Fungal entomopathogens in the rhizosphere

The ecology of fungal entomopathogens in the rhizosphere is an understudied area of insect pathology. The rhizosphere is the region of soil in which the release of root exudates influences the soil microbiota, and may provide a favorable environment for fungal entomopathogens. The objective of this review is to bring together the relatively scant data available to date on the subject of fungal entomopathogens colonizing the rhizosphere and to highlight the importance of these findings. Gaining a better understanding of the ecology of fungal entomopathogens in the rhizosphere will help in the development of successful microbial control strategies against root-feeding insect pests.     

The rhizosphere microbiome and plant health

The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.     

Fungal volatiles mediate cheese rind microbiome assembly

In vitro studies in plant, soil, and human systems have shown that microbial volatiles can mediate microbe–microbe or microbe–host interactions. These previous studies have often used artificially high concentrations of volatiles compared to in situ systems and have not demonstrated the roles volatiles play in mediating community-level dynamics. We used the notoriously volatile cheese rind microbiome to identify bacteria responsive to volatiles produced by five widespread cheese fungi. Vibrio casei had the strongest growth stimulation when exposed to all fungi. In multispecies community experiments, fungal volatiles caused a shift to a Vibrio-dominated community, potentially explaining the widespread occurrence of Vibrio in surface-ripened cheeses. RNA sequencing identified activation of the glyoxylate shunt as a possible mechanism underlying volatile-mediated growth promotion and community assembly. Our study demonstrates how airborne chemicals could be used to control the composition of microbiomes and illustrates how volatiles may impact the development of cheese rinds.     

根际微生物组中细菌趋化系统的生态功能

在根际微环境中,特定的土壤微生物能够利用自身独特的趋化系统感应根系分泌物,响应植物的选择性招募。细菌的趋化系统介导了植物-微生物以及微生物间相互作用,在植物对根际微生物组的选择中发挥着关键的生态学功能。综述了根际微生物组中细菌趋化系统的研究进展,从生态学的角度提出了未来针对根际细菌趋化系统的研究方向,旨在阐明根际细菌趋化系统的生态学功能,为增进理解作物根际微生物组的募集过程,以及未来农业中根际微生物组的重组构建奠定理论基础。     

烟草根际土壤真菌多样性的研究

烟草土传病害发生普遍,危害严重。为深入了解烟草根际土壤真菌区系与土传病害间的相互关系,选取黑龙江、山东、广西和云南四省区的代表性烟田,开展了烟草根际土壤真菌多样性的研究。对采自上述四省区12个县市的224份烟草根际土壤样品进行了真菌的分离和培养,共分离获得1,278株真菌,通过形态学特征鉴定出真菌25属86种。其中接合菌门4属6种,子囊菌门1属1种,无性型真菌20属79种。通过分析发现,烟草根际土壤中的优势真菌种群及其菌株数量所占分离真菌总菌株数量的比例分别为：青霉属Penicillium 16.74%,木霉属Trichoderma 14.32%,镰孢菌属Fusarium 13.54%和曲霉属Aspergillus 11.50%。在12个采样地点中,山东诸城的多样性指数（H￠=2.0666）和均匀度指数（J=0.6898）最高,云南玉溪的丰富度指数（R=4.0687）最高。不同采样地点的烟草根际土壤真菌种群的相似性水平也存在差异,其中云南永胜和大理的烟草根际土壤真菌种群的相似性系数最高（Cj=0.9375）,山东沂水和云南玉溪间的相似性最低（Cj=0.5217）。     

小蓬竹根际土壤真菌多样性研究

为认识喀斯特山地适应竹种小蓬竹根际土壤微生物多样性,本文采用稀释平板法研究小蓬竹根际土壤真菌多样性。结果表明,菌落具有表型差异的真菌共33株,r DNA‐ITS进行BLAST划分为12个属24个种,相似度为75%–100%。子囊菌门真菌11个属、23个种、32株;担子菌门仅有1株,属多年卧孔菌属。子囊菌门的青霉属的菌株数量最多,占总菌株数21.21%。小蓬竹根际真菌数量为9.19×105/cfu?g,Shannon‐Wiener多样性指数H为2.2180,Margalef丰富度指数R为12,Pielou均匀度指数J为0.8926。     

Fungal invasion of epithelial cells

Interaction between host cells and invasive Candida plays a large role in the pathogenicity of Candida species. Fungal-induced endocytosis and active penetration are the two distinct, yet complementary invasion mechanisms of invasive candidiasis. Induced endocytosis is a microorganism-triggered, epithelial-driven, clathrin-mediated and actin-dependent process. During the fundamental pathological process of induced endocytosis, invasins (Als3 and Ssa1), which mediate the binding of host epithelial surface proteins, are expressed by Candida species on the hyphal surface. Sequentially, the interaction between invasins and host epithelial surface proteins stimulates the recruitment of clathrin, dynamin and cortactin to the sites where Candida enters epithelial cells, which in turn induce the actin cytoskeleton reorganization. Actin cytoskeleton provides the force required for fungal internalization. Parallely, active penetration of Candida can directly pass through epithelial cells possibly due to progressive elongation of hyphae and physical forces. Several molecules, such as secreted hydrolases and Als3, can affect the protective barrier of the epithelium and make Candida actively penetrate into epithelial cells through intercellular gaps of epithelial layers.     

Harnessing the rhizosphere microbiome through plant breeding and agricultural management

Background

The need to enhance the sustainability of intensive agricultural systems is widely recognized One promising approach is to encourage beneficial services provided by soil microorganisms to decrease the inputs of fertilizers and pesticides. However, limited success of this approach in field applications raises questions as to how this might be best accomplished.

Scope

We highlight connections between root exudates and the rhizosphere microbiome, and discuss the possibility of using plant exudation characteristics to selectively enhance beneficial microbial activities and microbiome characteristics. Gaps in our understanding and areas of research that are vital to our ability to more fully exploit the soil microbiome for agroecosystem productivity and sustainability are also discussed.

Conclusion

This article outlines strategies for more effectively exploiting beneficial microbial services on agricultural systems, and cals attention to topics that require additional research.     

Fungal morphogenesis and host invasion

Many fungal pathogens undergo morphological transformations during host invasion. However, the significance of this for fungal pathogenesis is not clear. Both yeast and hyphal cells have properties well suited to tissue invasion and evasion of the immune system. However, molecular control circuits that regulate morphogenesis also regulate the expression of other virulence traits. To establish the extent to which morphogenesis impacts on pathogenesis, it is necessary to characterise the morphology of the fungus at different stages and locations during the natural history of a disease and to untangle how gene expression is modulated at these stages. This review considers the role of morphogenesis in fungal infection and argues that no simple, universal relationship can be drawn between morphology and the invasive potential of a fungus.     

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome

The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.     

马铃薯全生育期内根际微生物组变化规律

[目的]陆生植物根际环境与土壤中的微生物菌群关系密切,其根际微生物群落动态极可能直接影响着植物健康及养分高效利用。虽然根际益生菌已被证实可用于提高作物生产力,但由于缺乏对这些菌群组成动态变化规律的认识了解,它们的开发受到限制。研究马铃薯全生育期根际菌群的动态变化规律,探讨根际菌群变化与马铃薯发育时期的相关性,为针对马铃薯不同生长时期开发专用生物益生菌肥奠定理论基础。[方法]本研究着眼于马铃薯田间全生命周期微生物组动态变化,通过Illumina MiSeq高通量测序技术对不同时间点马铃薯根际细菌16S rRNA基因V3-V4区和真菌ITS区测序并对操作分类单位(OTU)进行聚类,分析样品间微生物群落的多样性特征,并通过机器学习的方法建立模型,将根际菌群与田间马铃薯发育时间相关联。[结果]根际菌群在马铃薯各个发育阶段随时间变化明显,营养生长阶段的微生物群落结构发生了显著变化,随着结薯期的开始逐渐稳定,直到块茎成熟后期根际菌群再次出现较大变化,且在不同施肥处理间呈现较大差异。进一步基于模型挖掘了与马铃薯发育时间相关联的22个特征细菌类群和16个特征真菌类群,其中苗期和结薯末期的特征类群分别为梭菌(Clostridium)和放线菌(Actinobacteria)。[结论]马铃薯的生长发育时期是影响根际微生物群落组成的主要因素,益生菌肥的添加主要影响马铃薯结薯末期的细菌微生物菌群结构。     

Salinity-induced changes in the rhizosphere microbiome improve salt tolerance of Hibiscus hamabo

Plant and Soil - Different grazing management practices have a significant impact on the sustainability of grassland ecosystems. This study invested the vertical distribution of soil nitrogen (N)...     

Fungal invasion of normally non-phagocytic host cells

Many fungi that cause invasive disease invade host epithelial cells during mucosal and respiratory infection, and subsequently invade endothelial cells during hematogenous infection. Most fungi invade these normally non-phagocytic host cells by inducing their own uptake. Candida albicans hyphae interact with endothelial cells in vitro by binding to N-cadherin on the endothelial cell surface. This binding induces rearrangement of endothelial cell microfilaments, which results in the endocytosis of the organism. The capsule of Cryptococcus neoformans is composed of glucuronoxylomannan, which binds specifically to brain endothelial cells, and appears to mediate both adherence and induction of endocytosis. The mechanisms by which other fungal pathogens induce their own uptake are largely unknown. Some angioinvasive fungi, such as Aspergillus species and the Zygomycetes, invade endothelial cells from the abluminal surface during the initiation of invasive disease, and subsequently invade the luminal surface of endothelial cells during hematogenous dissemination. Invasion of normally non-phagocytic host cells has different consequences, depending on the type of invading fungus. Aspergillus fumigatus blocks apoptosis of pulmonary epithelial cells, whereas Paracoccidioides brasiliensis induces apoptosis of epithelial cells. This review summarizes the mechanisms by which diverse fungal pathogens invade normally non-phagocytic host cells and discusses gaps in our knowledge that provide opportunities for future research.     

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.Subject terms: Agricultural genetics, Plant ecology, Soil microbiology     

Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome

Recruitment of microorganisms to the rhizosphere varies among plant genotypes, yet an understanding of whether the microbiome can be altered by selection on the host is relatively unknown. Here, we performed a common garden study to characterize recruitment of rhizosphere microbiome, functional groups, for 20 expired Plant Variety Protection Act maize lines spanning a chronosequence of development from 1949 to 1986. This time frame brackets a series of agronomic innovations, namely improvements in breeding and the application of synthetic nitrogenous fertilizers, technologies that define modern industrial agriculture. We assessed the impact of chronological agronomic improvements on recruitment of the rhizosphere microbiome in maize, with emphasis on nitrogen cycling functional groups. In addition, we quantified the microbial genes involved in nitrogen cycling and predicted functional pathways present in the microbiome of each genotype. Both genetic relatednesses of host plant and decade of germplasm development were significant factors in the recruitment of the rhizosphere microbiome. More recently developed germplasm recruited fewer microbial taxa with the genetic capability for sustainable nitrogen provisioning and larger populations of microorganisms that contribute to N losses. This study indicates that the development of high-yielding varieties and agronomic management approaches of industrial agriculture inadvertently modified interactions between maize and its microbiome.Subject terms: Microbial ecology, Plant sciences, Agricultural genetics     

Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health

Metagenomic has been explored in investigating microbiome diversity. However, there is limited available information on its application towards securing plant health. Hence, this study adopts the metagenomic approach to unravel the microbiome diversity associated with healthy (LI and MA) and Northern corn leaf blight (NCLB) infected (LID and MAD) maize rhizosphere in the maize growing field at Lichtenburg and Mafikeng, North-West province of South Africa. The extraction of whole DNA from the respective healthy and diseased rhizosphere soils was conducted and sequenced using shotgun metagenomics. A total of 12 bacteria, 4 archaea and 2 fungal phyla were found as predominant across the fields with the use of the SEED subsystem database. The most predominant bacteria phyla included Proteobacteria, Dienococcus-Thermus, Gemmatimonadetes, Chlorobi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Acidobacteria, Firmicutes, Chloroflexi and Bacteroidetes. Archaea consisted of Euryarchaeota, Thaumarchaeota, Crenarchaeota and Korachaeota, while Ascomycota and Basidiomycota were the dominant fungal phyla. Microbial abundance and diversity were higher in the rhizosphere of healthy maize (LI and MA) rhizosphere as compared to the NCLB diseased (LID and MAD), in the order LI > MA > LID > MAD. At phylum and genus level, alpha diversity index showed no significant (p > 0.05) difference in the abundance of the microbial community of healthy and NCLB infected maize rhizosphere, while beta analysis produced a significant (p = 0.01) difference in the microbial diversity in the soil. Taken together, the study revealed that the abundance of microbial diversity in the maize rhizosphere influences the efficacy of the rhizosphere microbiome to modulate microbial functions towards managing and sustaining plant health.     

根际微生物与植物再植病的发生发展关系

植物再植病严重危害农作物的生长发育,形成原因复杂,最新的研究显示它与根际微生态的变化相关,其中主要涉及根际微生物菌群结构的变化。现代高通量测序技术的迅速推广使得根际微生物和再植病间关系成为新的研究热点;本文根据国内外植物再植病病因、根际土壤微生物多样性以及它们与植物生长发育关系等多方面的研究成果,综合分析植物再植病与根际微生物间的关系,以期从根际微生物种群动态变化的角度认识植物再植病的病因并为防治提供新的思路。     

Fungal populations in the rhizosphere of peanut (Arachis hypogaea L.)

Summary A comparison of fungal populations in the rhizospheres of eight varieties of peanut grown in a red lateritic soil amended with farmyard manure was made by the dilution-plate technique. There was a marked increase in fungi in the rhizospheres of TMV 2, TMV 4, Pollachi Red and EC 1698, the increase was smaller in Spanish Improved and RS 1 while very little rhizosphere effect was shown by TMV 3 and Pondicherry 8. Age of the plant had a significant influence on numbers of fungi in the rhizosphere. High R/S ratios were obtained when the plants were 30 days old, at which time attained maximum vegetative growth and started to flower. The ratios gradually decreased after that age until the plants were three months old when there was again a small increase. This later rise in fungal populations is interpreted to be due to an increase in microbial activity around dead or senescent roots. No correlation could be established between numbers of root nodules produced by a variety and its rhizosphere effect. Preferential stimulation of certain fungi in the rhizosphere of some of the varieties was noticed.