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Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere., (© FEMS 2020.)

Background: Stress-induced hormones are essential for plants to modulate their microbiota and dynamically adjust to the environment. Despite the emphasis of the role of the phytohormone ethylene in the plant physiological response to heterospecific neighbour detection, less is known about how this activated signal mediates focal plant rhizosphere microbiota to enhance plant fitness. Here, using 3 years of peanut (Arachis hypogaea L.), a legume, and cyanide-containing cassava (Manihot esculenta Crantz) intercropping and peanut monocropping field, pot and hydroponic experiments in addition to exogenous ethylene application and soil incubation experiments, we found that ethylene, a cyanide-derived signal, is associated with the chemical identification of neighbouring cassava and the microbial re-assemblage in the peanut rhizosphere., Results: Ethylene production in peanut roots can be triggered by cyanide production of neighbouring cassava plants. This gaseous signal alters the microbial composition and re-assembles the microbial co-occurrence network of peanut by shifting the abundance of an actinobacterial species, Catenulispora sp., which becomes a keystone in the intercropped peanut rhizosphere. The re-assembled rhizosphere microbiota provide more available nutrients to peanut roots and support seed production., Conclusions: Our findings suggest that root ethylene acts as a signal with a dual role. It plays a role in perceiving biochemical cues from interspecific neighbours, and also has a regulatory function in mediating the rhizosphere microbial assembly, thereby enhancing focal plant fitness by improving seed production. This discovery provides a promising direction to develop novel intercropping strategies for targeted manipulations of the rhizosphere microbiome through phytohormone signals. Video abstract.

Summary: Plants impact the development of their rhizosphere microbial communities. It is yet unclear to what extent the root cap and specific root zones contribute to microbial community assembly.To test the roles of root caps and root hairs in the establishment of microbiomes along maize roots (Zea mays), we compared the composition of prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) microbiomes of intact or decapped primary roots of maize inbred line B73 with its isogenic root hairless (rth3) mutant. In addition, we tracked gene expression along the root axis to identify molecular control points for an active microbiome assembly by roots.Absence of root caps had stronger effects on microbiome composition than the absence of root hairs and affected microbial community composition also at older root zones and at higher trophic levels (protists). Specific bacterial and cercozoan taxa correlated with root genes involved in immune response.Our results indicate a central role of root caps in microbiome assembly with ripple‐on effects affecting higher trophic levels and microbiome composition on older root zones. [ABSTRACT FROM AUTHOR]

Aims: Different drivers are known to shape rhizosphere microbiome assembly. How soil texture (Texture) and presence or lack of root hairs (Root Hair) of plants affect the rhizosphere microbiome assembly and soil potential extracellular enzyme activities (EEA) at defined rooting depth (Depth) is still a knowledge gap. We investigated effects of these drivers on microbial assembly in rhizosphere and on potential EEA in root-affected soil of maize. Methods: Samples were taken from three depths of root hair defective mutant rth3 and wild-type WT maize planted on loam and sand in soil columns after 22 days. Rhizosphere bacterial, archaeal, fungal and cercozoan communities were analysed by sequencing of 16S rRNA gene, ITS and 18S rRNA gene fragments. Soil potential EEA of ß-glucosidase, acid phosphatase and chitinase were estimated using fluorogenic substrates. Results: The bacterial, archaeal and cercozoan alpha- and beta-diversities were significantly and strongly altered by Texture, followed by Depth and Root Hair. Texture and Depth had a small impact on fungal assembly, and only fungal beta-diversity was significantly affected. Significant impacts by Depth and Root Hair on beta-diversity and relative abundances at taxonomic levels of bacteria, archaea, fungi and cercozoa were dependent on Texture. Likewise, the patterns of potential EEA followed the trends of microbial communities, and the potential EEA correlated with the relative abundances of several taxa. Conclusions: Texture was the strongest driver of rhizosphere microbiome and of soil potential EEA, followed by Depth and Root Hair, similarly to findings in maize root architecture and plant gene expression studies. [ABSTRACT FROM AUTHOR]

Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their "microbiome." Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology. [ABSTRACT FROM AUTHOR]

It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil – their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important. [ABSTRACT FROM AUTHOR]

Rhizosphere metabolite concentration gradients serve as cues for rhizosphere organisms, including plant pathogens (Bouwmeester et al., [5]; Baker et al., [2]). Keywords: soil properties; modeling; biosensor; network analysis; community assembly; process rate EN soil properties modeling biosensor network analysis community assembly process rate 1 3 3 11/22/21 20211118 NES 211118 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. Rhizosphere soil can be less porous than bulk soil due to increased aggregation and compression (Daly et al., [8]), but the immediate root-soil interface is a zone of high porosity (Helliwell et al., [10]). According to the simulation results, the modification of rhizosphere bulk density and mucilage concentration by plant roots appear as a means to reduce water stress and to reduce root water uptake under drought. [Extracted from the article]

Summary: In nature, beneficial and pathogenic fungi often simultaneously colonise plants. Despite substantial efforts to understand the composition of natural plant−microbe communities, the mechanisms driving such multipartite interactions remain largely unknown.Here we address how the interaction between the beneficial root endophyte Serendipita vermifera and the pathogen Bipolaris sorokiniana affects fungal behaviour and determines barley host responses using a gnotobiotic soil‐based split‐root system.Fungal confrontation in soil resulted in induction of B. sorokiniana genes involved in secondary metabolism and a significant repression of genes encoding putative effectors. In S. vermifera, genes encoding hydrolytic enzymes were strongly induced. This antagonistic response was not activated during the tripartite interaction in barley roots. Instead, we observed a specific induction of S. vermifera genes involved in detoxification and redox homeostasis. Pathogen infection but not endophyte colonisation resulted in substantial host transcriptional reprogramming and activation of defence. In the presence of S. vermifera, pathogen infection and disease symptoms were significantly reduced despite no marked alterations of the plant transcriptional response.The activation of stress response genes and concomitant repression of putative effector gene expression in B. sorokiniana during confrontation with the endophyte suggest a reduction of the pathogen's virulence potential before host plant infection. See also the Commentary on this article by Franken et al., 224: 547–549. [ABSTRACT FROM AUTHOR]

The response of the biocontrol bacterium Pseudomonas fluorescens CHA0 to a common predator, the free-living amoeba Acanthamoeba castellanii, is examined. The results have shown that predator-prey interactions are a determinant of toxin production by rhizosphere Pseudomonas fluorescens and might have an impact on its biocontrol potential.

Abstract: Cercomonads are among the most abundant and diverse groups of heterotrophic flagellates in terrestrial systems and show an affinity to plants. However, we still lack basic knowledge of plant‐associated protists. We isolated 75 Cercomonadida strains from the phyllosphere and rhizosphere of plants from three functional groups: grasses (Poa sp.), legumes (Trifolium sp.) and forbs (Plantago sp.), representing 28 OTUs from the genera Cercomonas, Neocercomonas and Paracercomonas. The community composition differed clearly between phyllosphere and rhizosphere, but was not influenced by plant species identity. From these isolates we describe three novel cercomonad species including Neocercomonas epiphylla that was consistently and exclusively isolated from the phyllosphere. For each new species we provide a detailed morphological description as well as an 18S rDNA gene sequence as a distinct marker of species identity. Our data contribute to a better resolution of the systematics of cercomonads and their association with plants, by describing three novel species and adding gene sequences of 10 new cercomonad genotypes and of nine previously described species. In view of the functional importance of cercozoan communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of their composition, function and predator–prey interactions are clearly required. [ABSTRACT FROM AUTHOR]

Cercozoa are a highly diverse protist phylum in soils and in the phyllosphere of plants. Many families are still poorly described and the vast majority of species are still unknown. Although testate amoebae are among the better-studied protists, only little quantitative information exists on the morphology, phylogeny and ecology of cercozoan Rhogostomidae. We cultured four different strains of Rhogostoma spp. isolated from Arabidopsis leaves, agricultural soil and rhizosphere soil of Ocimum basilicum and Nicotiana sp. We describe Rhogostoma epiphylla sp. nov. and R. cylindrica sp. nov. and present their morphology, studied their food spectra in food range experiments and obtained two SSU rDNA gene sequences resulting in an updated thecofilosean phylogeny. Short generation times, desiccation resistance and the ability to prey on a wide range of algae and yeasts from the phyllosphere were seen as crucial traits for the phyllosphere colonization by Rhogostoma . In contrast, the soil-dwelling R. cylindrica did not feed on eukaryotes in our experiment. [ABSTRACT FROM AUTHOR]

In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'. [ABSTRACT FROM AUTHOR]

Plants foster diverse assemblages of bacteria in the rhizosphere serving important functions which may result in enhanced plant growth. Microbial diversity is increasingly recognized to shape the functionality of microbial communities. This leads to the assumption that there is a positive relationship between rhizosphere diversity and plant growth. Here we investigate how bacterial diversity affects the mineralization of organic matter and plant nutrient acquisition., We hypothesized that altered bacterial diversity will affect nitrogen mineralization, uptake by plants and ultimately plant growth. We set up a controlled model system with Arabidopsis thaliana colonized by defined assemblages of fluorescent pseudomonads, a well-characterized plant-beneficial rhizosphere taxon. The growth substrate contained casein as sole nitrogen source, making the plant nitrogen uptake dependant on breakdown by bacterial enzymes., Bacterial diversity was associated with a higher enzyme activity which increased nitrogen mineralization and enhanced plant growth. The effect of bacterial diversity on plant growth increased with time, pointing to a positive feedback between bacteria and plants: bigger plants associated with species-rich bacterial communities supported more bacterial growth, which further enhanced the impact of bacteria on plant growth., We demonstrate that plant-soil feedbacks establish rapidly during one single growth season and that bacterial diversity modulates this interaction. Preserving soil microbial diversity therefore may improve positive plant-soil feedbacks and thereby plant growth. [ABSTRACT FROM AUTHOR]

Plant residues provide a major source of nitrogen (N) for plant growth. Litter N mineralization varies with litter carbon-to-nitrogen (C-to-N) ratio and presence of bacterial-feeding fauna. We assessed the effect of amoebae, major bacterial feeders in soil, on mineralization of litter of low (high quality) and high C-to-N ratio (low quality) and evaluated consequences for plant growth. We used stable isotopes to determine plant N uptake from litter and plant C partitioning. Stable isotope probing of phospholipid fatty acids was used to follow incorporation of plant C into microorganisms. Amoebae increased plant N uptake independent of litter quality and thereby the biomass of shoots and roots by 33% and 66%, respectively. Plant allocation of total 13C to roots in low (42%) exceeded that of high-quality litter treatments (26%). Amoebae increased plant allocation of 13C to roots by 37%. Microbial community structure and incorporation of 13C into PLFAs varied significantly with litter quality and in the low-quality litter treatment also with the presence of amoebae. Overall, the results suggest that in particular at low nutrient conditions, root-derived C fosters the mobilization of bacterial N by protozoa, thereby increasing plant growth when microorganisms and plants compete for nutrients. [ABSTRACT FROM AUTHOR]

Dead organic matter ( OM) is a major source of nitrogen ( N) for plants. The majority of plants support N uptake by symbiosis with arbuscular mycorrhizal ( AM) fungi. Mineralization of N is regulated by microfauna, in particular, protozoa grazing on bacteria. We hypothesized that AM fungi and protozoa interactively facilitate plant N nutrition from OM., In soil systems consisting of an OM patch and a root compartment, plant N uptake and consequences for plant carbon ( C) allocation were investigated using stable isotopes., Protozoa mobilized N by consuming bacteria, and the mobilized N was translocated via AM fungi to the host plant. The presence of protozoa in both the OM and root compartment stimulated photosynthesis and the translocation of C from the host plant via AM fungi into the OM patch. This stimulated microbial activity in the OM patch, plant N uptake from OM and doubled plant growth., The results indicate that protozoa increase plant growth by both mobilization of N from OM and by protozoa-root interactions, resulting in increased C allocation to roots and into the rhizosphere, thereby increasing plant nutrient exploitation. Hence, mycorrhizal plants need to interact with protozoa to fully exploit N resources from OM. [ABSTRACT FROM AUTHOR]

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 diffi cult. We discuss mistakes, pitfalls 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 confl ict 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. [ABSTRACT FROM AUTHOR]

We constructed an experimental model system to study the effects of grazing by a common soil amoeba, Acanthamoeba castellanii, on the composition of bacterial communities in the rhizosphere of Arabidopsis thaliana. Amoebae showed distinct grazing preferences for specific bacterial taxa, which were rapidly replaced by grazing tolerant taxa in a highly reproducible way. The relative proportion of active bacteria increased although bacterial abundance was strongly decreased by amoebae. Specific bacterial taxa had disappeared already two days after inoculation of amoebae. The decrease in numbers was most pronounced in Betaproteobacteria and Firmicutes. In contrast, Actinobacteria, Nitrospira, Verrucomicrobia and Planctomycetes increased. Although other groups, such as betaproteobacterial ammonia oxidizers and Gammaproteobacteria did not change in abundance, denaturing gradient gel electrophoresis with specific primers for pseudomonads (Gammaproteobacteria) revealed both specific changes in community composition as well as shifts in functional genes (gacA) involved in bacterial defence responses. The resulting positive feedback on plant growth in the amoeba treatment confirms that bacterial grazers play a dominant role in structuring bacteria–plant interactions. This is the first detailed study documenting how rapidly protozoan grazers induce shifts in rhizosphere bacterial community composition.The ISME Journal (2009) 3, 675–684; doi:10.1038/ismej.2009.11; published online 26 February 2009 [ABSTRACT FROM AUTHOR]

Decomposer animals stimulate plant growth by indirect effects such as increasing nutrient availability or by modifying microbial communities in the rhizosphere. In grasslands, the spatial distribution of organic matter (OM) rich in nutrients depends on agricultural practice and the bioturbation activities of large detritivores, such as earthworms. We hypothesized that plants of different functional groups with contrasting nutrient uptake and resource allocation strategies differentially benefit from sites in soil with OM accumulation and the presence of decomposer animals. In a greenhouse experiment we investigated effects of spatial distribution of 15N-labelled grass litter, earthworms and collembola on a simple grassland community consisting of Lolium perenne (grass) and Trifolium repens (legume). Litter aggregates (compared to homogeneous litter distribution) increased total shoot biomass, root biomass and 15N uptake by the plants. Earthworms and collembola did not affect total N uptake of T. repens; however, the presence of both increased 15N uptake by T. repens and L. perenne. Earthworms increased shoot biomass of T. repens 1.11-fold and that of L. perenne 2.50 fold. Biomass of L. perenne was at a maximum in the presence of earthworms, collembola and with litter concentrated in a single aggregate. Shoot biomass of T. repens increased in the presence of collembola, with L. perenne generally responding opposingly. The results indicate that the composition of the decomposer community and the distribution of OM in soil affect plant competition and therefore plant community composition. [Copyright &y& Elsevier]

Abstract: Fluorescent pseudomonads show great potential as biological control agents due to their capability to produce antifungal toxins such as 2,4-diacetylphloroglucinol (DAPG). DAPG is synthesized from the precursor monoacetyl-phloroglucinol (MAPG) and its production depends on the metabolic state of the bacteria as well as on their interaction with other organisms. In this study we show that Pseudomonas fluorescens responds to the bacterivorous amoeba Acanthamoeba castellanii by upregulating the production of phloroglucinol derivates in a density-dependent manner. Living amoebae caused moreover a distortion of the MAPG to DAPG balance in favor of the latter, suggesting that amoebae may interfere with the first steps of DAPG synthesis. Predator–prey interactions appear thus to be an important factor for the regulation of antibiotics production in biocontrol microorganisms. [Copyright &y& Elsevier]

Increased plant growth due to protozoa-bacteria interactions in the rhizosphere is well documented. Protozoan stimulation of plant growth has generally been attributed to nutritional effects based on release of nutrients during grazing on bacterial biomass, i.e. the microbial loop. Here I review our recent findings indicating that protozoan effects on plant growth are more complex than previously assumed. Protozoan grazing alters microbial diversity and function in the rhizosphere and also strongly affects root architecture and root foraging abilities of plants. Instead of regarding protozoa merely as consumers of bacterial prey, they should be also seen as mutualists, affecting plant growth by stimulation of plant growth-promoting rhizobacteria. This has important consequences for other plant mutualists like mycorrhizal fungi; plants presumably allocate their carbon resources to optimize simultaneous exploitation of both mutualistic relationships. [Copyright &y& Elsevier]

Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10–30 cm (topsoil) and 60–75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between topsoil and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies are now needed to describe and isolate these possibly subsoil specific phylotypes and better understand their ecology and function. [ABSTRACT FROM AUTHOR]

In the context of the soil food web, the transfer of plant-fixed energy and carbon to higher trophic levels has traditionally been attributed to two main energy channels: the fungal energy channel and the bacterial energy channel. Historically, protists were overlooked in the fungal energy channel, which was believed to be controlled by fungivorous microarthropods and nematodes. In this study, we investigated fungivorous protists in the rhizosphere of Arabidopsis thaliana. Our findings revealed a notable abundance and diversity of protists that have developed specialized strategies to overcome the protective cell wall of fungi. Among the identified species were two Vampyrellida (Rhizaria) species, namely Theratromyxa weberi and Platyreta germanica , as well as one Arcellinida (Amoebozoa) species, called Cryptodifflugia oviformis. While T. weberi typically consumed entire fungal cells, the other two species perforated fungal cell walls and extracted the cellular contents. We elucidate the feeding strategies and dietary ranges of the amoebae, highlighting the non-uniform nature of fungivory in protists, as different taxa have evolved distinct approaches to access fungi as a food source. Moreover, we provide publicly available cultures of these protists to facilitate further experimental investigations within the research community. • Arabidopsis thaliana accommodates three species of specialized fungivorous protists. • Fungivorous protists differ in their food spectra and mechanisms to access their prey. • Theratromyxa weberi engulfs fungal cells. • Cryptodifflugia oviformis and Platyreta germanica perforate fungal cell walls. • Publicly available cultures are provided for further experimental exploration. [ABSTRACT FROM AUTHOR]

Abstract Numerous 13CO 2 labeling studies have traced the flow of carbon from fresh plant exudates into rhizosphere bacterial communities. However, the succession of the uptake of carbon leaving the roots by distinct rhizosphere microbiota has rarely been resolved between microbial kingdoms. This can provide valuable insights on the niche partitioning of primary rhizodeposit consumption, as well as on community interactions in plant-derived carbon flows in soil. Here, we have traced the flow of fresh plant assimilates to rhizosphere microbiota of maize (Zea mays L.) by rRNA-stable isotope probing (SIP). Carbon flows involving bacteria, unicellular fungi, as well as protists were observed over 5 and 8 days. Surprisingly, labeling of Paraglomerales and several bacteria including Opitutus, Mucliaginibacter and Massilia spp. was especially apparent in soil surrounding the strict rhizosphere after 5 d. This highlights the central role of arbuscular mycorrhizal fungi (AMF) as a shunt for fresh plant assimilates to soil microbes not directly influenced by root exudation. Distinct trophic webs involving different flagellates, amoeba and ciliates were also observed in rhizosphere and surrounding soil, while labeling of filamentous saprotrophic Ascomycota or Basidiomycota was not apparent. This challenges the proposed "sapro-rhizosphere" concept and demonstrates the utility of rRNA-SIP to disentangle inter-kingdom microbial relationships in the rhizosphere. Graphical abstract Image 1 Highlights • rRNA-SIP was used to trace plant-derived carbon flows in the rhizosphere of maize. • 13C-labeling of mycorrhiza was stronger in surrounding soil than in the rhizosphere. • Labelling of bacteria incl. Opitutus spp. was also stronger in surrounding soil. • AMF are a shunt of plant assimilates to microbes outside the strict rhizosphere. [ABSTRACT FROM AUTHOR]

Soil texture, i.e. the fractions of different sized mineral particles, is critical to root growth and an important determinant of the occurrence and distribution of soil microbiota. More recently it was shown that individual plant species and even different cultivars harbor highly distinct rhizosphere associated microbiota, but it is still an open question how soil texture and its influence on root growth feeds back on root microbial assembly. We manipulated soil texture by stepwise additions of quartz sand to an agricultural loam. We grew maize (Zea mays L.) in these soils, measured changes in root traits and sampled bulk soil and rhizosphere to apply amplicon based high-throughput sequencing. We investigated changes in root morphology of maize and the concomitant shift in prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) diversity, community composition and co-occurrence in the maize rhizosphere along the soil texture gradient. A linear relationship between loam fraction and root morphology and a shift in microbial diversity along the soil texture gradient, as well as a stronger selection effect of the rhizosphere in soils with a high sand fraction (and high bulk density) were found. Co-occurrence network analysis revealed high modularity in fine textured soil, demonstrating that bulk density and texture are important factors affecting the recruitment of the core rhizosphere microbiome of maize. • Compensatory root growth in maize caused by soil texture and bulk density. • Linear shift of microbial community structure with changes in soil texture. • Amplified soil texture effects on community composition in the rhizosphere. • Less recruitment of bulk soil taxa into the rhizosphere microbiome with increasing bulk density. • Network analysis indicated the formation of small, isolated sub-communities in fine textured soil. [ABSTRACT FROM AUTHOR]

Elevated atmospheric CO 2 concentrations (eCO 2 ) often increase plant growth but simultaneously lead to the nitrogen (N) limitation in soil. The corresponding mitigation strategy such as supplementing N fertilizer and growing high-yielding cultivars at eCO 2 would further modify soil ecosystem structure and function. Little attention has, however, been directed toward assessing the responses of soil food web. We report results from a long-term free air CO 2 enrichment (FACE) experiment in a rice paddy agroecosystem that examined the responses of soil micro-food webs to eCO 2 and exogenous nitrogen fertilization (eN) in the rhizosphere of two rice cultivars with distinctly weak and strong responses to eCO 2 . Soil micro-food web parameters, including microfauna (protists and nematodes) and soil microbes (bacteria and fungi from phospholipid fatty acid (PLFA) analysis), as well as soil C and N variables, were determined at the heading and ripening stages of rice. Results showed that eCO 2 effects on soil micro-food webs depended strongly on N fertilization, rice cultivar and growth stage. eCO 2 stimulated the fungal energy channel at the ripening stage, as evidenced by increases in fungal biomass (32%), fungi:bacteria ratio (18%) and the abundance of fungivorous nematodes (64%), mainly due to an enhanced carbon input. The eN fueled the bacterial energy channel by increasing the abundance of flagellates and bacterivorous nematodes, likely through alleviating the N-limitation of plants and rhizosphere under eCO 2 . While eCO 2 decreased the abundance of herbivorous nematodes under the weak-responsive cultivar by 59% and 47% with eN at the heading and ripening stage, respectively, the numbers of herbivorous nematodes almost tripled (×2.9; heading) and doubled (×1.6; ripening) under the strong-responsive cultivar with eCO 2 at eN due to higher root quantity and quality. Structural equation model (SEM) showed that lower trophic-level organisms were affected by bottom-up forces of altered soil resources induced by eCO 2 and eN, and effects on higher trophic level organisms were driven by bottom-up cascades with 69% of the variation being explained. Taken together, strategies to adapt climate change by growing high-yielding crop cultivars under eCO 2 may face a trade-off by negative soil feedbacks through the accumulation of root-feeding crop pest species. [ABSTRACT FROM AUTHOR]

Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa, across four seasons, and four soil compartments - rhizosphere, root, soil and litter. The sampling was replicated in two forests in Norway and the Czech Republic, in order to test our results across biogeographic scales. Compartment had a major influence in shaping protistan communities, over and above spatial distance and seasonal variation. Protistan diversity was highest in the bulk soil while lowest in the roots, suggesting that the plants select for restricted assemblages of protists. Accordingly, only the root compartment harboured a subset of the bulk soil protistan diversity. In addition, protistan communities showed markedly different distributions according to their feeding modes, with opposite patterns for bacterivores versus omnivores and eukaryvores. The small bacterivorous flagellates (mostly Glissomonadida) were more abundant in roots, while the larger amoeboid eukaryvores (e.g. some of the Cryomonadida and vampyrellids) dominated in soil and in the rhizosphere, and the omnivores (e.g. Euglyphida and part of the Cercomonadida), also large and mostly amoeboid, were more abundant in litter. The current view of the soil microbiome is mostly focused on bacteria and fungi: this detailed study on the community distribution of protists according to their feeding modes reveals the essential role they play in each of the soil compartments, an essential precondition for a detailed understanding of the soil food web and nutrient cycling in forest. [Display omitted] • Compartments are the main drivers of the distribution of soil protists in forest • Protistan diversity is lowest in root, suggesting plant-driven selection • Protistan distribution is shaped by their feeding modes • Protists, especially predators, are essential players in the rhizosphere biome [ABSTRACT FROM AUTHOR]