Identification and functional roles of amoeboid protozoa in soil

Protozoa are the major consumers of bacterial production in soil, forming the base of the heterotrophic eukaryotic food web that channels the energy flow via bacteria to higher trophic levels in soil (i.e. the bacterial energy channel). Among them, amoebae and amoeboid flagellates are of major importance due to their small size, high abundance, fast turnover and ability to penetrate even the smallest pores with their flexible pseudopodia, making them key regulators of bacterial biomass and nutrient cycling. Despite these important functions for soils we have only a vague idea on the identity of the dominant taxa of amoeboid organisms in soils. Major reasons for the general ignorance in environmental studies of these key eukaryotes are methodological difficulties in cultivation and quantification in the opaque soil environment as well as a lack of taxonomic expertise. However, recent developments in molecular techniques now allow closing the methodological gap on this functionally important trophic link in the soil food web. Within my PhD project as part of the EU-project EcoFINDERS we aim at designing DNA-based barcodes for dominant taxa of amoeboid organisms, eventually to determine their diversity across soils throughout Europe and China using high-throughput sequencing. Cultivation of amoeboid organisms from several soils already indicated an enormous hidden diversity. Morphological and molecular information retrieved from these cultures indicates deep phylogenetic relationships among many amoeboid organisms and the existence of high numbers of new taxa and even genera. This information is crucial to develop effective genetic barcodes targeting broader protozoan taxa for pyrosequencing. First ecological studies investigating grazing of amoebae have confirmed strong impacts on total bacterial biomass and community composition. Further we found grazing differences even between closely related taxa suggesting niche specialisation, making it difficult to treat protozoa as a single functional black box in soil food webs

ZOOTAXA

www.mapress.com/zootaxa

Interactions of Mycorrhiza and Protists in the Rhizosphere Systemically Alter Microbial Community Composition, Plant Shoot-to-Root Ratio and Within-Root System Nitrogen Allocation

Arbuscular mycorrhizal fungi (AMF) are important symbionts for plant nutrient uptake, but their exact role in plant nitrogen (N) nutrition is unclear. Protists on the other hand play an acknowledged role in plant N acquisition, and there is increasing evidence for a close interaction with AMF. In a split root set up, we investigated the distinct roles of mycorrhiza (Rhizophagus irregularis), protists (Acanthamoeba castellanii), and their interaction on plant N uptake, within-root system allocation patterns, and shoot-to-root ratio of winter wheat. In addition, we applied a quantitative metabolomics approach to characterize associated changes in soil microbial communities by microbial phospholipid fatty acid (PLFA) analysis from rhizosphere soil. AMF markedly altered plant shoot-to-root allometry by reducing root biomass of wheat, and mycorrhiza partly took over root system functioning. Protists promoted shoot and root growth, and improved plant N uptake by the release of N from consumed bacterial biomass, a mechanism known as microbial loop. The shoot system however responded little to these alterations of the root system and of the rhizosphere community composition, indicating that the plants optimized shoot growth despite varying investment into roots. Mycorrhiza reduced root biomass and plant N, especially in the combined treatments with protists by changing within root system allocation of N and root biomass. These systemic effects on root allocation pattern suggest that mycorrhiza also gained control over N provided by protist grazers. Protists and mycorrhiza altered rhizosphere bacterial communities in contrasting but consistent ways as shown by quantitative shifts in microbial PLFA profiles. Remarkably, the changes in bacterial community composition were systemically conveyed within the root system to the split-root chamber where the symbionts were lacking. Accordingly the synergistic effects of protists and mycorrhiza indicated systemic effects on nutrient- and on root-allocation within root systems as an emergent property that could not be predicted from single treatments with mycorrhiza or protists alone. The tight plant and microbial feed backs uncovered in this study have far reaching implications for understanding the assembly of plant microbiomes, and testify central roles of both protists and mycorrhizas in the assembly process

Stimulation of Plant Growth through Interactions of Bacteria and Protozoa: Testing the Auxiliary Microbial Loop Hypothesis

By feeding on bacterial biomass protozoa play an acknowledged role in the liberation of nutrients in the plant rhizosphere. In addition there are suggestions that plants have mechanisms working through changes in root architecture and initiation of active release from soil organic matter, which are used to improve uptake and recirculation of nutrients in the ecosystem. All processes are carried out on a local scale in soil with roots, bacteria and protozoa interacting. The many actors and the small scale of interactions make experimentation difficult. We discuss mistakes, pit falls and misinterpretations and provide suggestions for improvement. Recent methodological progress has opened new exciting avenues for protozoan research. New techniques have already helped to reveal protozoan regulation of cooperation as well as conflict in bacterial communities. These mechanisms in turn affect bacterial functioning and target molecular control points in rhizosphere food webs in relation to plants. Integrating nutritional and regulatory aspects into new concepts of protozoan functioning in soil is a challenging frontier in protozoology

Ecological importance of soil bacterivores for ecosystem functions

BackgroundBacterivores, mostly represented by protists and nematodes, are a key component of soil biodiversity involved in soil fertility and plant productivity. In the current context of global change and soil biodiversity erosion, it becomes urgent to suitably recognize and quantify their ecological importance in ecosystem functioning.ScopeUsing meta-analysis tools, we aimed at providing a quantitative synthesis of the ecological importance of soil bacterivores on ecosystem functions. We also intended to produce an overview of the ecological factors that are expected to drive the magnitude of bacterivore effects on ecosystem functions.ConclusionsBacterivores in soil contributed significantly to numerous key ecosystem functions. We propose a new theoretical framework based on ecological stoichiometry stressing the role of C:N:P ratios in soil, microbial and plant biomass as important parameters driving bacterivore-effects on soil N and P availability for plants, immobilization of N and P in the bacterial biomass, and plant responses in nutrition and growth

Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field

Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus‐level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere), we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere‐associated clade. We extended our approach to show that closely related Cercozoa encounter divergent arbuscular mycorrhizal (AM) fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field scale is driven by niche‐based processes shaped by evolutionary legacy of adaptation to conditions primarily related to the soil compartment, followed by the soil layer, giving a deeper understanding on the selection pressures that shaped their evolution

Editorial: Rhizosphere Spatiotemporal Organisation

Formation of the rhizosphere, interface between living plant roots and soil, leads to changes in soil properties, nutrient and water distribution and biogeochemical cycling, and to a selection of unique populations of microorganisms and invertebrates. Dynamic feedback processes between the plant, the soil and the biota govern rhizosphere formation. The Frontiers Research Topic on “Rhizosphere Spatiotemporal Organization” presents contributions which aim to advance our understanding of rhizosphere processes. All of the six articles took the challenge to elaborate on the dynamic interactions and feedback processes in both spatial and temporal contexts

From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies

Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible

Computational and experimental studies of diffusion in monoclinic HfO2

Research on hafnia and zirconia has received a boost in the last two decades, mainly because of their electrical properties. As materials with high dielectric permittivity and a wide band-gap, they can replace SiO2 in Si-based semiconductor devices as the gate dielectric, and they can be employed as the insulator in metal—insulator—metal structures, showing memristive behavior.[1,2] Anion, and possibly cation, transport is of fundamental importance for the annealing of such devices and the proposed mechanism of resistive switching (filament switching in the case of HfO2).[2,3] In this study, we investigated both cation and anion diffusion in HfO2 using diffusion experiments, with subsequent determination of the diffusion profiles by Secondary Ion Mass Spectrometry (SIMS). For the diffusion of oxygen in dense ceramics of monoclinic HfO2,, (18O/16O) isotope exchange anneals were performed in the temperature range 573 ≤ T / K ≤ 973 at an oxygen partial pressure of pO2 = 200 mbar.[4] All measured isotope profiles exhibited two features: the first feature, closer to the surface, was attributed to slow oxygen diffusion in an impurity silicate phase; the second feature, deeper in the sample, was attributed to oxygen diffusion in a homogeneous bulk phase. The activation enthalpy of oxygen tracer diffusion in bulk HfO2 was found to be ΔHD* ≈ 0.5 eV. In contrast to oxygen diffusion, diffusion of cations in HfO2 and other oxide-ion conductors is experimentally much more challenging. It is slow, requiring, therefore, high temperatures and long diffusion times. In the case of HfO2, there is also the problem of Si impurities (see above), which are hard to get rid of in ceramic samples. To alleviate these problems somewhat, we directly investigated the diffusion of Zr in thin films of nanocrystalline, monoclinic HfO2, prepared by Atomic Layer Deposition (ALD) and coupled with a sputtered top layer of ZrO2 as a diffusion source. Diffusion experiments were performed in the temperature range 1173 ≤ T / K ≤ 1323 in air. All measured diffusion profiles exhibited bulk diffusion and fast grain-boundary diffusion. Using numerical simulations, we were able to describe the profiles and extract diffusion coefficients for Zr diffusion in bulk HfO2 and along its grain boundaries. The activation enthalpies of diffusion in both cases were, surprisingly, the same at ΔHDb/Dgb ≈ 2.1 eV. They are also much lower than activation energies predicted by static atomistic simulations.[5] In order to aid the interpretation of the experimental data, we conducted atomistic simulations of cation diffusion in HfO2. Specifically we performed Molecular Dynamics (MD) simulations using the empirical pair potentials derived by Catlow and Lewis.[6,7] These potentials are suitable for describing defect behaviour in HfO2.[8,9] The activation enthalpy of Hf diffusion in bulk HfO2 we obtained from the MD simulations agrees exceedingly well with the experimental results: ΔHD* ≈ 2 eV. The reasons for this behaviour are discussed. [1]: V. A. Gritsenko et al., Phys. Rep 613, 1 (2016). [2]: R. Waser et al., Adv. Mater. 21, 2632 (2009). [3]: S. Uhlenbruck et al., Solid State Ionics 180, 418 (2009). [4]: M. P. Mueller, R. A. De Souza, Appl. Phys. Lett. 112, 051908 (2018). [5]: S. Beschnitt et al., J. Phys. Chem. C 119, 27307 (2015). [6]: C. R. A. Catlow, Proc. R. Soc. Lond. A. 353(1675), 533 (1977). [7]: G. Lewis, C. R. A. Catlow, J. Phys. C: Solid State Phys. 18(6), 1149 (1985). [8]: M. Schie et al., J. Chem. Phys. 146, 094508 (2017). [9]: M. Schie et al., Phys. Rev. Mat. 2, 035002 (2018

Larval development and breeding ecology of Ziegler's crocodile newt, Tylototriton ziegleri Nishikawa, Matsui and Nguyen, 2013 (Caudata: Salamandridae), compared to other Tylototriton representatives

We describe for the first time the larval development and stages of the recently described Ziegler's Crocodile Newt (Tylototriton ziegleri), an endemic species to northern Vietnam. Diagnostic morphological characters are provided for Grosse (1997, 2013) stages 27-32, 35-36, and 44-45, as well as comparisons with larval stages of other Tylototriton representatives. In addition, natural history data and an ecological assessment of the breeding niche are presented for T. ziegleri as well as for T. vietnamensis, from whom the former species was only recently taxonomically separated. We provide data extending the known breeding season of these two cryptic species in the North of Vietnam, which in fact lasts from April until July. On average, the clutches of T. ziegleri consisted of 67 +/- 32 eggs, were found on rock and soil substrates with a distance of 50 +/- 28 cm from water, whereas the clutches of T. vietnamensis were significantly smaller (43 +/- 19 eggs), found only on soil and were further distant from water (80 +/- 41 cm). The known maximum altitudinal distribution of T. vietnamensis is herein increased to 980 m above sea level. Based on the examples of T. ziegleri and T. vietnamensis, this study highlights how important it is to uncover cryptic species, define their exact distribution range, and investigate potential differences in ecological adaptations in order to assess the conservation status, develop proper conservation planning and provide suitable conditions for potential ex situ breeding programs