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Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology. [ABSTRACT FROM AUTHOR]

In terrestrial ecosystems decomposing cadavers act as resource patches affecting nutrient cycling and soil communities, but the effects on soil communities are not well known. In this study we investigated nematode community response to decomposing pig cadavers ( Sus scrofa ) over a one-year period. As nematodes play key roles in soil food webs and are known to respond to disturbances and nutrient enrichment, we hypothesised that they would respond to decomposing cadavers and that this response would change over time. We compared the temporal patterns of nematode density and community structure under pig cadavers, either placed directly on the ground or hung 1 m aboveground (for effects of cadaveric fluids only), with two controls, i.e., bare soil and bags filled with soil placed on the ground (fake pigs – for microclimatic effects only). In the control and fake pig treatments nematode densities, community patterns and maturity indices did not change significantly. In contrast, density increased significantly underneath the ground and hanging pigs two weeks after the beginning of the experiment, and nematode family richness, Simpson diversity and maturity index were significantly reduced in the cadaver treatments. Most nematode families responded negatively to cadavers with the notable exceptions of Rhabditidae, Neodiplogasteridae and Diplogasteroididae. The latter two were found exclusively underneath the decomposing cadavers and are promising bioindicators of vertebrate cadaver decomposition. Even though diversity, density and communities were recovering after one year, the impact of cadavers was still significant for the maturity index. These contrasting patterns illustrate how decomposing cadavers contribute to increasing local biodiversity and suggest that soil nematodes could be used as a tool to document the presence of a decomposing cadaver, or to estimate the time elapsed since death (post-mortem interval). Patterns should, however, be compared in different settings and seasons before such a tool can be validated. [ABSTRACT FROM AUTHOR]

Energy dynamics within ecological communities are important in delivering ecosystem services. However, it remains elusive how the energy fluxes within soil food webs respond to agricultural fertilization regimes. Here, we studied the effects of long-term organic amendments and mineral fertilizers on the energetic structure of soil nematodes from a food-web perspective. We replicated our experiment in a rice paddy and in an upland maize cropping system. Results showed that the abundance of most trophic groups was higher in organically amended soils compared with mineral fertilizer treatments in both systems. Organic amendments, but not mineral fertilizers, increased the energy flux of total nematodes and most trophic groups compared with the no-fertilizer treatment. Furthermore, organic amendments increased the relative allocation of energy flux to microbivores but decreased the relative allocation to herbivores, supporting a higher flow uniformity than mineral fertilizers. We further found that organic amendments favored a higher total energy flux by supporting a greater nematode diversity, while sustained a higher flow uniformity by altering nematode community composition. Taken together, the result provides the evidence that a complex and species-rich community could transfer more energy to support ecosystem services. A broader perspective on linkages of biodiversity and energy dynamics spanning multitrophic groups is crucial for sustainable management, particularly in the light of non-random species loss under future environmental change. [Display omitted] • Organic amendments increased total energy flux and flow uniformity. • High flow uniformity resulted from increasing relative energy flux of microbivores. • Energy fluxes and flow uniformity were positively linked with nematode diversity. • Effect of diversity decline on energy loss was stronger in paddy than upland fields. [ABSTRACT FROM AUTHOR]

Energy flux in food webs, i.e., energy consumption by different trophic groups and describing their energetic structure, has been proposed as a powerful tool to understand the relationships between biodiversity and multiple ecosystem functions (ecosystem multifunctionality). Here we examined how different fertilization regimes affected the energy flux across multitrophic levels of soil nematodes in the paddy rice and upland maize fields. We considered 13 ecosystem functions of four ecological processes related to plant productivity, nutrient cycling processes and drivers, and functional stability, which are central to energy and nutrient flow across trophic levels. To confirm whether multitrophic flux would underpin the relationships between biodiversity and multifunctionality, we compared energy flux with other approaches including taxonomic diversity, functional diversity and community composition. Results showed that organic fertilizer supported 33–340% greater multitrophic energy flux of soil nematode community and enhanced 41–264% of ecosystem multifunctionality in both fields compared with mineral fertilizer treatments. Organic fertilization enhanced ecosystem multifunctionality by favoring energy flux in multitrophic levels of soil nematodes, while fertilization-mediated changes in other facets of biodiversity were less related to multifunctionality. Our study provides empirical evidence that energy flux within food webs can be used to understand the impacts of environmental change drivers on ecosystem multifunctionality. • Organic fertilization increased ecosystem multifunctionality. • Energy flux of soil nematodes was positively related to multifunctionality. • Energy flux underpinned the link between biodiversity and multifunctionality. [ABSTRACT FROM AUTHOR]

Previous results from a long-term grassland trial, located in south-east Ireland indicated conserved (homeostatic) nutrient stoichiometry of the soil microbial biomass despite widely varying soil C:N:P ratios. To determine whether this was associated with a change in microbial community structure, rather than a change in microbial physiology, this study characterized the responses of below-ground microbial and nematode community structure to P fertilization. The trial site maintained a range of P fertilisation rates (0-30 kg P ha−1 yr−1) which had been applied since 1968 and soil samples were collected in spring 2009, autumn 2010 and spring 2011. The microbial biomass demonstrated homeostatic stoichiometry over all sampling occasions, particularly of the C:P ratio, despite a 50-fold difference in soil solution C:P ratio. However, microbial and nematode community structure also varied with P fertilisation, indicating that nutrient ratios are maintained even though there were changes in microbial community structure. P fertilization induced a shift from fungal to bacterial dominated decomposition pathways, as indicated by the proportion of bacterial-feeding to fungal-feeding nematodes and bacterial: fungal phospholipid fatty acids (PLFAs). The altered microbial community structure was considered to result from bottom-up control of nutrient quality and quantity by altered vegetation structure and fertilizer inputs, as well as top-down pressures from the nematode community. [ABSTRACT FROM AUTHOR]

Abstract: Plant-mediated effects of aboveground herbivory on the belowground ecosystem are well documented, but less attention has been paid to agro-ecosystems and in particular how crop cultivars with different traits (i.e. resistance to pests) shape such interactions. A fully factorial experiment was conducted using four rice cultivars with different insect-resistance, with and without the aboveground herbivore Nilaparvata lugens (brown planthopper), and to test two hypotheses (1) aboveground herbivory affects the soil microbial biomass and nematode community by altering plant performance and soil resource availability and (2) herbivory effects will depend on cultivar resistance traits. Our results suggested that cultivar resistance mediated both herbivory intensity and herbivore effects on plant performance. N. lugens decreased the availability of soil resources (soluble sugars, amino acids, organic acids, dissolved organic carbon and nitrogen), microbial biomass and percentages of bacterivores when feeding on a susceptible cultivar but increased them in a resistant cultivar. However, total nematode abundance and the percentage of plant-parasitic nematodes responded in the opposite way, increasing under a susceptible cultivar and decreasing under a resistant cultivar. The development of plant-parasites under resistant cultivars before aboveground herbivory might contribute to their resistance traits. Our findings provide evidence that N. lugens significantly reversed the pattern of soil resource availability, microbial biomass and nematode community structure (abundance and trophic composition) across cultivars with distinct resistance. In the presence of aboveground pests, the agronomic use of resistant rice cultivars could also control populations of plant-parasites and promote soil resource availability, further extended to higher trophic level of soil food web. [Copyright &y& Elsevier]

Abstract: Re-vegetation of eroded soil restores organic carbon concentrations and improves the physical stability of the soil, which may then extend the range of microhabitats and influence soil microbial activity and functional stability through its effects on soil bacterial community structure. The objectives of this study were (i) to evaluate the restorative effect of re-vegetation on soil physical stability, microbial activity and bacterial community structure; (ii) to examine the effects of soil physical microhabitats on bacterial community structure and diversity and on soil microbial functional stability. Soil samples were collected from an 18-year-old eroded bare soil restored with either Cinnamomum camphora (“Eroded Cc”) or Lespedeza bicolour (“Eroded Lb”). An uneroded soil planted with Pinus massoniana (“Uneroded Pm”) and an eroded bare soil served as references. The effect of microhabitats was assessed by physical destruction with a wet shaking treatment. Soil bacterial community structure and diversity were measured using a terminal restriction fragment length polymorphism (T-RFLP) approach, while soil microbiological stability (resistance and resilience) was determined by measuring short-term (28 days) decomposition rate of added barley (Hordeum vulgare) powder following copper and heat perturbations. The results demonstrated that re-vegetation treatment affected the recovery of physical and biological stability, microbial decomposition and the bacterial community structure. Although the restored soils overshot the Uneroded Pm sample in physical stability, they had lower microbial decomposition and less resilience to copper and heat perturbations than the Uneroded Pm samples. Soil physical destruction by shaking had the same effect on soil physical stability, but different effects on soil microbial functional stability. There were significant effects of vegetation treatment and perturbation type, and interactive effects among vegetation treatment, shaking and perturbation type on bacterial community structure. The destruction of aggregate structure increased resilience of the Eroded Lb sample and also altered its bacterial community structure. Both copper and heat perturbations resulted in significantly different community structure from the unperturbed controls, with a larger effect of copper than heat perturbation. Bacterial diversity (Shannon index) increased following the perturbations, with a more profound effect in the Uneroded Pm sample than in the restored soils. The interactive effects of vegetation treatment and shaking on microbial community and stability suggest that soil aggregation may contribute to the generation of bacterial community structure and mediation of biological stability via the protection afforded by soil organic carbon. Differential effects of re-vegetation treatment suggest that the long-term effects are mediated through changes in the quality and quantity of C inputs to soil. [Copyright &y& Elsevier]

One of the greatest challenges in soil ecology is to disentangle the plant-mediated bottom-up factors regulating soil biodiversity and community composition. The soil food web, fundamentally driving nearly all ecosystem functions, is controlled by the quantity and quality of root-mediated resources. Here, a trait-based approach was adopted to explore the divergence of soil nematode functional guilds and their connections to root traits belonging to distinct plant resource-use strategies. Root traits and rhizosphere nematode functional guilds were measured on four plant species in an ex-arable field. Results showed that plant species exhibiting acquisitive strategies promoted nematode abundance in contrast to species with conservative strategies. Further, the results also supported that plant resource-use strategies could regulate nematode life strategies in a bottom-up manner. However, lower proportions of opportunist nematodes in rhizosphere were found in acquisitive plants rather than conservative plants, mainly attributed to the stronger top-down regulation as a dominant control within the former than the later ones. Structure equation modeling revealed that root length density could primarily modulate nematode abundance and functional guilds mainly through changes in nitrogen availability of rhizosphere, as indicated by mineral N and enzymatic stoichiometry. Overall, our findings extend the conceptual framework based on a trait-centred view spanning plants to the soil food web, and this knowledge is critical to understand the mechanisms of ecosystem process. • Acquisitive plants promoted nematode abundance and K-strategist nematodes. • Conservative plants supported mainly r-strategist nematodes. • Root length density was the key root trait for regulating soil nematodes. [ABSTRACT FROM AUTHOR]