Characterization of Root Surface and Endorhizosphere Pseudomonads in Relation to Their Colonization of Roots

An extensive colonization of the endorhizosphere by fluorescent pseudomonads was observed in tomato plants grown on artificial substrates. These studies reveal that a significantly higher percentage of pseudomonads obtained from the endorhizosphere (30%) reduced plant growth than those obtained from the root surface (4%). Lipopolysaccharide patterns, cell envelope protein patterns, and other biochemical characteristics indicated that Pseudomonas isolates obtained from the endorhizosphere are distinct from Pseudomonas isolates obtained from the root surface. Isolates from the endorhizosphere especially were able to recolonize the endorhizosphere of both sterile and nonsterile tomato roots. The ability of the endorhizosphere isolates to colonize the endorhizosphere significantly correlated with their agglutination by tomato root agglutinin but did not correlate with chemotaxis to seed exudates of tomato. No correlation between colonization of the endorhizosphere and agglutination by root agglutinin could be demonstrated for the root surface isolates. We propose that agglutination of specific Pseudomonas strains by root agglutinin is of importance in the initial phase of adherence of bacteria to the root surface.     

粪产碱菌（Alcaligenes faecalis）对稻根氧化还原特性及水稻多元酚和内根际激素水平的影响

联合固氮粪产碱菌结合于水稻根表时能增强水稻根部还原力和稻根超氧化物歧化酶（ＳＯＤ）活性。实验室和田间试验证明粪产碱菌能提高水稻幼苗对高、低温不良环境的抗逆性。经浸种处理的水稻幼苗植株内多元酚含量增加了１２．５％。粪产以菌对接种水稻多元酚抽提物有强烈的趋化性,而该抽提物对粪产碱菌的固氮活性有明显的刺激作用。多元酚抽提物经双向纸层析和薄层层析表明接种诱导了至少一个特征组分含量提高。采用粪产减菌野生型Ａ１５０１（ｎｉｆ＋）和固氮缺陷型Ａ１５０６（Ｎｉｆ－）浸种能改变宿主水稻内源激素水平,提高内根际的ＩＡＡ和Ｚ的含量,促进植株及根系的生长发育,使其侧根和根毛数目明显增多。在根际联合体系形成过程中,多元酚或激素可能充当植物与细菌间相互作用的一类特异信号分子。     

External and Internal Root Colonization of Maize by Two Pseudomonas Strains: Enumeration by Enzyme-Linked Immunosorbent Assay (ELISA)

Maize root colonization by two fluorescent Pseudomonas strains M.3.1. and TR335, isolated respectively from maize and tomato roots, were studied in hydroponic conditions. Each bacterium was inoculated separately, and three different colonization areas were studied: nutrient solution, rhizoplane, and endorhizosphere. The two Pseudomonas strains established large rhizosphere populations, and rhizoplane colonization of the entire root system was similar for both strains. However, strain M.3.1. colonized the endorhizosphere more efficiently than strain TR335. Seminal root cuttings from the tip to the seed allowed the assessment of colonization of three different root areas (i.e., root cap and elongation area, root-hair zone, and mature zone). Rhizoplane colonizations of all these three areas by M.3.1. were significantly the same, whereas strain TR335 colonized the rhizoplane of the root cap and elongation area more actively than the root-hair zone and mature zone. Population size of the strain M.3.1. in the internal tissue of these areas was greater than that of strain TR335. Co-inoculations of the two strains indicated a stimulation of the population size of strain M.3.1. regardless of root area studied, whereas population size of strain TR335 remained unchanged. These results demonstrated that external and internal maize root tissues were colonized to a greater extent by a strain isolated from a maize rhizosphere than by one isolated from another rhizosphere. Received: 26 September 1996 / Accepted: 1 November 1996     

Variation in Nitrogen Fixing Ability among Natural Isolates of Azospirillum

Abstract A total of 285 strains of Azospirillum were isolated from soils from seven geographic regions in New South Wales, Australia, using an immunomagnetic separation procedure which does not select strains according to their nitrogen-fixing ability. By combining amplification and restriction analysis of 16S rDNA (ARDRA) patterns with serological, morphological and biochemical results, we found that almost all isolates were A. brasilense and A. lipoferum. There was wide variation in the nitrogenase (acetylene reduction) activity of isolates grown in nitrogen-free, semisolid medium, with differences in average activities between regions. Isolates with zero or negligible nitrogenase activity were found in samples from only two regions, one of which had two out of 26 strains with no activity. Representative isolates, having the highest, the lowest, and intermediate nitrogen fixation rates for each site, were used to inoculate the roots of wheat plants in a model system. Most of the isolates, in association with wheat roots, reduced between 1 and 5 nmol C₂H₄· mg dry root⁻¹· day⁻¹, but certain strains gave considerably higher activities. The rank order of nitrogen fixation activity on wheat roots did not correlate well with that of nitrogen fixation in pure culture; some strains that fixed nitrogen vigorously in pure culture had low rates of fixation on roots, and vice versa. This inconsistency could not be explained by variations in the root colonizing ability of different strains. However, isolates of A. lipoferum had a higher average nitrogenase activity than A. brasilense, both in Nfb medium and in association with wheat roots. The majority of the most active nitrogen fixers were A. lipoferum. When wheat plants were inoculated with mixtures of two or four strains, nitrogen fixation rates were generally between the rates for the component strains when inoculated individually. There was no benefit from using mixtures of different strains. Received: 23 July 1997; Accepted: 4 December 1997     

Close Association of Azospirillum and Diazotrophic Rods with Different Root Zones of Kallar Grass

The populations of diazotrophic and nondiazotrophic bacteria were estimated in the endorhizosphere and on the rhizoplane of Kallar grass (Leptochloa fusca) and in nonrhizosphere soil. Microaerophilic diazotrophs were counted by the most-probable-number method, using two semisolid malate media, one of them adapted to the saline-sodic Kallar grass soil. Plate counts of aerobic heterotrophic bacteria were done on nutrient agar. The dominating N₂-fixing bacteria were differentiated by morphological, serological, and physiological criteria. Isolates, which could not be assigned to a known species, were shown to fix nitrogen unequivocally by ¹⁵N₂ incorporation. On the rhizoplane we found 2.0 × 10⁷ diazotrophs per g (dry weight) of root, which consisted in equal numbers of Azospirillum lipoferum and Azospirillum-like bacteria showing characteristics different from those of known Azospirillum species. Surface sterilization by NaOCI treatment effectively reduced the rhizoplane population, so that bacteria released by homogenization of roots could be regarded as endorhizosphere bacteria. Azospirillum spp. were not detected in the endorhizosphere, but diazotrophic, motile, straight rods producing a yellow pigment occurred with 7.3 × 10⁷ cells per g (dry weight) of root in the root interior. In nonrhizosphere soil we found 3.1 × 10⁴ nitrogen-fixing bacteria per g. Diazotrophs were preferentially enriched in the Kallar grass rhizosphere. In nonrhizosphere soil they made up 0.2% of the total aerobic heterotrophic microflora, on the rhizoplane they made up 7.1%, and in the endorhizosphere they made up 85%. Owing to high numbers in and on roots and their preferential enrichment, we concluded that diazotrophs are in close association with Kallar grass. They formed entirely different populations on the rhizoplane and in the endorhizosphere.     

Enhancement of polygalacturonase activity during auxin induced para nodulation and endorhizosphere colonization of Azospirillum in rice roots

Effect of different auxins, namely, 2,4-dichlorophenoxyacetic acid (2,4-D), naphthalene acetic acid (NAA) and indole acetic acid (IAA) and Azospirillum brasilense bioinoculation on the enhancement of polygalacturonase (PG) activity in rice roots during para nodulation and endorhizosphere colonization of Azospirillum was studied under in vitro condition. It was observed that Azospirillum bioinoculation could augment PG activity of rice roots to a lesser extent without any root morphogenesis whereas auxin application together with Azospirillum bioinoculation enhanced PG activity of rice roots to a higher level which resulted in better root morphogenesis (para nodule) and endorhizosphere colonisation of A. brasilense. Among the three auxins tested, 2,4-D, even at lower concentration (0.5 ppm) enhanced the rice root PG activity, root morphogenesis and endorhizosphere colonization of Azospirillum while it was 2.0 ppm with NAA and variable with IAA. It is concluded that there is a positive correlation existing among PG activity, degree of root morphogenesis and endorhizosphere colonization of Azospirillum brasilense in rice roots and the degree of correlation is determined by the chemical composition, concentration and mode of action of the auxin utilised.     

Relationship between root colonization and initial adsorption ofAzospirillum to plant roots

Four strains ofAzospirillum were ranked according to numbers of cells adsorbed on the roots of seedlings in liquid medium, and the rankings were evaluated for their usefulness in predicting success of colonization of the roots of pot-grown plants. Different rankings were observed on different parts of the roots and on different host plants. Rhizosphere colonization results for rice were similar to those for clover and showed little difference between bacterial strains. The population densities were approximately equal to those of the most dense strains in the wheat rhizosphere, whereas the highest concentrations in the root interior of clover and rice were only about one-tenth of those in wheat. Rankings of initial adsorptive ability on various parts of the roots showed potential for predicting the best strains for colonizing the root interiors of wheat and clover. On wheat, the two strains (Cd and SpBr14) which showed best initial adsorption to the root cap were best at colonizing the endorhizosphere of pot-grown plants. For rice, strains Cd and SpBr14 gave lowest and highest values, respectively, both for adsorption to the terminal 2 cm of roots and for subsequent colonization of the root interior. Data on initial adsorption were of no value in predicting the relative success of strains in colonizing the root surface of any host plants or the interior of clover roots.     

Regional distribution and pH sensitivity ofAzospirillum associated with wheat roots in Eastern Australia

In a survey ofAzospirillum spp. on the roots and associated soil of wheat grown in eastern Australia, azospirilla were isolated from approximately 40% of samples from areas of soil pH between 5.0 and 6.6. However, azospirilla isolates were rare in soil between pH 4.5 and 5.0 and absent below pH 4.5. Of 25 independent isolates, 17 wereA. brasiliense and eight wereA. lipoferum. No selection forA. brasiliense Nir^– strains by wheat roots was observed. Only one of six endorhizosphere isolates wereA. brasiliense Nir^–, compared with three of nine from unsterilized roots plus associated soil, and three of eight from soil. With a medium buffered with 0.05 M malate and 0.05 M phosphate, it was found that allAzospirillum isolates had a lower minimum pH for growth when supplied with fixed nitrogen than when grown under nitrogen-fixing conditions. Strains isolated from soils had a minimum pH for growth that was less than the pH of the soil from which they were isolated. However, a significant proportion of strains isolated from roots had a minimum pH for growth that was higher than the pH of the associated soil suggesting that the wheat roots provided an ecological niche protecting against soil acidity.     

Sugar-binding activity of pea lectin enhances heterologous infection of transgenic alfalfa plants by Rhizobium leguminosarum biovar viciae

Transgenic alfalfa (Medicago sativa L. cv Regen) roots carrying genes encoding soybean lectin or pea (Pisum sativum) seed lectin (PSL) were inoculated with Bradyrhizobium japonicum or Rhizobium leguminosarum bv viciae, respectively, and their responses were compared with those of comparably inoculated control plants. We found that nodule-like structures formed on alfalfa roots only when the rhizobial strains produced Nod factor from the alfalfa-nodulating strain, Sinorhizobium meliloti. Uninfected nodule-like structures developed on the soybean lectin-transgenic plant roots at very low inoculum concentrations, but bona fide infection threads were not detected even when B. japonicum produced the appropriate S. meliloti Nod factor. In contrast, the PSL-transgenic plants were not only well nodulated but also exhibited infection thread formation in response to R. leguminosarum bv viciae, but only when the bacteria expressed the complete set of S. meliloti nod genes. A few nodules from the PSL-transgenic plant roots were even found to be colonized by R. leguminosarum bv viciae expressing S. meliloti nod genes, but the plants were yellow and senescent, indicating that nitrogen fixation did not take place. Exopolysaccharide appears to be absolutely required for both nodule development and infection thread formation because neither occurred in PSL-transgenic plant roots following inoculation with an Exo(-) R. leguminosarum bv viciae strain that produced S. meliloti Nod factor.     

Endophytic colonization of rice by a diazotrophic strain of Serratia marcescens

Six closely related N2-fixing bacterial strains were isolated from surface-sterilized roots and stems of four different rice varieties. The strains were identified as Serratia marcescens by 16S rRNA gene analysis. One strain, IRBG500, chosen for further analysis showed acetylene reduction activity (ARA) only when inoculated into media containing low levels of fixed nitrogen (yeast extract). Diazotrophy of IRBG500 was confirmed by measurement of 15N2 incorporation and by sequence analysis of the PCR-amplified fragment of nifH. To examine its interaction with rice, strain IRBG500 was marked with gusA fused to a constitutive promoter, and the marked strain was inoculated onto rice seedlings under axenic conditions. At 3 days after inoculation, the roots showed blue staining, which was most intense at the points of lateral root emergence and at the root tip. At 6 days, the blue precipitate also appeared in the leaves and stems. More detailed studies using light and transmission electron microscopy combined with immunogold labeling confirmed that IRBG500 was endophytically established within roots, stems, and leaves. Large numbers of bacteria were observed within intercellular spaces, senescing root cortical cells, aerenchyma, and xylem vessels. They were not observed within intact host cells. Inoculation of IRBG500 resulted in a significant increase in root length and root dry weight but not in total N content of rice variety IR72. The inoculated plants showed ARA, but only when external carbon (e.g., malate, succinate, or sucrose) was added to the rooting medium.     

Symbiotic and competitive properties of motility mutants of Rhizobium trifolii TA1

Non-motile mutants of Rhizobium trifolii defective in either flagellar synthesis or function were isolated by transposon Tn5 mutagenesis. they were indistinguishable from motile control strains in growth in both laboratory media and in the rhizosphere of clover roots. When each non-motile mutant was grown together with a motile strain in continuous culture, the numbers of motile and non-motile organisms remained in constant proportion, implying that their growth rates were essentially identical. When inoculated separately onto clover roots, the mutants and wildtype did not differ significantly in the number of nodules produced or in nitrogen fixing activity. However, when mixtures of equal numbers of mutant and wild-type cells were inoculated onto clover roots, the motile strain formed approximately five times more nodules than the flagellate or non-flagellate, non-motile mutants, suggesting that motility is a factor in competition for nodule formation.     

Root-Zone-Specific Oxygen Tolerance of Azospirillum spp. and Diazotrophic Rods Closely Associated with Kallar Grass

The effect of oxygen on N₂-dependent growth of two Azospirillum strains and two diazotrophic rods closely associated with roots of Kallar grass (Leptochloa fusca) was studied. To enable precise comparison, bacteria were grown in dissolved-oxygen-controlled batch and continuous cultures. Steady states were obtained from about 1 to 30 μM O₂, some of them being carbon limited. All strains needed a minimum amount of oxygen for N₂-dependent growth. Nitrogen contents between 10 and 13% of cell dry weight were observed. The response of steady-state cultures to increasing O₂ concentrations suggested that carbon limitation shifted to internal nitrogen limitation when N₂ fixation became so low that the bacteria could no longer meet their requirements for fixed nitrogen. For Azospirillum lipoferum Rp5, increase of the dilution rate resulted in decreased N₂ fixation in steady-state cultures with internal nitrogen limitation. Oxygen tolerance was found to be strain specific in A. lipoferum with strain Sp59b as a reference organism. Oxygen tolerance of strains from Kallar grass was found to be root zone specific. A. halopraeferens Au 4 and A. lipoferum Rp5, predominating on the rhizoplane of Kallar grass, and strains H6a2 and BH72, predominating in the endorhizosphere, differed in their oxygen tolerance profiles. Strains H6a2 and BH72 still grew and fixed nitrogen in steady-state cultures at O₂ concentrations exceeding those which absolutely inhibited nitrogen fixation of both Azospirillum strains. It is proposed that root-zone-specific oxygen tolerance reflects an adaptation of the isolates to the microenvironments provided by the host plant.     

Acetylene reduction (nitrogen fixation) associated with corn inoculated with Spirillum.

Sorghum and corn breeding lines were grown in soil in field and greenhouse experiments with and without an inoculum of N2-fixing in Spirillum strains from Brazil. Estimated rates of N2 fixation associated with field-grown corn and sorghum plants were less than 4 g of N2/ha per day. The mean estimated N2-fixation rates determined on segments of roots from corn inoculated with Spirillum and grown in the greenhouse at 24 to 27 degrees C were 15 g of N2/ha per day (16 inbreds), 25 g of N2/ha per day (six hybrids), and 165 g of N2/ha per day for one hybird which was heavily inoculated. The corresponding mean rates determined from measurements of in situ cultures of the same series of corn plants (i.e., 16 inbreds, six hybrids, and one heavily inoculated hybrid) were 0.4, 2.3, and 1.1 g of N2/ha per day, respectively. Lower rates of C2H2 reduction were associated with control corn cultures which had been treated with autoclaved Spirillum than with cultures inoculated with live Spirillum. No C2H2 reduction was detected in plant cultures treated with ammonium nitrate. Numbers of nitrogen-fixing bacteria on excised roots of corn plants increased an average of about 30-fold during an overnight preincubation period, and as a result acetylene reduction assays of root samples after preincubation failed to serve as a valid basis for estimating N2 fixation by corn in pot cultures. Plants grown without added nitrogen either with or without inoculum exhibited severe symptoms of nitrogen deficiency and in most cases produced significantly less dry weight than those supplied with fixed nitrogen. Although substantial rates of C2H2 reduction by excised corn roots were observed after preincubation under limited oxygen, the yield and nitrogen content of inoculated plants and the C2H2-reduction rates by inoculated pot cultures of corn, in situ, provided no evidence of appreciable N2 fixation.     

耐氨固氮菌在水稻根际的存活时间

耐氮固氮菌接种水稻后,能够附着秧苗根系移动而迁移,其数量随时间增长逐渐减少,耐氨固氮菌在水稻根际存活时间早造为７—８周,晚造５—８周．它们在水稻根际附近的泥土中存在时间较短,为５周左右。初步测定结果表明,当水稻根际有耐氨固氮菌存在时,接种耐氨固氮菌的水稻根际乙炔还原活性比对照高１－２倍。     

Inoculation with the Plant-Growth-Promoting Rhizobacterium Azospirillum brasilense Causes Little Disturbance in the Rhizosphere and Rhizoplane of Maize (Zea mays)

Inoculation with Azospirillum brasilense exerts beneficial effects on plant growth and crop yields. In this study, a comparative analysis of maize (Zea mays) root inoculated or not inoculated with A. brasilense strains was performed in two soils. Colonization dynamics of the rhizobacteria were tracked in various root compartments using 16S rRNA-targeted probes and 4′,6′diamidino-2-phenylindole staining, and the structure of bacterial populations in the same samples was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction products of the 16S rRNA gene. Based on whole cell hybridization, a large fraction of the bacterial community was found to be active in both the rhizoplane–endorhizosphere and rhizosphere soil compartments, in both soil types. A DGGE fingerprint analysis revealed that plant inoculation with A. brasilense had no effect on the structural composition of the bacterial communities, which were also found to be very similar at the root tip and at zones of root branching. However, rhizobacterial populations were strongly influenced by plant age, and their complexity decreased in the rhizoplane–endorhizosphere in comparison to rhizosphere soil. A clone library generated from rhizosphere DNA revealed a highly diverse community of soil and rhizosphere bacteria, including an indigenous Azospirillum-like organism. A large proportion of these clones was only distantly related to known species. Herschkovitz and Lerner contributed equally to this work.     

Cotton roots and vitamin-requiring and amino acid-requiring bacteria

Summary The rhizosphere effects of diploid and amphidiploid strains of cotton in black cotton soils have been investigated with reference to vitamin-requiring bacteria and amino acid-requiring bacteria. Influence of cotton roots on amino acid-requiring bacteria was found to be greater than on vitamin-requiring bacteria. The rhizosphere effects of diploid strains were greater than those of amphidiploid strains. The effects were also influenced by the initial proportions of these bacterial groups in the two soils. The rhizosphere effects of inoculated plants were lower than the respective healthy controls; but those of apparently healthy (disease escapes) diploid plants and those of inoculated amphidiploid plants in PLD soil (wilt-sick) were strikingly higher than the healthy controls. Differences in the rhizosphere effects between diploid and amphidiploid plants could be correlated with the amino acid and vitamin exudations by roots of these strains, but not with reference to soil types.Part of Doctoral Thesis, University of Madras.     

Characterization of bacterial endophytes of sweet potato plants

Endophytic bacteria associated with sweet potato plants (Ipomoea batatas (L.) Lam.) were isolated, identified and tested for their ability to fix nitrogen, produce indole acetic acid (IAA), and exhibit stress tolerance. Eleven different strains belonging to the genera, Enterobacter, Rahnella, Rhodanobacter, Pseudomonas, Stenotrophomonas, Xanthomonas and Phyllobacterium, were identified. Four strains were shown to produce IAA (a plant growth hormone) and one strain showed the ability to grow in nitrogen free medium and had the nitrogenase subunit gene, nifH. To determine if IAA production by the endophytes had any role in protecting the cells against adverse conditions, different stress tests were conducted. The IAA producer grew well in the presence of some antibiotics, UV and cold treatments but the response to pH, osmotic shock, thermal and oxidative treatments was the same for both the IAA producer and the no IAA producer. To determine if IAA produced by the strains was biologically relevant to plants, cuttings of poplar were inoculated with the highest IAA producing strain. The inoculated cuttings produced roots sooner and grew more rapidly than uninoculated cuttings. These studies indicate that endophytes of sweet potato plants are beneficial to plant growth.     

Evaluation of host and pathogen responses for screening soil amendments to control Sclerotium rolfsii

Three strains of Bradyrhizobium, 280A, 2209A and 32H1, that nodulated peanuts (Arachis hypogaea L.), were tested for their ability to grow and survive at elevated temperatures of up to 42°C in laboratory culture. Strain 32H1 was unable to grow at 37°C and was more sensitive to elevated temperatures than the other two strains. All three produced heat-shock proteins of molecular weights 17 kDa and 18 kDa. Two greenhouse experiments were conducted to determine the effect of high root temperature on nodulation, growth and nitrogen fixation of peanut. Two peanut varieties (Virginia cv NC7 and Spanish cv Pronto) were inoculated and exposed to root temperatures of 30°, 37° and 40°C. Nodulation and nitrogen fixation were strongly affected by root temperature but there was no variety × temperature interaction. At a constant 40°C root temperature no nodules were formed. Nodules were formed when roots were exposed to this temperature with diurnal cycling but no nitrogen fixation occurred. Highest plant dry weight, shoot nitrogen content and total nitrogen were observed at a constant root temperature of 30°C. Increasing root temperature to 37°C reduced average nitrogen content by 37% and total nitrogen by 49% but did not reduce nodulation. The symbiotic performance of the strains corresponded to their abilities to grow and survive at high temperature in culture.     

Susceptibility of Paulownia elongata to Agrobacterium and production of transgenic calli and hairy roots by in vitro inoculation

Susceptibility of Paulownia elongata S.Y. Hu (princess tree) to Agrobacterium tumefaciens and A. rhizogenes was demonstrated by inoculating in vitro shoots. Shoots had a gall formation frequency of ≥83% when inoculated with any of three A. tumefaciens strains (542, A281, or C58). Timing of gall appearance and type of callus proliferation differed among A. tumefaciens strains. Rapidly proliferating callus was produced from explants that were inoculated with A. tumefaciens. Hairy roots were produced directly from wound sites on 33% of shoots inoculated with A. rhizogenes strain R1601. Rapidly growing detached roots were produced from explants that were inoculated with A. rhizogenes. Opine analyses demonstrated the expression of foreign genes in proliferating galls/hairy roots shortly after emergence from wound sites and in callus and roots after 12 weeks of in vitro culture. Southern analyses demonstrated the presence of tDNA in long-term callus and root cultures. This revised version was published online in June 2006 with corrections to the Cover Date.     

Soil-plant compartments affect fungal microbiome diversity and composition in grapevine

Plant compartments provide unique niches that lead to specific microbial associations. The microbiota colonizing the endophytic compartment (endorhizosphere) and the rhizosphere contribute to productivity, plant growth, phytoremediation and carbon sequestration. The main objective of this study was to investigate how fungal communities are enriched in different habitats outside and inside of grapevine roots. For this purpose, the spatial dynamics of the fungal communities associated with three soil-plant compartments (bulk soil, rhizosphere and endorhizosphere) were characterized by ITS high-throughput amplicon sequencing (HTAS). Fungal communities were largely affected in their diversity and composition by soil-plant compartments, whereas the spatial variation (i.e. across five vineyards) was low. The endorhizosphere compartment differed most from the other two, suggesting that the root tissues entail a barrier for fungal colonization. The results of functional prediction via FUNGuild suggested an increase in the relative abundances of potential plant pathogens, endophytes and arbuscular mycorrhiza, and a decrease in wood, dung and undefined saprotrophs from bulk soil towards the endorhizosphere. Roots of asymptomatic vines were a microbial niche that is inhabited by soilborne fungi associated with grapevine trunk diseases, which opens up new perspectives in the study of the endophytic role of these pathogens on grapevines. Results obtained in this study provide helpful information to better know how the host shapes its microbiome and the implications for vineyard productivity and management.