Ecological and taxonomic diversity of nematode communities in soils of the Zarafshan Valley (Uzbekistan) and its edaphic determinants

Environmental variables such as soil moisture and phosphorus (P) might influence above- and below-ground biodiversity. In this study, we investigated the rarely reported individual and interactive multifactor effects of soil moisture and phosphorus addition with the type of above-ground tree species (biological interactions) on the soil nematode community structure. We established a completely randomized experimental design with two plant types (N2-fixer and non-nitrogen fixer) and different combinations of water treatments and P additions (i.e., water with P addition, water only, drought with P addition, and drought only) in a greenhouse and investigated their effects on the soil chemical properties and nematode community. Soil samples were collected at the end of the experiment and were analyzed for soil moisture content (SM), available phosphorus (aP), nitrate nitrogen (NO3−–N), ammonium nitrogen (NH4+–N), dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and nematode community. The following trophic groups were assigned to the nematodes: bacterivores (Ba), fungivores (Fu), omnivores–predators (Op), and plant parasites (PP). The channel index (CI), enrichment index (EI), maturity index (MI), genus richness (GR), and Simpson dominance (Ig) were adopted to indicate the indices of the nematode food web. Phosphorus addition and its interaction with water treatments had no statistically significant effects on the soil nematode community, but there were significant decreasing (p < 0.05) effects of P addition on the total density of nematodes of the N2-fixing tree under optimum water treatment. There were no significant interactive effects of P addition and water treatments on all the trophic groups, but plant type, water treatments, and their interactions significantly affected the density of most nematode trophic groups. The total nematode abundances of bacterivores, plant parasitic, omnivores, and enrichment index were significantly higher in the N2-fixers than in the non-nitrogen-fixing tree. Soil nematode abundance and community composition were more affected by the plant type than by the P addition and its interaction with water treatments. Drought exerted adverse effects on the total density of soil nematodes, the dominant genera, and the trophic groups. This study demonstrated that the rate of drought impact hinges more on the type of tree and that N2-fixing tree could still maintain the soil food web structure irrespective of the environmental changes.

The nematode community is an important component of soil biodiversity, which has a wide range of ecological functions, from nutrient cycling to plant parasitism. Although much effort has been made to describe the plant-parasitic nematode communities associated to soybean crop, little is known about the interactions between nematodes and soil microbiome. Here, two experiments under controlled conditions and analyses of 178 soil samples collected from the main soybean producing areas in Brazil, in four different biomes (Amazon Rainforest, Atlantic Rainforest, Cerrado, and Pampa), were used to assess the relationships between soil bacterial communities and (plant-parasitic and free-living) nematode communities in soybean crop. Soil bacterial and total nematode communities were analysed by sequencing of the 16S rRNA and 18S rRNA genes, respectively, while plant-parasitic nematode communities were analysed by light microscopy. Furthermore, we investigated the influence of soil physicochemical properties on the plant-parasitic nematode community and microbial activity by analysing 216 soil samples collected from no-till soybean crops. Our experimental results demonstrated the suppressive effect of soil bacterial diversity against Meloidogyne javanica in soybean plants and highlighted some groups of bacteria potentially antagonistic to this plant-parasitic nematode, such as Pseudomonas spp. and Microbacterium spp. Our sampling results showed significant negative correlations between population density of Pratylenchus sp. and relative abundance of several bacterial genera that naturally occur in soybean cultivated soils, such as Streptomyces and Paenibacillus, which are known antagonists of plant-parasitic nematodes. Our results also showed that the total nematode community in soils cultivated with soybean in Brazil is predominantly composed of the orders Rhabditida, Tylenchida, Dorylaimida, Triplonchida and Enoplida, while the plant-parasitic nematode community is predominantly composed of the genera Meloidogyne, Pratylenchus, Heterodera, Rotylenchulus, Helicotylenchus, Scutellonema, and Xiphinema. We also observed a positive correlation between the total nematode richness (predominantly composed by free-living nematodes) and soybean yields, which highlights the positive importance of the free-living nematode community in maintaining and increasing grain productivity. In addition, our results demonstrated that the clay content and the soil pH are the main soil physicochemical properties modulating the plant-parasitic nematodes community in soybean cultivated soils under the no-till system and the soil organic matter content and the pH are the main properties modulating the microbial activity in those soils. Our study is the first to provide insights into the interactions between soil bacterial diversity and nematode communities in soybean crop in Brazil, which may be useful for the design of new strategies to manage these organisms and for the development of new biological products based on bacteria potentially antagonistic to plant-parasitic nematodes.

The wide-scale adoption of transgenic crops has aroused public concern towards potential impacts to the ecological services of soil fauna, such as soil nematodes. However, few studies has examined whether the cultivation of transgenic rice would pose greater threats to soil nematode community and associated ecological functions than insecticides application. Moreover, what are determinants of soil nematode community in paddy fields remains unclear. During a 3-year field study, rhizosphere soil samples of transgenic-Bt rice, its counterpart non-Bt parental rice and not-Bt rice with insecticides application were taken at four times in the rice developmental cycle using a random block design with three replications for each treatment. We hypothesized that the effects of pest management practice on soil nematode abundance and metabolic footprint change with trophic group and sampling time. We also predicted there were significant differences in structure and composition of soil nematode community across the three treatments examined and sampling times. In agreement with our expectation, the effects of pest management practice on nematode abundance and metabolic footprints depend on trophic group and sampling time. However, pest management practice exerted no apparent effect on nematode diversity and community composition. Soil nutrient availability and C:N molar ratio are the primary regulating factor of soil nematode community in rice paddy fields. In conclusion, our findings implied that changes in abundance, diversity, metabolic footprints associated with the crop growth stage overweighed the application of Bt rice and insecticides. The cultivation of Bt rice Huahui-1 exerted no measurable adverse effect on soil nematode community in rhizosphere soil over 3 years of rice cropping.

The combined effects of warming and increased nitrogen (N) deposition in various ecosystems have become global issues. We used high‐throughput sequencing in an 8‐year field experiment to evaluate the impacts of the interactions between warming and nitrogen addition on soil nematode communities in a desert steppe. The soil nematode community presented with a certain degree of tolerance to warming. Warming mainly altered soil nematode diversity and community stability in deep soils whereas nitrogen addition primarily affected the nematode community in surface soils. Moreover, warming interacted with nitrogen addition exacerbated its negative effects on nematode richness and diversity. A Mantel analysis showed that soil pH was significantly negatively correlated with soil NH4+ and NO3− content. All three soil physicochemical (pH, NH4+ and NO3−) parameters were significantly correlated with desert steppe soil nematode community structure. Based on network and relative abundance analyses, we determined that Paratylenchus, Cervidellus, and Acrobeloides were the major hub soil nematode genera responding to soil warming and nitrogen addition in a desert steppe. The present study comprehensively analyzed the responses of desert steppe soil nematode communities to warming and nitrogen addition and provided an exemplar for studying the impact of environmental factors on soil nematodes communities worldwide.

Land use and temperature shape the beta diversity of soil nematodes across the Mollisol zone in northeast China

Plant species effects on soil nematode communities in experimental grasslands

Global warming and drying are important environmental issues. Our study aimed to investigate how warming and precipitation changes affect soil nematode communities in an Inner Mongolian desert steppe for 10 years. Soil nematodes were extracted by the Baermann funnel method. Changes in the nematode communities under artificial warming and precipitation conditions were assayed by analyzing their abundance and ecological indices. Soil nematode abundance decreased significantly by 37.47% under artificial warming; however, there was no significant effect of warming on the nematode community diversity. As for precipitation experiment, the decreased precipitation eliminated some of non-dominant nematode genera, such as Pratylenchus, Helicotylenchus, and Aphelenchus. It caused not only a significant decrease (37.65%) in soil nematode abundance but also a more structured food web and shorter food chain. However, nematode faunal analysis indicated that the soil nematode community was more resistant to drought. Both soil nematode abundance and community diversity increased significantly as increase of precipitation. In particular, the abundance of plant parasitic nematodes increased by 46.69%, which may due to the increase in total nitrogen content in soil. Nematode faunal analysis showed that increased precipitation improved soil environment for the nematodes, and increased food web connectivity and food chain length. However, bacterivorous nematode abundance decreased by 74.39%, and the decomposition pathway of the nematode community had switched from the bacterial channel to the fungal channel. In the Inner Mongolian steppe, both climate drying and warming had negative impacts on soil nematode abundance; however, only drying affected nematode community diversity and food web structure and slowly changed nematode ecological functions. Increased precipitation may aid soil nematode community recovery.

The basic taxonomy of nematodes and resources for nematode identification in Brazil are briefly discussed. Their communities were assessed based on: (i) abundance (population density and relative abundance); (ii) diversity (generic richness, Shannon-Weaver's and Simpson's diversity indices and evenness of both indices, trophic diversity and dominance); (iii) trophic habits (plant parasites, bacterial and fungal feeders, omnivores and predators); (iv) soil disturbance; (v) soil decomposition pathway (ratios of fungivores/bacterivores) and of (fungivores+bacteriovores)/plant parasites; (vi) index of similarity; and (vii) correspondence analysis. Nematode community structure is discussed in two areas, the Amazonian tropical and humid region with sampling sites in two western states, Rondônia and Acre, and the tropical savannah (cerrado) region in the 3 central states of Goiás, Minas Gerais and Districto Federal. In the Amazon, community structure for periodically flooded and non-flooded ecosystems (in four sites near Manaus), and for five land use types in the western states (forest, annual crops, pasture, fallow and agroforestry) are considered. In the savannah region, nematode communities are discussed with reference to native and cultured systems, managed soybean plantations, temporal and spatial samplings and edaphic factors. It was shown that nematode diversity is closely related to vegetation diversity (both in natural and in agricultural systems), with, somewhat counterintuitively, plant parasites the most important functional group in native vegetation versus bacterial feeders in agricultural systems. Nematode abundance is generally greater in agricultural systems.

Higher taxa vs. functional guilds vs. trophic groups as indicators of soil nematode diversity and community structure

Soybean cyst nematode (SCN), Heterodera glycines, remains a major yield-limiting pathogen of soybean. Natural suppression of SCN exists and becomes increasingly attractive; however, ecological mechanisms leading to the suppressive state are rarely studied. A glasshouse experiment was performed to determine the effects of soil disturbance and biocides on nematode community and extracellular enzyme activities in the SCN-suppressive soil collected in 2007 and 2008. Soil disturbance was simulated by passing soil through a sieve (aperture 5 mm) and compared with no-disturbance (non-sieve) treatment. Composition of microbial communities was manipulated by applying captan (fungicide), streptomycin (bactericide), captan plus streptomycin, or no biocide. SCN egg population density, proportion of second-stage juveniles (J2) parasitised by fungi, nematode communities in the soil, and plant weight in each pot were determined 70 days after planting soybean. In addition, the activities of six selected hydrolytic and oxidative extracellular enzymes representing cellulase, chitinase, serine protease, collagenase and peroxidase were measured. Soil disturbance resulted in an increase in SCN egg population density and reduction in the proportion of J2 parasitised by fungi. Biocide treatments increased SCN egg population density and the proportion of J2 parasitised by fungi at the end of experiment. Values of nematode community diversity index decreased and dominance and maturity indices increased in the disturbed soil compared with the no-disturbance treatment. Biocide treatments reduced maturity index values exclusively. With soil disturbance, the activity of extracellular enzyme L-proline aminopeptidase activity declined to less than half of that under no-disturbance in 2007. This experiment showed that both bacteria and fungi were potentially involved in the soil suppressiveness to SCN: soil disturbance and biocide application may reduce natural soil suppressiveness that was potentially associated with soil nematode community diversity and microbial enzyme activities.

Effect of compost and chemical fertilizer on soil nematode community in a Chinese maize field

Effects of long-term turfgrass management practices on soil nematode community and nutrient pools

Effects of wild boar grubbing on the soil nematode community subject to seasonal variation in a broad-leaved Korean pine forest in Northeast China

Changes in diversity patterns and assembly processes of soil nematode communities during forest secondary succession on the Loess Plateau

Influences of organic and synthetic soil fertility amendments on nematode trophic groups and community dynamics under tomatoes