Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds.     

Impact of Endochitinase-Transformed White Spruce on Soil Fungal Biomass and Ectendomycorrhizal Symbiosis

The impact of transgenic white spruce [Picea glauca (Moench) Voss] containing the endochitinase gene (ech42) on soil fungal biomass and on the ectendomycorrhizal fungi Wilcoxina spp. was tested using a greenhouse trial. The measured level of endochitinase in roots of transgenic white spruce was up to 10 times higher than that in roots of nontransformed white spruce. The level of endochitinase in root exudates of three of four ech42-transformed lines was significantly greater than that in controls. Analysis soil ergosterol showed that the amount of fungal biomass in soil samples from control white spruce was slightly larger than that in soil samples from ech42-transformed white spruce. Nevertheless, the difference was not statistically significant. The rates of mycorrhizal colonization of transformed lines and controls were similar. Sequencing the internal transcribed spacer rRNA region revealed that the root tips were colonized by the ectendomycorrhizal fungi Wilcoxina spp. and the dark septate endophyte Phialocephala fortinii. Colonization of root tips by Wilcoxina spp. was monitored by real-time PCR to quantify the fungus present during the development of ectendomycorrhizal symbiosis in ech42-transformed and control lines. The numbers of Wilcoxina molecules in the transformed lines and the controls were not significantly different (P > 0.05, as determined by analysis of covariance), indicating that in spite of higher levels of endochitinase expression, mycorrhization was not inhibited. Our results indicate that the higher levels of chitinolytic activity in root exudates and root tissues from ech42-transformed lines did not alter the soil fungal biomass or the development of ectendomycorrhizal symbiosis involving Wilcoxina spp.White spruce [Picea glauca (Moench) Voss] is a tree species with an extensive distribution in boreal and subboreal forests and with significant ecological roles (37, 38). It is also an important commercial species for production of pulpwood and construction-grade lumber. However, in nurseries and plantations, white spruce is sensitive to multiple fungal diseases (23, 29, 42, 62, 76). Climate change scenarios suggest that diseases could result in increased mortality in conifer forests (22, 48). Genetic engineering offers a potential means to mitigate biotic and abiotic stresses.During the last 2 decades, chitinase genes isolated from plants, fungi, or bacteria have been studied and used to transform crops or trees in order to increase their resistance to plant-pathogenic fungi. One potential goal is improving white spruce tolerance to fungal infection through insertion of a chitinase gene. Chitin is a biopolymer of β-(1-4)-linked molecules of N-acetylglucosamine (NAG), a derivative of glucose, and is the primary constituent of the fungal cell wall and arthropod exoskeleton (3, 51). Chitinases are plant defense pathogenesis-related proteins (6, 11) that break down the chitin chain either by cleavage of internal glycoside bonds (endochitinases), by hydrolysis of the nonreducing end of the chitin chain (exochitinases), or by hydrolysis of NAG oligomers and trimers into NAG monomers (chitobiases). Endo- and exochitinase genes have been well characterized using sugar beet (Beta vulgaris) (44) and the filamentous fungal genus Trichoderma (14, 24, 69). Chitinolytic genes have been inserted into the genomes of cultivated plants and trees in an attempt to boost plant chitinase activity. Among the different genes involved in the production of chitinolytic enzymes, the ech42 endochitinase gene from Trichoderma harzianum has been inserted into plant genomes to enhance their resistance against phytopathogenic fungi. In McIntosh apple cultivars transformed with the ech42 gene there was limited attack by the apple scab fungus Venturia inaequalis (5). Transgenic black spruce (Picea mariana) expressing the ech42 gene was more resistant to the root rot pathogen Cylindrocladium floridanum (45).However, field deployment of crops and trees genetically transformed to improve nonspecific resistance against phytopathogenic fungi has raised concerns about the impact on nontarget fungi, including potentially beneficial symbionts. This is particularly worrisome when nonspecific constitutive promoters control expression of the resistance gene and the gene is expressed in all tissues from roots to leaves. As a consequence, the natural colonization of such transformed plants by endophytic or mycorrhizal fungi can be altered.Mycorrhizal fungi play a key role in plant nutrition (55) by mobilizing and transferring nutrients to the host through an intimate and highly organized association with plant roots (52, 63). Furthermore, their involvement in soil nutrient recycling (56) makes mycorrhizal symbiosis a major ecological process that is important for the health of soil and forest ecosystems. Crops, fruits, and forest trees exhibit mycorrhizal colonization by arbuscular mycorrhizae, ectomycorrhizae, and ectendomycorrhizae (EEM). While numerous studies have addressed the impact of transgenic plants on arbuscular mycorrhizae (10, 26, 64, 68, 72, 73) and ectomycorrhizae (32, 43, 50, 60), no previous study focused on EEM.Ectendomycorrhizal fungi can be distinguished from ectomycorrhizae by the presence of a thin or fragmented mantle and intracellular penetration into root cortical cells. All EEM fungi identified so far belong to the Ascomycetes, and these fungi are represented by several genera of Helotiales and Pezizales (77). EEM fungi are prevalent in conifer and deciduous tree nurseries (27, 39, 40, 70) and are also very common on seedling root tips at disturbed sites (15, 16, 19). The prevalence of EEM fungi on seedling roots, from which the genus Wilcoxina is frequently recovered (16, 67), suggests that they can play a significant role in establishment and growth of seedlings (77) and provide protection against root diseases (31, 61). Consequently, the potentially negative effects of chitinase-transformed trees on ectendomycorrhizal fungi could be detrimental to plant health.The present study addressed the potential impact of ech42-transformed white spruce on soil fungal biomass and ectendomycorrhizal symbiosis. It was hypothesized that (i) the soil fungal biomass in a transgenic white spruce rhizosphere is less than the soil fungal biomass in a control tree rhizosphere and (ii) the development of Wilcoxina spp. on root tips of transgenic white spruce is less important than the development of Wilcoxina spp. on root tips of control trees. To test these hypotheses, 5-year-old white spruce trees transformed with the 35S promoter-ech42 construct were analyzed by performing a greenhouse trial. The amount of soil fungal biomass was estimated using measurements of ergosterol in soil. A real-time PCR method was developed to detect changes in the quantity of ectendomycorrhizal hyphae involved in colonization of transgenic white spruce root tips.     

Accelerated Transformation and Binding of 2,4,6-Trinitrotoluene in Rhizosphere Soil

Enhanced microbial activity and xenobiotic transformations take place in the rhizosphere. Degradation and binding of 2,4,6-trinitrotoluene (TNT) were determined in two rhizosphere soils (RS) and compared to respective unplanted control soils (CS). The rhizosphere soils were obtained after growing corn for 70 d in soils containing 2.8% (Soil A) or 5.9% (Soil B) organic matter. Aerobically agitated soil slurries (3:1, solution/soil) were prepared from RS and CS and amended with 75 mg TNT L^-1 (¹⁴C-labeled). TNT degraded more rapidly and formed more un-extractable bound residue in RS than in CS. In Soil A, total extractable TNT decreased from 225 to 1.0 mg kg^-1 in RS, whereas 11 mg kg^-1 remained in CS after 15 d. Unextractable bound ¹⁴C residues accounted for 40% of the added ¹⁴C-TNT in RS and 28% in CS. The smaller differences in Soil B were attributed partially to the higher organic matter content. The predominant TNT degradation products were monoaminodinitrotoluenes (ADNT), which accumulated and disappeared more rapidly in RS than in CS, and hydroxylaminodinitrotoluenes (HADNT). When sterilized by γ-irradiation, no significant differences between RS and CS were observed in TNT loss or bound residue formation. More rapid TNT degradation and enhanced bound residue formation in the unsterilized RS was attributed to micro-bial-facilitated production and transformation of HADNT and ADNT, which are potential precursors to bound residue formation. If plants can be established on TNT-contaminated soil, these results indicate that the rhizosphere can accelerate reductive transformation of TNT and promote bound residue formation.     

Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil

Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and chiA genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of chiA gene types in soil is enormous and (i) that different chiA gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in the immediate response to the added chitin (based on 16S rRNA gene abundance and chiA gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.     

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.     

Spatial Patterns of Soil Microbial Communities in a Norway Spruce (Picea abies) Plantation

The phospholipid fatty acid (PLFA) profiles of soil microbial communities were determined in relation to the patterns of tree cover in a mature Norway spruce plantation. Replicate samples of the surface organic layers were taken close to the trunk, at 1 m and at 2 m (under the edge of the canopy) beneath five trees. Samples were analyzed for standard PLFAs to assess the initial composition of the microbial communities. Replicate samples were then incubated under constant or fluctuating moisture conditions for 30 d to test the hypothesis that the patterns of microbial community structure (or its physiological state) might be determined by biophysical conditions under the tree canopies. The PLFA profiles near the trunks and at 2 m were similar, but samples taken 1 m from the bases of the trees contained lower concentrations of polyunsaturated (fungal) and monounsaturated PLFAs, and higher concentrations of saturated PLFAs. These differences in PLFA profiles were maintained during laboratory incubation under a regime of drying and wetting cycles, but there was some evidence of convergence in community structure under constant moisture conditions resulting from significant increases and decreases in specific bacterial PLFA concentrations. There were no effects of either moisture treatment on fungal PLFA concentrations. It is concluded that variation in the soil biophysical environment beneath the tree canopies resulted in the differentiation of spatially defined bacterial communities that were tolerant of moisture stress. The anomaly that differences in community structure were largest at an intermediate position of 1 m between the trunk and below the canopy edge was not explained but may relate to tree root distribution.     

Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (Picea mariana) Seedlings Grown in a Nursery

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.     

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.     

Genetic and Phenotypic Diversity of Bacillus polymyxa in Soil and in the Wheat Rhizosphere

Diversity among 130 strains of Bacillus polymyxa was studied; the bacteria were isolated by immunotrapping from nonrhizosphere soil (32 strains), rhizosphere soil (38 strains), and the rhizoplane (60 strains) of wheat plantlets growing in a growth chamber. The strains were characterized phenotypically by 63 auxanographic (API 50 CHB and API 20B strips) and morphological features, serologically by an enzyme-linked immunosorbent assay, and genetically by restriction fragment length polymorphism (RFLP) profiles of total DNA in combination with hybridization patterns obtained with an rRNA gene probe. Cluster analysis of phenotypic characters by the unweighted pair group method with averages indicated four groups at a similarity level of 93%. Clustering of B. polymyxa strains from the various fractions showed that the strains isolated from nonrhizosphere soil fell into two groups (I and II), while the third group (III) mainly comprised strains isolated from rhizosphere soil. The last group (IV) included strains isolated exclusively from the rhizoplane. Strains belonging to a particular group exhibited a similarity level of 96%. Serological properties revealed a higher variability among strains isolated from nonrhizosphere and rhizosphere soil than among rhizoplane strains. RFLP patterns also revealed a greater genetic diversity among strains isolated from nonrhizosphere and rhizosphere soil and therefore could not be clearly grouped. The RFLP patterns of sorbitol-positive strains isolated from the rhizoplane were identical. These results indicate that diversity within populations of B. polymyxa isolated from nonrhizosphere and rhizosphere soil is higher than that of B. polymyxa isolated from the rhizoplane. It therefore appears that wheat roots may select a specific subpopulation from the soil B. polymyxa population.     

No Evidence of an Impact on the Rhizosphere Diazotroph Community by the Expression of Bacillus thuringiensis Cry1Ab Toxin by Bt White Spruce

Nitrogen fixation is one of the most important roles played by soil bacterial communities, as fixation supplies nitrogen to many ecosystems which are often N limited. As impacts on this functional group of bacteria might harm the ecosystem's health and reduce productivity, monitoring that particular group is important. Recently, a field trial with Bt white spruce, which constitutively expresses the Cry1Ab insecticidal toxin of Bacillus thuringiensis, was established. The Bt white spruce was shown to be resistant to spruce budworm. We investigated the possible impact of these genetically modified trees on soil nitrogen-fixing bacterial communities. The trial consisted of untransformed controls, GUS white spruce (transformed with the β-glucuronidase gene), and Bt/GUS white spruce (which constitutively expresses both the Cry1Ab toxin and β-glucuronidase) in a random design. Four years after planting, soil samples from the control and the two treatments from plantation as well as from two natural stands of white spruce were collected. Diazotroph diversity was assessed by extracting soil genomic DNA and amplifying a region of the nitrogenase reductase (nifH) gene, followed by cloning and sequencing. Analysis revealed that nitrogen-fixing communities did not differ significantly among the untransformed control, GUS white spruce, and Bt/GUS white spruce. Nevertheless, differences in diazotroph diversity were observed between white spruce trees from the plantation site and those from two natural stands, one of which grew only a few meters away from the plantation. We therefore conclude, in the absence of evidence that the presence of the B. thuringiensis cry1Ab gene had an effect on diazotroph communities, that either site and/or field preparation prior to planting seems to be more important in determining diazotroph community structure than the presence of Bt white spruce.     

Alteration of Soil Carbon Pools and Communities of Mycorrhizal Fungi in Chaparral Exposed to Elevated Carbon Dioxide

We examined the effects of atmospheric carbon dioxide (CO₂) enrichment on belowground carbon (C) pools and arbuscular mycorrhizal (AM) fungi in a chaparral community in southern California. Chambers enclosing intact mesocosms dominated by Adenostoma fasciculatum were exposed for 3.5 years to CO₂ levels ranging from 250 to 750 ppm. Pools of total C in bulk soil and in water-stable aggregates (WSA) increased 1.5- and threefold, respectively, between the 250- and 650-ppm treatments. In addition, the abundance of live AM hyphae and spores rose markedly over the same range of CO₂, and the community composition shifted toward dominance by the AM genera Scutellospora and Acaulospora. Net ecosystem exchange of C with the atmosphere declined with CO₂ treatment. It appears that under CO₂ enrichment, extra C was added to the soil via AM fungi. Moreover, AM fungi were predominant in WSA and may shunt C into these aggregates versus bulk soil. Alternatively, C may be retained longer within WSA than within bulk soil. We note that differences between the soil fractions may act as a potential feedback on C cycling between the soil and atmosphere.     

玉米根际土壤中铜形态的动态变化

采用根垫法研究玉米根际土壤形态动态变化。结果表明：玉米生长过程中根际土壤铜形态发生显著变化。植物生长前期交换态和碳酸盐结合态铜含量逐渐增加,随后增加量减少。植物生长后期根际交换态和碳酸盐结合态铜含量低于非根际土壤。这种变化主要由根际环境变化与植物吸收引起。与根限土壤中铜形态变化,特别是交换态铜含量变化关系密切的因素包括土壤溶解性有机碳、pH和土壤微生物。随着植物生物量的增加,对铜的吸收速率不断增加,导致根限土壤中有效态铜的先增后减。     

Manipulation of Rhizosphere Bacterial Communities to Induce Suppressive Soils

Naturally occurring disease-suppressive soils have been documented in a variety of cropping systems, and in many instances the biological attributes contributing to suppressiveness have been identified. While these studies have often yielded an understanding of operative mechanisms leading to the suppressive state, significant difficulty has been realized in the transfer of this knowledge into achieving effective field-level disease control. Early efforts focused on the inundative application of individual or mixtures of microbial strains recovered from these systems and known to function in specific soil suppressiveness. However, the introduction of biological agents into non-native soil ecosystems typically yielded inconsistent levels of disease control. Of late, greater emphasis has been placed on manipulation of the cropping system to manage resident beneficial rhizosphere microorganisms as a means to suppress soilborne plant pathogens. One such strategy is the cropping of specific plant species or genotypes or the application of soil amendments with the goal of selectively enhancing disease-suppressive rhizobacteria communities. This approach has been utilized in a system attempting to employ biological elements resident to orchard ecosystems as a means to control the biologically complex phenomenon termed apple replant disease. Cropping of wheat in apple orchard soils prior to re-planting the site to apple provided control of the fungal pathogen Rhizoctonia solani AG-5. Disease control was elicited in a wheat cultivar-specific manner and functioned through transformation of the fluorescent pseudomonad population colonizing the rhizosphere of apple. Wheat cultivars that induced disease suppression enhanced populations of specific fluorescent pseudomonad genotypes with antagonistic activity toward R. solani AG-5, but cultivars that did not elicit a disease-suppressive soil did not modify the antagonistic capacity of this bacterial community. Alternatively, brassicaceae seed meal amendments were utilized to develop soil suppressiveness toward R. solani. Suppression of Rhizoctonia root rot in response to seed meal amendment required the activity of the resident soil microbiota and was associated with elevated populations of Streptomyces spp. recovered from the apple rhizosphere. Application of individual Streptomyces spp. to soil systems provided control of R. solani to a level and in a manner equivalent to that obtained with the seed meal amendment. These and other examples suggest that management of resident plant-beneficial rhizobacteria may be a viable method for control of specific soilborne plant pathogens.     

Genetic Diversity of Bacterial Communities of Serpentine Soil and of Rhizosphere of the Nickel-Hyperaccumulator Plant <Emphasis Type="Italic">Alyssum bertolonii</Emphasis>

Serpentine soils are characterized by high levels of heavy metals (Ni, Co, Cr), and low levels of important plant nutrients (P, Ca, N). Because of these inhospitable edaphic conditions, serpentine soils are typically home to a very specialized flora including endemic species as the nickel hyperaccumulator Alyssum bertolonii. Although much is known about the serpentine flora, few researches have investigated the bacterial communities of serpentine areas. In the present study bacterial communities were sampled at various distances from A. bertolonii roots in three different serpentine areas and their genetic diversity was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The obtained results indicated the occurrence of a high genetic diversity and heterogeneity of the bacterial communities present in the different serpentine areas. Moreover, TRFs (terminal restriction fragments) common to all the investigated A. bertolonii rhizosphere samples were found. A new cloning strategy was applied to 27 TRFs that were sequenced and taxonomically interpreted as mainly belonging to Gram-positive and -Proteobacteria representatives. In particular, cloned TRFs which discriminated between rhizosphere and soil samples were mainly interpreted as belonging to Proteobacteria representatives.This revised version was published online in November 2004 with corrections to Volume 48.     

伊贝根际微生物

<正>土壤微生物是土壤中最活跃的因子,一方面是土壤天然有机体的转化者,另一方面是土壤养分的源和库,与植物营养和土壤肥力密切相关,在土壤物质和能量循环转化过程中起着重要作用。在植物的整个生长期间,根系进行着活跃的代谢作用,向根外不断分泌有机物质,这些分泌物是根际微生物的重要营养和能量来源,其成分和数量影响着根际微生物的种类和繁殖。根际微生物的数量、活性和群落结构及其变化直接影响到植物吸收水分和养分。因此,植物、土壤和微生物之间存在着相互依赖、相互作用的复杂的三边关系[1-2]。     

Removal of Cyanide Contaminants from Rhizosphere Soil

Cyanide and cyanide-containing compounds from anthropogenic sources can be an environmental threat because of their potential toxicity. A remediation option for cyanide-contaminated soil may be through the use of plants and associated rhizosphere microorganimsms that have the ability to degrade cyanide compounds. Cyanogenic plant species are known to produce cyanide, but they also have the ability to degrade these compounds. In addition, the presence of these plants in soil may result in an increase in cyanide degrading microorganisms in the rhizosphere. Two cyanogenic species (Sorghum bicolor and Linum usitassium) and a noncyanogenic species (Panicum virgatum) were selected for a 200-day phytoremediation study to assess their potential use for removal of cyanide from soil. For both cyanogenic species, approximately 85% of the iron cyanide in soil was removed, whereas very little iron cyanide was removed in the unvegetated control or in the presence of Panicum virgatum. In addition, the activity of microbial communities in the rhizosphere of cyanogenic plants was higher than in cyanide-contaminated soil from unvegetated soil.     

Soil Nitrogen Availability and Plant Genotype Modify the Nutrition Strategies of M. truncatula and the Associated Rhizosphere Microbial Communities

Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM). First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability.     

Urea Transformation of Wetland Microbial Communities

Transformation of urea to ammonium is an important link in the nitrogen cycle in soil and water. Although microbial nitrogen transformations, such as nitrification and denitrification, are well studied in freshwater sediment and epiphytic biofilm in shallow waters, information about urea transformation in these environments is scarce. In this study, urea transformation of sedimentary, planktonic, and epiphytic microbial communities was quantified and urea transformation of epiphytic biofilms associated with three different common wetland macrophyte species is compared. The microbial communities were collected from a constructed wetland in October 2002 and urea transformation was quantified in the laboratory at in situ temperature (12°C) with the use of the ¹⁴C-urea tracer method, which measures the release of ¹⁴CO₂ as a direct result of urease activity. It was found that the urea transformation was 100 times higher in sediment (12–22 mmol urea-N m⁻² day⁻¹) compared with the epiphytic activity on the surfaces of the submerged plant Elodea canadensis (0.1–0.2 mmol urea-N m⁻² day⁻¹). The epiphytic activity of leaves of Typha latifolia was lower (0.001–0.03 mmol urea-N m⁻² day⁻¹), while urea transformation was negligible in the water column and on the submerged leaves of the emergent plant Phragmites australis. However, because this wetland was dominated by dense beds of the submerged macrophyte E. canadensis, this plant provided a large surface area for epiphytic microbial activity—in the range of 23–33 m² of plant surfaces per square meter of wetland. Thus, in the wetland system scale at the existing plant distribution and density, the submerged plant community had the potential to transform 2–7 mmol urea-N m⁻² day⁻¹ and was in the same magnitude as the urea transformation in the sediment.