Root cap is an important determinant of rhizosphere microbiome assembly

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

Pseudomonas fluorescens CHA0 maintains carbon delivery to Fusarium graminearum-infected roots and prevents reduction in biomass of barley shoots through systemic interactions

Soil bacteria such as pseudomonads may reduce pathogen pressure for plants, both by activating plant defence mechanisms and by inhibiting pathogens directly due to the production of antibiotics. These effects are hard to distinguish under field conditions, impairing estimations of their relative contributions to plant health. A split-root system was set up with barley to quantify systemic and local effects of pre-inoculation with Pseudomonas fluorescens on the subsequent infection process by the fungal pathogen Fusarium graminearum. One root half was inoculated with F. graminearum in combination with P. fluorescens strain CHA0 or its isogenic antibiotic-deficient mutant CHA19. Bacteria were inoculated either together with the fungal pathogen or in separate halves of the root system to separate local and systemic effects. The short-term plant response to fungal infection was followed by using the short-lived isotopic tracer 11CO2 to track the delivery of recent photoassimilates to each root half. In the absence of bacteria, fungal infection diverted carbon from the shoot to healthy roots, rather than to infected roots, although the overall partitioning from the shoot to the entire root system was not modified. Both local and systemic pre-inoculation with P. fluorescens CHA0 prevented the diversion of carbon as well as preventing a reduction in plant biomass in response to F. graminearum infection, whereas the non-antibiotic-producing mutant CHA19 lacked this ability. The results suggest that the activation of plant defences is a central feature of biocontrol bacteria which may even surpass the effects of direct pathogen inhibition

How to adequately represent biological processes in modeling multifunctionality of arable soils

Essential soil functions such as plant productivity, C storage, nutrient cycling and the storage and purification of water all depend on soil biological processes. Given this insight, it is remarkable that in modeling of these soil functions, the various biological actors usually do not play an explicit role. In this review and perspective paper we analyze the state of the art in modeling these soil functions and how biological processes could more adequately be accounted for. We do this for six different biologically driven processes clusters that are key for understanding soil functions, namely i) turnover of soil organic matter, ii) N cycling, iii) P dynamics, iv) biodegradation of contaminants v) plant disease control and vi) soil structure formation. A major conclusion is that the development of models to predict changes in soil functions at the scale of soil profiles (i.e. pedons) should be better rooted in the underlying biological processes that are known to a large extent. This is prerequisite to arrive at the predictive models that we urgently need under current conditions of Global Change

Soil texture is a stronger driver of the maize rhizosphere microbiome and extracellular enzyme activities than soil depth or the presence of root hairs

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

The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots

Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance

Litter chemistry influences earthworm effects on soil carbon loss and microbial carbon acquisition

Earthworms could affect soil C and N cycling process to balance their energy and nutrients requirements, and they could also regulate soil microbial community structure and microbial acquisition for C and N. However, the connection between faunal and microbial stoichiometry in the coupling soil C and N cycling remains poorly understood. In a controlled laboratory experiment, we amended soil with five litters differing in litter chemistry (clover, maize stover, wheat straw, Rurnex and bagasse fiber) including a no litter control and treated them without or with earthworms (Metaphire guillelmi). After 90 d incubation, we examined changes in earthworm tissue and microbial stoichiometry and different soil C and N fractions. Earthworm tissue C content was rather stable compared with the fluctuation in tissue N, implying that C is under stronger control and associated with higher demand than N. The presence of earthworm significantly enhanced CO2 emissions and decreased particulate organic carbon (POC) and soil organic carbon (SOC) contents in the low lignin litter species clover, maize stover and wheat straw. Meanwhile, earthworm presence increased N2O cumulative emissions but exerted negligible effects on particulate organic nitrogen (PON) and soil total nitrogen (TN) contents irrespective of litter species. Correspondingly, earthworm regulated microbial C and N acquisition as C to N-degrading enzyme activity ratio were nearly doubled in the low lignin litter species clover, maize stover and wheat straw, while it was decreased in the high lignin litter species Rumex and bagasse fiber. However, the structural equation modeling indicated C loss induced by earthworms was mainly attributed to their effects on soil fungi and bacteria abundance, while much less related to C-degrading enzyme activities. In conclusion, litter species controlled earthworm effects on soil C and N loss and associated microbial acquisition for C and N, highlighting the pivotal role of resource chemistry in the regulation of soil fauna impact on soil functioning and ecosystem services

Organic matter composition and the protist and nematode communities around anecic earthworm burrows

By living in permanent burrows and incorporating organic detritus from the soil surface, anecic earthworms contribute to soil heterogeneity, but their impact is still under-studied in natural field conditions. We investigated the effects of the anecic earthworm Lumbricus centralis on fresh carbon (C) incorporation, soil organic matter composition, protists, and nematodes of a Cambisol under grassland. We used plant material labelled with stable isotope tracers to detect fresh C input around earthworm-occupied burrows or around burrows from which the earthworm had been removed. After 50 days, we sampled soil (0–10 cm depth) in concentric layers around the burrows, distinguishing between drilosphere (0–8 mm) and bulk soil (50–75 mm). L. centralis effectively incorporated fresh C into the drilosphere, and this shifted soil organic matter amount and chemistry: total soil sugar content was increased compared to unoccupied drilosphere and bulk soil, and the contribution of plant-derived sugars to soil organic matter was enhanced. Earthworms also shifted the spatial distribution of soil C towards the drilosphere. The total abundance of protists and nematodes was only slightly higher in earthworm-occupied drilosphere, but strong positive effects were found for some protist clades (e.g. Stenamoeba spp.). Additional data for the co-occurring anecic earthworm species Aporrectodea longa showed that it incorporated fresh C less than L. centralis, suggesting that the two species may have different effects on soil C distribution and organic matter quality

Responses of rice paddy micro-food webs to elevated CO₂ are modulated by nitrogen fertilization and crop cultivars

Elevated atmospheric CO2 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 CO2 enrichment (FACE) experiment in a rice paddy agro-ecosystem 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 (x2.9; heading) and doubled (x1.6; 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. (C) 2017 Elsevier Ltd. All rights reserved

Disruption of Growth Hormone Receptor Prevents Calorie Restriction from Improving Insulin Action and Longevity

Most mutations that delay aging and prolong lifespan in the mouse are related to somatotropic and/or insulin signaling. Calorie restriction (CR) is the only intervention that reliably increases mouse longevity. There is considerable phenotypic overlap between long-lived mutant mice and normal mice on chronic CR. Therefore, we investigated the interactive effects of CR and targeted disruption or knock out of the growth hormone receptor (GHRKO) in mice on longevity and the insulin signaling cascade. Every other day feeding corresponds to a mild (i.e. 15%) CR which increased median lifespan in normal mice but not in GHRKO mice corroborating our previous findings on the effects of moderate (30%) CR on the longevity of these animals. To determine why insulin sensitivity improves in normal but not GHRKO mice in response to 30% CR, we conducted insulin stimulation experiments after one year of CR. In normal mice, CR increased the insulin stimulated activation of the insulin signaling cascade (IR/IRS/PI3K/AKT) in liver and muscle. Livers of GHRKO mice responded to insulin by increased activation of the early steps of insulin signaling, which was dissipated by altered PI3K subunit abundance which putatively inhibited AKT activation. In the muscle of GHRKO mice, there was elevated downstream activation of the insulin signaling cascade (IRS/PI3K/AKT) in the absence of elevated IR activation. Further, we found a major reduction of inhibitory Ser phosphorylation of IRS-1 seen exclusively in GHRKO muscle which may underpin their elevated insulin sensitivity. Chronic CR failed to further modify the alterations in insulin signaling in GHRKO mice as compared to normal mice, likely explaining or contributing to the absence of CR effects on insulin sensitivity and longevity in these long-lived mice

Carbon budgets of top- and subsoil food webs in an arable system

© 2018 This study assessed the carbon (C) budget and the C stocks in major compartments of the soil food web (bacteria, fungi, protists, nematodes, meso- and macrofauna) in an arable field with/without litter addition. The C stocks in the food web were more than three times higher in topsoil (0–10 cm) compared to subsoil (>40 cm). Microorganisms contained over 95% of food web C, with similar contributions of bacteria and fungi in topsoil. Litter addition did not alter C pools of soil biota after one growing season, except for the increase of fungi and fungal feeding nematodes in the topsoil. However, the C budget for functional groups changed with depth, particularly in the microfauna. This suggests food web resilience to litter amendment in terms of C pool sizes after one growing season. In contrast, the distinct depth dependent pattern indicates specific metacommunities, likely shaped by dominant abiotic and biotic habitat properties