Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.     

Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure

Plant-soil feedbacks are gaining attention for their ability to determine plant community development. Plant-soil feedback models and research assume that plant-soil interactions occur within days to weeks, yet, little is known about how quickly and to what extent plants change soil community composition. We grew a dominant native plant (Pseudoroegneria spicata) and a dominant non-native plant (Centaurea diffusa) separately in both native- and non-native-cultivated field soils to test if these species could overcome soil legacies and create new soil communities in the short-term. Soil community composition before and after plant growth was assessed in bulk and rhizosphere soils using phospholipid fatty acid analyses. Nematode abundance and mycorrhizal colonization were also measured following plant growth. Field-collected, native-cultivated soils showed greater bacterial, Gram (−), fungal, and arbuscular mycorrhizal PLFA abundance and greater PLFA diversity than field-collected, non-native-cultivated soils. Both plant species grew larger in native- than non-native-cultivated soils, but neither plant affected microbial composition in the bulk or rhizosphere soils after two months. Plants also failed to change nematode abundance or mycorrhizal colonization. Plants, therefore, appear able to create microbial legacies that affect subsequent plant growth, but contrary to common assumptions, the species in this study are likely to require years to create these legacies. Our results are consistent with other studies that demonstrate long-term legacies in soil microbial communities and suggest that the development of plant-soil feedbacks should be viewed in this longer-term context.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

黑土区大豆基因型的根际细菌群落结构时空动态变化

The dynamics of rhizosphere microbial communities is important for plant health and productivity, and can be influenced by soil type, plant species or genotype, and plant growth stage. A pot experiment was carried out to examine the dynamics of microbial communities in the rhizosphere of two soybean genotypes grown in a black soil in Northeast China with a long history of soybean cultivation. The two soybean genotypes, Beifeng 11 and Hai 9731, differing in productivity were grown in a mixture of black soil and siliceous sand. The bacterial communities were compared at three zone locations including rhizoplane, rhizosphere, and bulk soil at the third node (V3), early flowering (R1), and early pod (R3) stages using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rDNA. The results of principal component analyses (PCA) showed that the bacterial community structure changed with growth stage. Spatially, the bacterial communities in the rhizoplane and rhizosphere were significantly different from those in the bulk soil. Nevertheless, the bacterial communities in the rhizoplane were distinct from those in the rhizosphere at the V3 stage, while no obvious differences were found at the R1 and R3 stages. For the two genotypes, the bacterial community structure was similar at the V3 stage, but differed at the R1 and R3 stages. In other words, some bacterial populations became dominant and some others recessive at the two later stages, which contributed to the variation of the bacterial community between the two genotypes. These results suggest that soybean plants can modify the rhizosphere bacterial communities in the black soil, and there existed genotype-specific bacterial populations in the rhizosphere, which may be related to soybean productivity.     

The bacterial community of tomato rhizosphere is modified by inoculation with arbuscular mycorrhizal fungi but unaffected by soil enrichment with mycorrhizal root exudates or inoculation with Phytophthora nicotianae

Arbuscular mycorrhizal (AM) fungi have been shown to induce the biocontrol of soilborne diseases, to change the composition of root exudates and to modify the bacterial community structure of the rhizosphere, leading to the formation of the mycorrhizosphere. Tomato plants were grown in a compartmentalized soil system and were either submitted to direct mycorrhizal colonization or to enrichment of the soil with exudates collected from mycorrhizal tomato plants, with the corresponding negative controls. Three weeks after planting, the plants were inoculated or not with the soilborne pathogen Phytophthora nicotianae growing through a membrane from an adjacent infected compartment. At harvest, a PCR-Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments amplified from the total DNA extracted from each plant rhizosphere was performed. Root colonization with the AM fungi Glomus intraradices or Glomus mosseae induced significant changes in the bacterial community structure of tomato rhizosphere, compared to non-mycorrhizal plants, while enrichment with root exudates collected from mycorrhizal or non-mycorrhizal plants had no effect. Our results support that the effect of AM fungi on rhizosphere bacteria would not be mediated by compounds present in root exudates of mycorrhizal plants but rather by physical or chemical factors associated with the mycelium, volatiles and/or root surface bound substrates. Moreover, infection of mycorrhizal or non-mycorrhizal plants with P. nicotianae did not significantly affect the bacterial community structure suggesting that rhizosphere bacteria would be less sensitive to the pathogen invasion than to mycorrhizal colonization. Of 96 unique sequences detected in the tomato rhizosphere, eight were specific to mycorrhizal fungi, including two Pseudomonas, a Bacillus simplex, an Herbaspirilium and an Acidobacterium. One Verrucomicrobium was common to rhizospheres of mycorrhizal plants and of plants watered with mycorrhizal root exudates.     

Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions

Soil microbial community composition is determined by the soil type and the plant species. By sequencing the V3-V4 region of the bacterial 16S rRNA gene amplicons, the current study assessed the bacterial community assemblage in rhizosphere and bulks soils of wild (Glycine soja) and cultivated (Glycine max) soybeans grown in the suspensions of three important soil types in China, including black, red and soda-saline-alkali soils. The alpha-diversity of the bacterial community in the rhizosphere was significantly higher than that of the bulk soils suggesting that bulk soil lacks plant nurturing effect under the current study conditions. Black and red soils were enriched with nitrifying and nitrogen-fixing bacteria but the soda-saline-alkali soil suspension had more denitrifying bacteria, which may reflect agronomic unsuitability of the latter. We also observed a high abundance of Bradyrhizobium and Pseudomonas, enriched cellulolytic bacteria, as well as a highly connected molecular ecological network in the G. soja rhizosphere soil. Taken all, the current study suggest that wild soybeans may have evolved to recruit beneficial microbes in its rhizosphere that can promote nutrients requisition, biostasis and disease-resistance, therefore ecologically more resilient than cultivated soybeans.     

Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth

When plants establish in novel environments, they can modify soil microbial community structure and functional properties in ways that enhance their own success. Although soil microbial communities are influenced by abiotic environmental variability, rhizosphere microbial communities may also be affected by plant activities such as nutrient uptake during the growing season. We predicted that during the growing season, plant N uptake would explain much of the variation in rhizosphere microbial community assembly and functional traits. We grew the invasive C₃ grass Bromus tectorum and three commonly co-occurring native C₃ grasses in a controlled greenhouse environment, and examined rhizosphere bacterial community structural and functional characteristics at three different plant growth stages. We found that soil N availability and plant tissue N levels strongly correlated with shifts in rhizosphere bacterial community structure. It also appeared that the rapid drawdown of soil nutrients in the rhizosphere during the plant growing season triggered a selection event whereby only those microbes able to tolerate the changing nutrient conditions were able to persist. Plant N uptake rates inversely corresponded to microbial biomass N levels during periods of peak plant growth. Mechanisms which enable plants to influence rhizosphere bacterial community structure and function are likely to affect their competitive ability and fitness. Our study suggests that plants can alter their rhizosphere microbiomes through influencing nutrient availability. The ways in which plants establish their rhizosphere bacterial communities may now be viewed as a selection trait related to intrinsic plant species nutrient demands.     

Soil microbial dynamics and genetic diversity in soil under monoculture wheat grown in different long-term management systems

Organic matter incorporation into soil can increase nutrient availability to plants but it can affect soil microbial communities. These in turn influence soil fertility and plant growth. Soil biochemical and microbiological properties are indicators of soil quality, but there is still no consensus as to how these should be used. Recent developments in molecular biology have provided new tools to obtain a view of the whole microbial community. The long-term impact of crop residue management on the microbial biomass, and on the activity and community structure of soil bacteria was evaluated in a clay soil of Southern Italy, where a monoculture of durum wheat (Triticum durum Desf.) was grown in semiarid conditions, and burning or incorporation of post harvest plant residues were typical practices. The role of N-mineral fertilization, simultaneously with the ploughing in of crop residues and during the plant growth cycle was also investigated. Total bacterial counts of viable cells, biomass C, ATP content of soil microorganisms, genetic fingerprinting of the total eubacterial community and of ammonia oxidizers were evaluated. Burning and incorporation did not affect microbial biomass C, ATP content, and total bacterial counts of viable cells although statistically relevant changes were detected among rhizosphere and bulk soil samples regardless of the crop residue management used. Molecular fingerprinting confirmed that: no significant change in the composition and diversity of total bacteria, as well as of ammonia oxidizers was induced by the crop residue managements; that soil bacteria were more sensitive to N fertilizer application during the plant growth cycle; and that rhizosphere soil samples were significantly different from those of the bulk soil. As microbiological and genetic factors related to soil fertility were not affected significantly, the long-term incorporation of crop residues, under the field conditions investigated, is a sustainable practice to manage post-harvest residues.     

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

In both managed and natural ecosystems, beneficial plant-associated bacteria play a key role in supporting and/or increasing plant health and growth. Plant growth-promoting bacteria (PGPB) can be applied in agricultural production or for the phytoremediation of pollutants. However, because of their capacity to confer plant beneficial effects, efficient colonization of the plant environment is of utmost importance. The majority of plant-associated bacteria derives from the soil environment. They may migrate to the rhizosphere and subsequently the rhizoplane of their hosts before they are able to show beneficial effects. Some rhizoplane colonizing bacteria can also penetrate plant roots, and some strains may move to aerial plant parts, with a decreasing bacterial density in comparison to rhizosphere or root colonizing populations. A better understanding on colonization processes has been obtained mostly by microscopic visualisation as well as by analysing the characteristics of mutants carrying disfunctional genes potentially involved in colonization. In this review we describe the individual steps of plant colonization and survey the known mechanisms responsible for rhizosphere and endophytic competence. The understanding of colonization processes is important to better predict how bacteria interact with plants and whether they are likely to establish themselves in the plant environment after field application as biofertilisers or biocontrol agents.     

Impact of fresh root material and mature crop residues of oilseed rape (Brassica napus) on microbial communities associated with subsequent oilseed rape

Glasshouse bioassays were conducted to assess the impact of different inputs of oilseed rape plant material on soil and rhizosphere microbial diversity associated with subsequently grown oilseed rape (Brassica napus) plants. The first bioassay focussed on the effect of oilseed rape rhizodeposits and fresh detached root material on microbial communities, in a rapid-cycling experiment in which oilseed rape plants were grown successively in pots of field soil for 4 weeks at a time, with six cycles of repeated vegetative planting in the same pot. Molecular analyses of the microbial communities after each cycle showed that the obligate parasite Olpidium brassicae infected the roots of oilseed rape within 4 weeks after the first planting (irrespective of the influence of rhizodeposits alone or in the presence of fresh detached root material), and consistently dominated the rhizosphere fungal community, ranging in relative abundance from 43 to 88 % when oilseed rape was grown more than once in the same soil. Fresh detached root material also led to a reduction in diversity within the soil fungal community, due to the increased relative abundance of O. brassicae. In addition, rhizosphere bacterial communities were found to have a reduced diversity over time when fresh root material was retained in the soil. In the second glasshouse experiment, the effect of incorporating mature, field-derived oilseed rape crop residues (shoots and root material) on microbial communities associated with subsequently grown oilseed rape was investigated. As before, molecular analyses revealed that O. brassicae dominated the rhizosphere fungal community, despite not being prevalent in either the residue material or soil fungal communities.     

Proteomic studies of plant-bacterial interactions

Plants and bacteria can interact with one another in a variety of different ways. The interaction may be beneficial, harmful or neutral for the plant, and sometimes the impact of a bacterium may vary as the soil conditions change. While a number of different soil bacteria are phytopathogenic, the majority of the more agronomically important plant disease-causing soil microorganisms are fungi. On the other hand, plant growth-promoting bacteria are typically of three general types: those that form a symbiotic relationship with the plant, those that are endophytic and colonize the inner tissues of the plant, and those of soil bacteria, which have competitive abilities to colonize efficiently the rhizosphere and the surface of plant roots.While there have been significant advances in elucidating the mechanistic details of plant-bacterial interactions in recent years, many fundamental questions about these processes remain. Unfortunately, studies that focus on only a single biochemical pathway or mechanism often miss the multiplicity of effects that plants and bacteria have on one another, motivating the employment of broader proteome-wide approaches. On the other hand, using proteomics technology including high-resolution two-dimensional gel electrophoresis (2-DE) and high-sensitivity mass spectrometry (MS), it is possible to gain greater insight into the detailed impact that plants and soil bacteria have on one another.In this regard, of all of the proteomic studies of plant-bacterial interactions, the symbiotic interaction between nitrogen-fixing bacteria and legumes has been studied in the greatest detail. Studies of the proteome of plant-pathogen interactions have also received considerable attention. However, there are currently very few proteomic studies of endophytic and rhizosphere associated plant growth promoting bacteria.Here, some fundamental proteomic tools are introduced and the applications of one of these approaches (i.e., 2-DE coupled to MS) to the study of plant-bacterial interactions are discussed. This review specifically addresses the questions: what are the impacts of plants on the bacterial proteomes, and vice versa?     

Structural differences in the rhizosphere communities of legumes are not equally reflected in community-level physiological profiles

The relationship of structural diversity and differences in the functional potentials of rhizosphere communities of alfalfa, common bean and clover was investigated in microcosms. PCR-SSCP (single strand conformation polymorphism) analysis of 16S rRNA genes revealed significant differences in the composition of the leguminous rhizosphere communities at the shoot stage of plants grown in the same soil. Sequencing of dominant SSCP-bands indicated the presence of plant specific organisms. The partial rRNA gene sequences were related to members of the α- and γ-Proteobacteria, Bacteroidetes and Actinobacteria. Besides the plant species, the soil also affected the structural diversity in rhizospheres. The dominant bacterial populations of alfalfa grown in soils with different agricultural histories were assigned to different taxonomic groups. Addressing the functional potentials, community-level physiological profiles (CLPP) were generated using BIOLOG GN^®. The three leguminous rhizosphere communities could be differentiated by principle component analysis, though the overall analysis indicated that the metabolic potential of all rhizosphere samples was similar. The functional variation examined in rhizospheres of alfalfa was minor in response to the soil origin and was found not to be significant different at different growth stages. The results indicate that similar functional potentials may be provided by structurally different bacterial communities.     

不同年限毛竹林土壤固氮菌群落结构和丰度的演变

应用变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)和荧光定量PCR(real time fluorescent quantitative PCR,q PCR)方法研究了不同年限毛竹林土壤固氮菌群落结构和丰度的变化。结果表明:土壤p H、有机质、有效磷、速效钾和铵态氮含量在马尾松林改造成毛竹林5 a后明显提高,而后逐渐降低,并趋于稳定;土壤固氮菌多样性和nif H基因丰度也呈现相似的趋势。条带测序分析表明,毛竹林土壤固氮菌均为不可培养的固氮菌,与慢生根瘤菌(Bradyrhizobium sp.)具有较高的相似度。冗余分析结果表明,不同栽培年限毛竹林地土壤固氮菌群落组成发生了明显变化,长期栽培毛竹林引起的土壤养分变化对土壤固氮菌多样性具有重要影响。     

Shifts in soil bacterial communities associated with the potato rhizosphere in response to aromatic sulfonate amendments

Desulfonation is an important process in the sulfur cycle, through which organic sulfur compounds are mineralized, releasing S. Desulfonating bacteria are known to respond to inorganic S soil amendments. However, the extent to which these communities shift as a response to the addition of organic sulfur in the soil remains elusive. Here, we investigated how amendments of soil with inorganic or organic sulfur compounds influence the bacterial communities associated with potato, in a microcosm experiment. The soil was amended with two doses of linear alkylbenzene sulfonate (LAS), here used as a model aromatic sulfonate compound, or with sulfate. Degradation of LAS was observed already at the young plant stage, as in all treatments 10- to 50-fold reductions of the initial (background) LAS concentrations were noted. Quantitative PCR analyses showed no significant effects of treatment on the bacterial abundances, which tended to increase from the young plant to the flowering stages of plant development. The bacterial community structures, determined via PCR-DGGE, were strongly affected by the presence of plants. This rhizosphere effect became more apparent at the flowering stages. Both the bacterial and β-proteobacterial community structures were affected by the presence of LAS, but dose-related effects were not observed. LAS also caused significant changes in the community structures, as compared to those in inorganic sulfate amended soil. Sulfate did not influence the bacterial community structures and only affected the β-proteobacterial ones at the flowering stage. Surprisingly, the presence of LAS did not exert any significant effect on the abundance of the Variovorax asfA gene, although clone libraries revealed a dominance of Variovorax types in the rhizosphere, especially in the high-level LAS treatment. Our results suggest that rhizosphere communities are key players in LAS degradation in soils, and that desulfonator Variovorax spp. plays a minor role in the mineralization of aromatic sulfonates in soil cropped with potato.     

Photoperiod and Soil Munition Constituent Effects on Phytoaccumulation and Rhizosphere Interactions in Boreal Vegetation

Permafrost thaw is expected to alter biogeochemistry and hydrology, potentially increasing the mobility of soil constituents. Northern latitude boreal forests where permafrost thaw is occurring also experience extreme changes in day length during the growing season. As the effects of photoperiod on plant uptake of soil constituents or interactions with the rhizosphere are unknown, our objective was to determine these interactions with three plant species from different functional groups. A tree, forb, and grass common to military training ranges in this region were grown in soil spiked with or without lead, antimony, or 2,4-dinitrotoluene and grown under 16, 20, or 24 h of light. Plant biomass, soil constituent uptake, and rhizosphere bacterial communities were compared between treatments. Photoperiod had no effect on plant uptake of any soil constituent or on rhizosphere community, indicating that plants and their associated microbial communities adapted to this environment are resilient to extremes in photoperiod. Lead uptake was not significant in any plant species and had no effect on the rhizosphere. Antimony increased the percentage composition of Saprospirales in the rhizospheres of two of the three plants, indicating an interaction between this bacterial order and antimony. Antimony uptake by white spruce (Picea glauca) was considerable, with a mean concentration of 1731 mg kg^?1 in roots, while mean shoot concentration was only 155 mg kg^?1, indicating its potential to phytostabilize this heavy metal. Although antimony had the strongest impact on the rhizosphere bacterial community, it was also readily accumulated by the grass and tree.     

Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage

Three experiments were conducted in this study in order to investigate the impacts of soil type, soybean genotype, and the reproductive growth stage on bacterial communities in the soybean rhizosphere. Communities were evaluated by principal component analysis of denaturing gradient gel electrophoresis (DGGE) banding patterns and sequencing of partial 16S rDNA polymerase chain reaction (PCR) amplicons. A pot experiment analyzing three soybean genotypes grown in two different types of soil (Black soil and Dark Brown soil) indicated that soil type was the major factor in influencing the bacterial communities in the soybean rhizosphere, with a more significant effect observed in the Black soil samples than in the Dark Brown soil samples. A field experiment was conducted in Dark Brown soil using three soybean genotypes, and the results gleaned from both pot and field experiments indicated that bacterial communities in the soybean rhizosphere changed with growth stages, and higher number of DGGE bands observed in early reproductive growth stages, while surprisingly, a significant impact of genotype on the bacterial communities was not observed in these experiments. However, a plate culture experiment targeting the culturable bacterial communities detected a remarkable difference in the community structures of the rhizosphere between the two soybean genotypes, suggesting that a small portion of the total bacteria was influenced by genotype. Sequence analysis of DGGE bands indicated that bacterial phyla of Proteobacteria, Actinobacteria, Bacteroidetes, Nitrospirae, Firmicutes, Verrucomicrobia and Acidobacteria commonly inhabit the soybean rhizosphere.     

土壤与基质栽培系统对生菜(Lactuca sativa)根际细菌群落的影响

以生菜(Lactuca sativa)"申选5号"与"罗莎红"为材料,采用PCR-DGGE和Real-Time PCR技术,分析了土壤栽培系统和基质栽培系统根际细菌群落的差异。Real-Time PCR检测结果表明,基质栽培的两个生菜品种根际细菌数量均显著高于土壤(P0.05);PCR-DGGE图谱条带结果表明,根际细菌群落多样性基质高于土壤。栽培系统是造成多样性差异的主要原因,但也与品种有关:"申选5号"基质的Shannon-Wiener指数(H),Simpson指数(D)和均匀度(E)均显著高于土壤(P0.05);"罗莎红"基质的H显著高于土壤,而D和E无显著差异。结合土壤和基质理化性质的RDA分析结果,土壤和基质具有不同的细菌群落,p H值与硝态氮是塑造根际细菌群落的主要因子,含水量、碳氮比和有效磷与细菌群落的形成呈正相关。     

The mycorrhizal fungus (Glomus intraradices) affects microbial activity in the rhizosphere of pea plants (Pisum sativum)

Pea plants were grown in γ-irradiated soil in pots with and without addition of the AM fungus Glomus intraradices at sufficient N and limiting P. Depending on the growth phase of the plant presence of AM had negative or positive effect on rhizosphere activity. Before flowering during nutrient acquisition AM decreased rhizosphere respiration and number of protozoa but did not affect bacterial number suggesting top-down regulation of bacterial number by protozoan grazing. In contrast, during flowering and pod formation AM stimulated rhizosphere respiration and the negative effect on protozoa decreased. AM also affected the composition of the rhizosphere bacterial community as revealed from DNA analysis (DGGE). With or without mycorrhiza, rhizosphere respiration was P-limited on very young roots, not nutrient limited at more mature roots and C-limited at withering. This suggests changes in the rhizosphere community during plant growth also supported by changes in the bacteria (DGGE).     

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.     

黄河三角洲刺槐根际与非根际细菌结构及多样性

为精确分析黄河三角洲刺槐根际与非根际土壤细菌群落定殖情况,本研究采用高通量测序方法对刺槐根际与非根际土壤细菌结构及多样性进行了研究。研究表明,根际土壤细菌共有36门214属,非根际土壤细菌共有33门153属。变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)细菌丰度超过15%,是根际与非根际土壤中的优势菌落。根际与非根际土壤中酸杆菌门、硝化螺旋菌门(Nitrospirae)丰度差异显著。根际土壤中红游动菌属(Rhodoplanes)、溶杆菌属(Lysobacter)、热单胞菌属(Thermomonas)、链霉菌属(Streptomyces)及非根际土壤中红游动菌属、溶杆菌属、链霉菌属、Kaistobacter细菌丰度超过4%。根际土壤中固氮菌丰度显著高于非根际土壤,解磷、解钾细菌丰度差异不显著。根际与非根际土壤细菌Chao丰富度分别为2 054、2 376,差异显著。根际与非根际土壤细菌之间的权重(Weighted Unifrac)距离在0.12~0.25之间。综上所述,黄河三角洲刺槐根际与非根际土壤细菌结构具有一定差异,多样性差异显著。