode communities were found in the four areas evaluated. Regarding trophic groups, the coffee AFS treated with either cow manure or poultry litter favored the trophic group of bacterivores. Plant-parasitic nematodes were more abundant in soils of both the naturally fertilized coffee AFS and the Atlantic rainforest fragment. The maturity and structural indexes indicated that the Atlantic rainforest fragment and the naturally fertilized coffee AFS had similar ecological functions. On the other hand, soils fertilized with cow manure were less diverse, had higher dominance in the community, and showed less ecological stability. The nematode communities found in the AFS were similar to those seen in the forest fragment indicating that is possible to produce coffee sustainably without negatively affecting soil quality.

Plant signals differentially affect rhizosphere nematode populations

This article comments on: Sikder MM, Vestergård M, Kyndt T, Fomsgaard IS, Kudjordjie EN, Nicolaisen M. 2021. Benzoxazinoids selectively affect maize root-associated nematode taxa. Journal of Experimental Botany 72,3835–3845.

The Use of Plant Growth-Promoting Bacteria to Prevent Nematode Damage to Plants

Simple Summary

It has been estimated that 100 g of bulk soil can host about 2000–4000 nematodes and this amount is increased 5-fold in the rhizosphere. A certain number of these nematodes are pathogenic for plants and cause yield and economic losses. Application of chemical nematicides is the most common method used to reduce nematode populations, but these chemicals can have a negative impact on both the environment and human health. Therefore, other more environmentally friendly methods of suppression of plant-parasitic nematodes have been proposed. Among them, the use of plant beneficial soil bacteria, behaving as biocontrol agents against nematodes, represent a potential alternative to chemicals.

Abstract

Plant-parasitic nematodes have been estimated to annually cause around US $173 billion in damage to plant crops worldwide. Moreover, with global climate change, it has been suggested that the damage to crops from nematodes is likely to increase in the future. Currently, a variety of potentially dangerous and toxic chemical agents are used to limit the damage to crops by plant-parasitic nematodes. As an alternative to chemicals and a more environmentally friendly means of decreasing nematode damage to plants, researchers have begun to examine the possible use of various soil bacteria, including plant growth-promoting bacteria (PGPB). Here, the current literature on some of the major mechanisms employed by these soil bacteria is examined. It is expected that within the next 5–10 years, as scientists continue to elaborate the mechanisms used by these bacteria, biocontrol soil bacteria will gradually replace the use of chemicals as nematicides.

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

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

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene

Nematodes are representative soil metazoans with diverged species that play crucial roles in nutrient recycling in the pedosphere. Qualitative and quantitative information on nematode communities is useful for assessing soil quality, and DNA barcode-mediated taxonomic analysis is a powerful tool to investigate taxonomic compositions and changes in nematode communities. Here, we investigated four regions (regions 1-4) of the 18S small subunit ribosomal RNA (SSU) gene as PCR targets of deep amplicon sequencing for the taxonomic profiling of individual soil nematodes. We determined the sequence variants (SVs) of 4 SSU regions for 96 nematodes (total 384 amplicons) isolated from copse soils and assigned their taxonomy using the QIIME2 software with dada2 or deblur algorithm and the SILVA database. Dada2 detected approximately 2-fold more nematode-derived SVs than deblur, and a larger number of SVs were obtained in regions 1 and 4 than those in other regions. These results and sufficient reference sequence coverage in region 4 indicated that DNA barcoding using a primer set for region 4 followed by dada2-based analysis would be most suitable for soil nematode taxonomic analysis. Eighteen SSU-derived operational taxonomic units (rOTUs) were obtained from 68 isolates, and their orders were determined based on the phylogenetic trees built by four regional sequences of rOTUs and 116 nematode reference species as well as the BLASTN search. The majority of the isolates were derived from three major orders Dorylaimida (6 rOTUs, 51.5% in 68 isolates), Rhabditida (4 rOTUs, 29.4%), and Triplonchida (7 rOTUs, 17.6%). The predicted feeding types of the isolates were fungivores (38.2% in total nematodes), plant feeders (32.4%), and 14.7% for both bacterivores and omnivores/predators. Additionally, we attempted to improve the branch structure of phylogenetic trees by using long nucleotide sequences artificially prepared by connecting regional sequences, but the effect was limited.