Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

Two Pythium-infested soils were used to compare the wheat root and rhizosphere soil microbial communities from plants grown in the field or in greenhouse trials and their stability in the presence of biocontrol agents. Bacteria showed the highest diversity at early stages of wheat growth in both field and greenhouse trials, while fungal diversity increased later on, at 12 weeks of the crop cycle. The microbial communities were stable in roots and rhizosphere samples across both soil types used in this study. Such stability was also observed irrespective of the cultivation system (field or greenhouse) or addition of biocontrol coatings to wheat seeds to control Pythium disease (in this study soil infected with Pythium sp. clade F was tested). In greenhouse plant roots, Archaeorhizomyces, Debaryomyces, Delftia, and unclassified Pseudeurotiaceae were significantly reduced when compared to plant roots obtained from the field trials. Some operational taxonomic units (OTUs) represented genetic determinants clearly transmitted vertically by seed endophytes (specific OTUs were found in plant roots) and the plant microbiota was enriched over time by OTUs from the rhizosphere soil. This study provided key information regarding the microbial communities associated with wheat roots and rhizosphere soils at different stages of plant growth and the role that Paenibacillus and Streptomyces strains play as biocontrol agents in supporting plant growth in infested soils.     

供磷水平和根际效应协同影响含碱性磷酸酶基因细菌群落的网络复杂性和稳定性北大核心

【目的】通过研究长期不同供磷水平下根际、土体土壤中编码碱性磷酸酶基因(alkaline phosphatase gene,phoD)细菌群落特征、网络复杂性、群落的稳定性及其与磷酸酶活性之间的关系,揭示供磷水平和根际效应在调控土壤有机磷矿化中的微生物学机制。【方法】选取华北平原长期施磷的小麦-玉米轮作体系石灰性土壤为基质土壤,开展根箱试验。选取的试验处理包括3个供磷水平,分别是0、50.0、200.0 kg P/hm^(2)(分别表示为P0、P50、P200)。玉米种子播种30 d后,采集玉米的根际土和土体土。采用高通量测序技术分析根际和土体土壤中编码碱性磷酸酶基因(phoD)细菌群落,探究施肥及根际效应对含phoD基因细菌的群落特征、网络特征的影响及其与磷酸酶活性的关系。【结果】随着施磷量的增加,速效磷(available P,AP)和碱性磷酸酶(alkaline phosphatase,ALP)活性在根际、土体土壤中均显著提高,且两者呈显著正相关。phoD基因丰度在P0、P200处理的根际土壤中显著高于土体土壤。含phoD基因细菌群落的α多样性在P50处理下的根际土壤显著高于土体土壤。冗余分析(redundancy analysis,RDA)表明,土壤中AP、有机磷(organic P,Po)和全磷(total P,Pt)是影响微生物群落的主要因素。与不施磷处理(P0)相比,施磷处理(P50、P200)下根际土壤中网络节点数和连接数降低,而土体土壤中网络节点数和连接数增加;同时,施磷处理含phoD基因细菌群落的鲁棒性(robustness)在根际土壤中显著提高,而在土体土壤中显著降低。Mantel检验表明,含phoD基因微生物群落中的优势物种在根际土壤与AP、酸性磷酸酶(acid phosphatase,ACP)、内聚力(cohesion)和网络的鲁棒性显著相关,在土体土壤中无显著性。【结论】供磷水平及根际效应协同影响phoD基因丰度、含phoD基因细菌群落的α多样性、群落结构、优势物种、网络的复杂性及群落的稳定性,进而影响磷酸酶活性,调控了土壤中有机磷的矿化。     

Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long‐term biodiversity experiment

Soil microbes are known to be key drivers of several essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition in the rhizosphere is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this time frame plants with a monoculture or mixture history changed in the bacterial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same field monocultures or mixtures (plant history in monoculture vs. mixture) in pots inoculated with microbes extracted from the field monoculture and mixture soils attached to the roots of the host plants (soil legacy). After 5 months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Bacterial community structure in the plant rhizosphere was primarily determined by soil legacy and by plant species identity, but not by plant history. In seven of the eight plant species the number of individual operational taxonomic units with increased abundance was larger when inoculated with microbes from mixture soil. We conclude that plant species richness can affect below‐ground community composition and diversity, feeding back to the assemblage of rhizosphere bacterial communities in newly establishing plants via the legacy in soil.     

Effects of using different host plants and long-term fertilization systems on population sizes of infective arbuscular mycorrhizal fungi

The effect of cultivation of mycorrhizal and non-mycorrhizal plants and mineral fertilization on the arbuscular mycorrhizal fungal (AMF) community structure of maize (Zea mays L.) plants was studied. Soil samples were collected from two field experiments treated for 5 years with three fertilization systems (Control – no fertilization; Mineral – NPK fertilization; and Organic – Farmyard manure fertilization). Soil samples containing soil and root fragments of rapeseed (Brassica napus L., non-mycorrhizal plant) and wheat (Triticum aestivum L., mycorrhizal plant) collected from the field plots were used as native microbial inoculum sources to maize plants. Maize plants were sown in pots containing these inoculum sources for four months under glasshouse conditions. Colonization of wheat roots by AMF, AMF community structure, AMF diversity (Shannon’s index), AMF dominance (Simpson’s index) and growth of maize were investigated. Sixteen AMF species were identified from rhizosphere soil samples as different species of genera Acaulospora, Claroideoglomus, Dentiscutata, Funneliformis, Gigaspora, Quatunica, Racocetra, and Rhizoglomus. Maize plants grown in manure-fertilized soils had a distinct AMF community structure from plants either fertilized with mineral NPK-fertilizer or non-fertilized. The results also showed that inoculum from non-mycorrhizal plants combined with mineral fertilization decreased AMF diversity (Shannon’s index), AMF dominance (Simpson’s index) and growth of maize. Our findings suggest that non-mycorrhizal plants, such as B. napus, can negatively affect the presence and the effects of soil inoculation on maize growth. Also, our results highlight the importance of considering the long-term effect of rapeseed cultivation system on the reduction of population sizes of infective AMF, and its effect on succeeding annual crops.     

Interactions among plants,bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Atmospheric nitrogen (N) deposition has enhanced soil carbon (C) stocks in temperate forests. Most research has posited that these soil C gains are driven primarily by shifts in fungal community composition with elevated N leading to declines in lignin degrading Basidiomycetes. Recent research, however, suggests that plants and soil microbes are dynamically intertwined, whereby plants send C subsidies to rhizosphere microbes to enhance enzyme production and the mobilization of N. Thus, under elevated N, trees may reduce belowground C allocation leading to cascading impacts on the ability of microbes to degrade soil organic matter through a shift in microbial species and/or a change in plant–microbe interactions. The objective of this study was to determine the extent to which couplings among plant, fungal, and bacterial responses to N fertilization alter the activity of enzymes that are the primary agents of soil decomposition. We measured fungal and bacterial community composition, root–microbial interactions, and extracellular enzyme activity in the rhizosphere, bulk, and organic horizon of soils sampled from a long‐term (>25 years), whole‐watershed, N fertilization experiment at the Fernow Experimental Forest in West Virginia, USA. We observed significant declines in plant C investment to fine root biomass (24.7%), root morphology, and arbuscular mycorrhizal (AM) colonization (55.9%). Moreover, we found that declines in extracellular enzyme activity were significantly correlated with a shift in bacterial community composition, but not fungal community composition. This bacterial community shift was also correlated with reduced AM fungal colonization indicating that declines in plant investment belowground drive the response of bacterial community structure and function to N fertilization. Collectively, we find that enzyme activity responses to N fertilization are not solely driven by fungi, but instead reflect a whole ecosystem response, whereby declines in the strength of belowground C investment to gain N cascade through the soil environment.     

Field‐grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry,microbiology, and carbon storage potential

Cell wall recalcitrance poses a major challenge on cellulosic biofuel production from feedstocks such as switchgrass (Panicum virgatum L.). As lignin is a known contributor of recalcitrance, transgenic switchgrass plants with altered lignin have been produced by downregulation of caffeic acid O‐methyltransferase (COMT). Field trials of COMT‐downregulated plants previously demonstrated improved ethanol conversion with no adverse agronomic effects. However, the rhizosphere impacts of altering lignin in plants are unknown. We hypothesized that changing plant lignin composition may affect residue degradation in soils, ultimately altering soil processes. The objective of this study was to evaluate effects of two independent lines of COMT‐downregulated switchgrass plants on soils in terms of chemistry, microbiology, and carbon cycling when grown in the field. Over the first two years of establishment, we observed no significant differences between transgenic and control plants in terms of soil pH or the total concentrations of 19 elements. An analysis of soil bacterial communities via high‐throughput 16S rRNA gene amplicon sequencing revealed no effects of transgenic plants on bacterial diversity, richness, or community composition. We also did not observe a change in the capacity for soil carbon storage: There was no significant effect on soil respiration or soil organic matter. After five years of establishment, δ¹³C of plant roots, leaves, and soils was measured and an isotopic mixing model used to estimate that 11.2 to 14.5% of soil carbon originated from switchgrass. Switchgrass‐contributed carbon was not significantly different between transgenic and control plants. Overall, our results indicate that over the short term (two and five years), lignin modification in switchgrass through manipulation of COMT expression does not have an adverse effect on soils in terms of total elemental composition, bacterial community structure and diversity, and capacity for carbon storage.     

淋洗与植物作用耦合对盐渍化土壤的改良效应

以甘肃秦王川引大灌区盐渍化土壤为背景,以当地5种耐盐植物为材料,采用根袋法盆栽试验动态研究了淋洗结合植物种植对盐渍化土壤改良的效应。结果表明:与种前相比,单纯的淋洗作用对土壤pH值影响不大,而淋洗结合植物种植明显降低了土壤pH值,且根际土壤pH值小于非根际土壤的,5种耐盐植物中霸王根际土壤pH值降低幅度最大,达0.6个单位。K+、Ca2+、Na+、Mg2+、Cl-和SO2-4在5种植物根际土壤中均有不同程度的富集,富集程度因物种的不同而不同,随培养时间的延长而呈波动状态。5种供试植物和对照组土壤中的6种主要的可溶性盐分离子随淋洗次数和培养时间的延长呈下降趋势。在培养120d后,单纯淋洗的土壤中K+、Ca2+、Na+、Mg2+、Cl-和SO2-4的含量相比种前平均分别降低了33.3%、26.1%、35.6%、32.5%、35.5%和36.3%,植物吸收带走的上述各离子的含量平均分别占种前的46.2%、8.1%、30.2%、7.2%和21.6%,其中霸王吸收带走的盐分离子最多,而淋洗结合种植植物的土壤中上述各离子的含量与种前相比平均分别降低了67.25%、63.73%、83.8%、67.5%、81.55%和78.46%,由此可见,淋洗结合植物种植的脱盐效果优于单纯淋洗,且土壤中主要的盐分离子Na+、Cl-和SO2-4的含量降低幅度最大,通过计算得出,在Cl-、SO2-4和Na+减少的总量中还有37.73%的Na+、38.22%的Cl-和35.14%的SO2-4的减少量是由植物根系的物理化学作用机制引起的。     

两种盐生植物根际土壤细菌多样性和群落结构

应用高通量测序技术对西北干旱区两种盐生植物黑果枸杞和里海盐爪爪根际土壤细菌的多样性和群落结构进行研究,旨在揭示两种耐盐植物根际土壤细菌之间以及根际与非根际细菌群落结构间的差异,为深入研究盐生植物根际土壤微生物与耐盐性之间的关系提供理论基础。结果表明:黑果枸杞、里海盐爪爪根际细菌多样性丰度高于非根际土,黑果枸杞根际土壤细菌多样性丰度高于里海盐爪爪。根际和非根际土壤细菌群落的组成和丰度存在差异,从黑果枸杞和里海盐爪爪根际土壤中分别检测出细菌21门289属和22门304属,而从非根际土壤中分别检测出28门285属和24门336属;在两种盐生植物根际土壤中,变形菌门和厚壁菌门均为优势门;拟杆菌门、放线菌门、蓝细菌门及浮霉菌门在根际土壤中的丰度显著高于非根际土壤,而厚壁菌门在根际土壤中的丰度低于非根际土壤。两种植物根际土壤中的细菌优势门和优势属的数量均高于非根际土壤,在黑果枸杞和里海盐爪爪的根际土壤中的细菌优势属分别有10个和9个,而二者非根际土壤中的细菌优势属各有4个,其中假单胞菌属是根际和非根际土壤中的共有优势属。黑果枸杞和里海盐爪爪根系细菌群落组成和丰度存在差异,只有假单胞菌属和盐单胞菌属是两种植物根际土壤中的共有优势属。Unifrac分析和聚类分析表明,两种盐生植物根际土壤细菌之间的相似性大于根际和非根际细菌群落间的相似性。细菌多样性与土壤有机碳、有机质、总氮正相关,与pH、电导率负相关,电导率和pH,有机碳和总氮分别是非根际土,根际土壤细菌群落物种组成的主要影响因素。     

三峡库区消落带4种适生植物根际与非根际土壤养分与酶活性特征研究

三峡库区消落带植被修复过程中,物种的更替对库区土壤的地球化学循环产生潜在影响。以三峡库区忠县石宝寨汝溪河消落带植被修复示范基地165-170 m海拔段人工种植狗牙根、牛鞭草、落羽杉以及立柳根际与非根际土为试验对象,探究其根际与非根际土壤的养分含量及酶活性差异,以阐明不同物种的生长适应性及其根际养分利用策略,比较不同物种对库区土壤的营养改良作用。结果表明：（1）三峡库区消落带4种适生植物根系活动导致根际与非根际土壤养分因子以及土壤酶活性产生差异,不同物种的栽植均在一定程度上使库区土壤营养条件得以改善;（2）碳、氮两种元素在4种适生植物根际土壤中发生不同程度的富集,但磷素与钾素在不同物种根际与非根际土壤之间的变化不一致;（3）蔗糖酶、脲酶以及酸性磷酸酶在4种适生植物根际土中均表现出一定程度的根际正效应（R/S>1）,且狗牙根对3种土壤酶的根际活化效果最为明显,其根际效应分别高达2.39、1.89和2.7;（4）在植物根系的调控下,根际土中有机质与氮素、磷素以及钾素的相关性更为显著,而非根际土壤中,仅钾素与有效氮、有效磷呈显著负相关,其余各土壤养分因子之间均无显著相关性;（5）与落羽杉和立柳两木本植物相比,狗牙根与牛鞭草两草本植物根际具有更为合理的养分调节模式,对库区土壤的改良效果更好。     

Rhizosphere microbial community and hexachlorocyclohexane degradative potential in contrasting plant species

The organochlorine 1,2,3,4,5,6 hexachlorocyclohexane (HCH) is a broad-spectrum insecticide that was used on a large-scale worldwide. The soil–plant–microbe system and its influence on HCH biodegradation are evaluated. A greenhouse experiment was designed to evaluate HCH dissipation and several microbial parameters among rhizosphere and bulk soil of two contrasting plants, Cytisus striatus (Hill) Rothm and Holcus lanatus L. Plants were grown for 180 days in three treatments: uncontaminated soil (control), uncontaminated soil inoculated with soil (3% w/w) from a HCH-contaminated site (INOC), and uncontaminated soil inoculated with soil (3% w/w) from the HCH-contaminated site and artificially contaminated to obtain 100 mg HCH kg⁻¹ dry soil (100HCH-INOC). At harvest, plant biomass, soil water-extractable organic C, pH and Cl concentration, rhizosphere microbial densities (total heterotrophs, ammonifiers, amylolytics) and C substrate utilization patterns, and degradation of α-, β-, δ- and γ-HCH isomers were determined in bulk and rhizosphere soils. Soil solution Cl concentration was determined every 30 days throughout the entire growth period. Results demonstrate that both Cytisus striatus and Holcus lanatus can grow in soils with up to 100 mg HCH kg⁻¹. An enhanced degradation of α-HCH, but not β- or δ-HCH, was observed in the rhizosphere. Significant changes in the microbial densities were observed between bulk and rhizosphere soils of Cytisus, and an increase in C source utilization indicated changes in community level physiological profiles (CLPP) in the rhizosphere of this species when grown in contaminated soils. HCH dissipation was also greater in soils planted with this species. In accordance, increases in soil extractable C, Cl concentration and acidity were greater at the rhizosphere of Cytisus. Concentration of Cl in soil solutions also indicates greater HCH dechlorination in soils planted with Cytisus than Holcus. Results suggest that phytostimulation of bacteria present or added to soil is a promising approach to cleaning HCH-contaminated sites, and especially for biodegradation of α-HCH.     

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant–microbe interactions/rhizosphere microbiota/selection.     

Herbicide residues in soil decrease microbe-mediated plant protection

• The residues of glyphosate are found to remain in soils longer than previously reported, affecting rhizosphere microbes. This may adversely affect crop and other non-target plants because the plant's resilience and resistance largely rely on plant-associated microbes. Ubiquitous glyphosate residues in soil and how they impact mutualistic microbes inhabiting the aboveground plant parts are largely unexplored.
• We studied the effects of herbicide residues in soil on Epichloë sp., which are common endophytic symbionts inhabiting aerial parts of cool-season grasses. In this symbiosis, the obligate symbiont subsists entirely on its host plant, and in exchange, it provides alkaloids conferring resistance to herbivores for the host grass that invests little in its own chemical defence.
• We first show decreased growth of Epichloë endophytes in vitro when directly exposed to two concentrations of glyphosate or glyphosate-based herbicides. Second, we provide evidence for a reduction of Epichloë-derived, insect-toxic loline alkaloids in endophyte-symbiotic meadow fescue (F. pratensis) plants growing in soil with a glyphosate history. Plants were grown for 2 years in an open field site, and natural herbivore infestation was correlated with the glyphosate-mediated reduction of loline alkaloid concentrations.
• Our findings indicate that herbicides residing in soil not only affect rhizosphere microbiota but also aerial plant endophyte functionality, which emphasizes the destructive effects of glyphosate on plant symbiotic microbes, here with cascading effects on plant–pest insect interactions.

     

Phosphorus pools and other soil properties in the rhizosphere of wheat and legumes growing in three soils in monoculture or as a mixture of wheat and legume

Background and aims

Phosphorus and nitrogen availability and forms are affected by soil properties as well as by plant species and further modulated by soil microbes. Additionally, close contact of the roots of two plant species may affect concentrations and forms of N and P. The aim of this study was to assess properties related to N and P cycling in the rhizosphere of wheat and legumes grown in monoculture or in wheat/legume mixtures in three soils differing in pH.

Methods

Faba bean, white lupin and wheat were grown in three soils differing in pH (4.8, 7.5 and 8.8) in monoculture or in mixed culture of wheat and legumes. Rhizosphere soil was collected at flowering and analyzed for P pools by sequential fractionation, available N as well as community structure of bacteria, fungi, ammonia oxidizers, N₂-fixers and P mobilizers by polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE).

Results

Soil type was the major factor determining plant growth, rhizosphere nutrient dynamics and microbial community structure. Among the crop species, only faba bean had a significant effect on nitrification potential activity (PNA) in all three soils with lower activity compared to the unplanted soil. Soil type and plant spieces affected the community composition of ammonia-oxidizing archaea (AOB), ammonia-oxidizing archaea (AOA), N₂-fixers (nifH), P mobilizers (ALP gene) and fungi, but not that of bacteria. Among the microbial groups, the AOA and nifH community composition were most strongly affected by crop species, cropping system and soil type, suggesting that these groups are quite sensitive to environmental conditions. All plants depleted some labile as well as non-labile P pools whereas the less labile organic P pools (NaOH extractable P pools, acid extractable P pools) accumulated in the rhizosphere of legumes. The pattern of depletion and accumulation of some P pools differed between monoculture and mixed culture as well as among soils.

Conclusions

Plant growth and rhizosphere properties were mainly affected by soil type, but also by crop species whereas cropping system had the least effect. Wheat and the legumes depleted less labile inorganic P pools in some soils whereas less labile organic P pools (NaOH extractable P, acid extractable P) accumulated in the rhizosphere of legumes.     

黄河三角洲不同类型盐生植物土壤真菌群落结构特征

盐生植物种类及其所具有的不同耐盐调节方式影响着根际微生物群落的结构与组成。为明确不同类型盐生植物根际与非根际土壤中真菌群落结构与组成的差异及其与土壤环境间的相互关系,该研究采集了黄河三角洲地区芦苇、盐地碱蓬、獐毛3种不同类型盐生植物0～20 cm土层的根际和非根际土壤,通过高通量测序对其真菌群落多样性和结构进行了分析,以探究真菌群落特征与土壤理化因子间的关系。结果表明：(1)3种不同类型盐生植物根际土壤真菌群落丰富度显著大于各自非根际土,且獐毛根际土壤真菌群落丰富度显著大于芦苇和盐地碱蓬的根际土。(2)距离热图分析表明,芦苇和盐地碱蓬非根际土壤真菌群落间的相似性最大。(3)土壤真菌多样性和丰富度与土壤总碳、总氮、有效磷、pH呈正相关关系,与土壤盐分含量呈负相关关系。(4)3种不同类型盐生植物的根际与非根际土壤中,球囊菌门(Glomeromycota)均为绝对优势门,盾巨孢囊霉属(Scutellospora)为优势属。(5)RDA分析表明,土壤盐分含量是影响土壤真菌群落结构的重要因子,球囊菌门丰度与土壤总氮、总碳、有效磷、有机碳、pH呈正相关关系,与盐分呈负相关关系。(6)植物土壤真菌群...     

Soil Microbial Community Associated with an Invasive Grass Differentially Impacts Native Plant Performance

This study is one of the first to show that invasive plant-induced changes in the soil microbial community can negatively impact native plant performance. This greenhouse experiment tested whether soil microbial communities specific to the rhizospheres of an invasive grass (Aegilops triuncialis) and two native plants (Lasthenia californica and Plantago erecta) affected invasive and/or native plant performance. Each of these species were grown in separate pots for 2 months to prime the soils with plant-specific rhizosphere microbial communities. Each plant species was then planted in native- and invasive-primed soil, and effects on plant performance were monitored. At 5 months, differences in microbial biomarker fatty acids between invaded and native soils mirrored previous differences found in field-collected soil. L. californica performance was significantly reduced when grown in invaded soil compared to native soil (flowering date was delayed, aboveground biomass decreased, specific root length increased, and root mass ratio increased). In contrast, P. erecta and A. triuncialis performance were unaffected when grown in invaded vs native soil. These results suggest that in some cases, invasion-induced changes in the soil microbial community may contribute to a positive feedback loop, leading to the increased dominance of invasive species in an ecosystem.     

Effects of Bacillus amyloliquefaciens FZB42 on Lettuce Growth and Health under Pathogen Pressure and Its Impact on the Rhizosphere Bacterial Community

The soil-borne pathogen Rhizoctonia solani is responsible for crop losses on a wide range of important crops worldwide. The lack of effective control strategies and the increasing demand for organically grown food has stimulated research on biological control. The aim of the present study was to evaluate the rhizosphere competence of the commercially available inoculant Bacillus amyloliquefaciens FZB42 on lettuce growth and health together with its impact on the indigenous rhizosphere bacterial community in field and pot experiments. Results of both experiments demonstrated that FZB42 is able to effectively colonize the rhizosphere (7.45 to 6.61 Log ₁₀ CFU g⁻¹ root dry mass) within the growth period of lettuce in the field. The disease severity (DS) of bottom rot on lettuce was significantly reduced from severe symptoms with DS category 5 to slight symptom expression with DS category 3 on average through treatment of young plants with FZB42 before and after planting. The 16S rRNA gene based fingerprinting method terminal restriction fragment length polymorphism (T-RFLP) showed that the treatment with FZB42 did not have a major impact on the indigenous rhizosphere bacterial community. However, the bacterial community showed a clear temporal shift. The results also indicated that the pathogen R. solani AG1-IB affects the rhizosphere microbial community after inoculation. Thus, we revealed that the inoculant FZB42 could establish itself successfully in the rhizosphere without showing any durable effect on the rhizosphere bacterial community.     

Nitrogen fertilization has minimal influence on rhizosphere effects of smooth crabgrass (Digitaria ischaemum) and bermudagrass (Cynodon dactylon)

Aims Plants generally respond to nitrogen (N) fertilization with increased growth, but N addition can also suppress rhizosphere effects, which consequently alters soil processes. We quantified the influence of N addition on rhizosphere effects of two C₄ grasses: smooth crabgrass (Digitaria ischaemum) and bermudagrass (Cynodon dactylon).Methods Plants were grown in nutrient-poor soil for 80 days with either 20 or 120 μg NH 4 NO 3 -N g dry soil^-1. N mineralization rates, microbial biomass, extracellular enzyme activities and bacterial community structure were measured on both rhizosphere and bulk (unplanted) soils after plant harvest.Important findings Fertilization showed nominal differences in net N mineralization, extracellular enzyme activity and microbial biomass between the rhizosphere and bulk soils, indicating minimal influence of N on rhizosphere effects. Instead, the presence of plant roots showed the strongest impact (up to 80%) on rates of net N mineralization and activities of three soil enzymes indicative of N release from organic matter. Principal component analysis of terminal restriction fragment length polymorphism (T-RFLP) also reflected these trends by highlighting the importance of plant roots in structuring the soil bacterial community, followed by plant species and N fertilization (to a minor extent). Overall, the results indicate minor contributions of short-term N fertilization to changes in the magnitude of rhizosphere effects for both grass species.     

Changes and availability of P fractions following 65 years of P application to a calcareous soil in a Mediterranean climate

The fate and availability of P derived from granular fertilisers in an alkaline Calcarosol soil were examined in a 65-year field trial in a semi-arid environment (annual rainfall 325 mm). Sequential P fractionation was conducted in the soils collected from the trial plots receiving 0–12 kg P ha⁻¹crop⁻¹, and the rhizosphere soil after growing wheat (Triticum aestivum L. cv. Yitpi) and chickpea (Cicer arietinum L. cv. Genesis 836) for one or two 60-day cycles in the glasshouse. Increasing long-term P application rate over 65 years significantly increased all inorganic P (Pi) fractions except HCl–Pi. By contrast, P application did not affect or tended to decrease organic P (Po) fractions. Increasing P application also increased Olsen-P and resin-P but decreased the P buffer capacity and sorption maxima. Residual P, Pi and Po fractions accounted for an average of 32, 16 and 52% of total P, respectively. All soil P fractions including residual P in the rhizosphere soil declined following 60-day growth of either wheat or chickpea. The decreases were greater in soils with a history of high P application than low P. An exception was water-extractable Po, which increased following plant growth. Changes in various P fractions in the rhizosphere followed the same pattern for both plant species. Biomass production and P uptake of the plants grown in the glasshouse correlated positively with the residual P and inorganic fractions (except HCl–Pi) but negatively with Po in the H₂O-, NaOH- and H₂SO₄-fractions of the original soils. The results suggest that the long-term application of fertiliser P to the calcareous sandy soil built up residual P and non-labile Pi fractions, but these P fractions are potentially available to crops.     

Fertilization alters protistan consumers and parasites in crop-associated microbiomes

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant–soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.     

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. This revised version was published online in August 2006 with corrections to the Cover Date.