Functional Diversity of Culturable Bacterial Communities in the Rhizosphere in Relation to Fine-root and Soil Parameters in Alder Stands on Forest, Abandoned Agricultural, and Oil-shale Mining Areas

Grey alder (Alnus incana) and black alder (Alnus glutinosa) stands on forest land, abandoned agricultural, and reclaimed oil-shale mining areas were investigated with the aim of analysing the functional diversity and activity of microbial communities in the soil–root interface and in the bulk soil in relation to fine-root parameters, alder species, and soil type. Biolog Ecoplates were used to determine community-level physiological profiles (CLPP) of culturable bacteria in soil–root interface and bulk soil samples. CLPP were summarized as AWCD (average well color development, OD 48 h⁻¹) and by Shannon diversity index, which varied between 4.3 and 4.6 for soil–root interface. The soil–root interface/bulk soil ratio of AWCD was estimated. Substrate-induced respiration (SIR) and basal respiration (BAS) of bulk soil samples were measured and metabolic quotient (Q = BAS/SIR) was calculated. SIR and Q varied from 0.24 to 2.89 mg C g⁻¹ and from 0.12 to 0.51, respectively. Short-root morphological studies were carried out by WinRHIZO^TM Pro 2003b; mean specific root area (SRA) varied for grey alder and black alder from 69 to 103 and from 54 to 155 m² kg⁻¹, respectively. The greatest differences between AWCD values of culturable bacterial communities in soil–root interface and bulk soil were found for the young alder stands on oil-shale mining spoil and on abandoned agricultural land. Soil–root interface/bulk soil AWCD ratio, ratio for Shannon diversity indices, and SRA were positively correlated. Foliar assimilation efficiency (FOE) was negatively correlated with soil–root interface/bulk soil AWCD ratio. The impact of soil and alder species on short-root morphology was significant; short-root tip volume and mass were greater for black alder than grey alder. For the investigated microbiological characteristics, no alder-species-related differences were revealed.     

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

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

两种盐生植物根际土壤细菌多样性和群落结构

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

Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants

To study the effect of plant species on the abundance and diversity of bacterial antagonists, the abundance, the phenotypic diversity, and the genotypic diversity of rhizobacteria isolated from potato, oilseed rape, and strawberry and from bulk soil which showed antagonistic activity towards the soilborne pathogen Verticillium dahliae Kleb. were analyzed. Rhizosphere and soil samples were taken five times over two growing seasons in 1998 and 1999 from a randomized field trial. Bacterial isolates were obtained after plating on R2A (Difco, Detroit, Mich.) or enrichment in microtiter plates containing high-molecular-weight substrates followed by plating on R2A. A total of 5,854 bacteria isolated from the rhizosphere of strawberry, potato, or oilseed rape or bulk soil from fallow were screened by dual testing for in vitro antagonism towards VERTICILLIUM: The proportion of isolates with antagonistic activity was highest for strawberry rhizosphere (9.5%), followed by oilseed rape (6.3%), potato (3.7%), and soil (3.3%). The 331 Verticillium antagonists were identified by their fatty acid methyl ester profiles. They were characterized by testing their in vitro antagonism against other pathogenic fungi; their glucanolytic, chitinolytic, and proteolytic activities; and their BOX-PCR fingerprints. The abundance and composition of Verticillium antagonists was plant species dependent. A rather high proportion of antagonists from the strawberry rhizosphere was identified as Pseudomonas putida B (69%), while antagonists belonging to the Enterobacteriaceae (Serratia spp., Pantoea agglomerans) were mainly isolated from the rhizosphere of oilseed rape. For P. putida A and B plant-specific genotypes were observed, suggesting that these bacteria were specifically enriched in each rhizosphere.     

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

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

Nutrient composition of Douglas-fir rhizosphere and bulk soil solutions

Rhizosphere soil solution is the direct source of nutrients for plant uptake. The nutrient composition of rhizosphere soil solution can be very different from that of bulk soil solution due to root exudation, nutrient uptake and rhizosphere microorganism activity. This study examined the nutrient composition of Douglas-fir rhizosphere soil solution in two soils belonging to the Nisqually and Pitcher soil series and compared rhizosphere solution with that of bulk soil solution. Fertilized and unfertilized Nisqually soils were also compared. Soil solutions were collected using centrifugation. Results indicated that nutrient concentrations in the rhizosphere solutions were typically higher than that of bulk soil solutions when no fertilizer was applied. Differences in the concentrations of nutrients between the rhizosphere and bulk soil solutions were masked by the addition of fertilizers. Rhizosphere solution pH also appeared to be affected by the concentration of NH₄ and NO₃ in the solution. With a higher concentration of NH₄ relative to NO₃ in the rhizosphere soil solution, the solution pH of the rhizosphere was lower than that of the bulk soil, but with a lower concentration of NH₄ relative to NO₃, the solution pH of the rhizosphere was higher than that of the bulk soil solution.     

Application of targeted metagenomics to explore abundance and diversity of CO2-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea

Sequestration of CO₂ by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO₂. Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed < 95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real‐time PCR (qRT PCR), was 9.38 ± 0.75 × 10⁷ and 5.43 ± 0.79 × 10⁸ (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO₂‐fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management.     

Plant-Dependent Genotypic and Phenotypic Diversity of Antagonistic Rhizobacteria Isolated from Different Verticillium Host Plants

To study the effect of plant species on the abundance and diversity of bacterial antagonists, the abundance, the phenotypic diversity, and the genotypic diversity of rhizobacteria isolated from potato, oilseed rape, and strawberry and from bulk soil which showed antagonistic activity towards the soilborne pathogen Verticillium dahliae Kleb. were analyzed. Rhizosphere and soil samples were taken five times over two growing seasons in 1998 and 1999 from a randomized field trial. Bacterial isolates were obtained after plating on R2A (Difco, Detroit, Mich.) or enrichment in microtiter plates containing high-molecular-weight substrates followed by plating on R2A. A total of 5,854 bacteria isolated from the rhizosphere of strawberry, potato, or oilseed rape or bulk soil from fallow were screened by dual testing for in vitro antagonism towards Verticillium. The proportion of isolates with antagonistic activity was highest for strawberry rhizosphere (9.5%), followed by oilseed rape (6.3%), potato (3.7%), and soil (3.3%). The 331 Verticillium antagonists were identified by their fatty acid methyl ester profiles. They were characterized by testing their in vitro antagonism against other pathogenic fungi; their glucanolytic, chitinolytic, and proteolytic activities; and their BOX-PCR fingerprints. The abundance and composition of Verticillium antagonists was plant species dependent. A rather high proportion of antagonists from the strawberry rhizosphere was identified as Pseudomonas putida B (69%), while antagonists belonging to the Enterobacteriaceae (Serratia spp., Pantoea agglomerans) were mainly isolated from the rhizosphere of oilseed rape. For P. putida A and B plant-specific genotypes were observed, suggesting that these bacteria were specifically enriched in each rhizosphere.     

不同品种酿酒葡萄根围、叶围微生物群落结构特点解析

【目的】了解不同品种酿酒葡萄根围、叶围细菌群落结构。【方法】以不同品种酿酒葡萄根围、叶围样品为分析材料,采用末端限制性片段长度多态性(T-RFLP)技术研究根围、叶围细菌群落结构,并对细菌群落多样性进行分析。【结果】不同品种葡萄根围微生物优势菌群为变形菌门,不同品种葡萄叶围微生物优势菌群为放线菌目。根围Simpson指数大小顺序为白福尔琼瑶浆白诗南赛美蓉白玉霓米勒长相思,Shannon指数与Simpson指数基本保持一致。叶围Simpson指数最大的为白诗南,最小的为米勒,与Shannon指数基本吻合。【结论】葡萄细菌群落结构综合多样性指数和品种以及定殖部位密切相关。     

Rooting strategy of naturally regenerated beech in Silver birch and Scots pine woodlands

This study investigated the belowground development and strategy of late-successional European beech (Fagus sylvatica L.) in ageing natural Scots pine (Pinus sylvestris L.) and Silver birch (Betula pendula Roth.) woodlands in a French volcanic mid-elevation area. For this purpose root biomass, root profile and fine-root architecture of competitor trees were examined in 53 mixed pine–beech and 42 birch–beech woodlands along a stand maturation gradient, using the root auger technique (0–75-cm). The total beech fine-root biomass highly correlated with aerial dimensions such as stem height and girth, whereas it moderately correlated with its age, thus indicating the effects of competition. Basic stand biometric data such as stand density and basal area had no significant effect on beech root biomass. Conversely, competition indices taking into account the vertical dimensions of competitor trees were efficient, probably due to redundancy with beech height. At similar age and height, beeches under birch had a greater belowground development than beeches under pine. Each species exhibited specific rooting pattern and plasticity of fine-root architecture along the gradients of stand maturation and competition. Beech had a heart-shaped rooting habit in both mixings, which strongly increased along stand maturation. Its fine-root system adopted a foraging strategy to respond to increasing stand competition. The Scots pine fine-root system was plate-like and showed a low morphological plasticity, thus presumably a conservative strategy. Silver birch exhibited a high biomass and a foraging capacity in the topsoil but a loose root system in the subsoil. The coexistence of pine and beech roots in the upper soil presumably leads to a high belowground competition. Beech root system becomes predominant throughout the soil profile and it adopts an efficient foraging strategy, but at the expense of its belowground development. Conversely, the niche partitioning strategy between beech and birch may explain why beech develops strongly belowground in spite of the fact that birch has a dense rooting and a competitive fine-root architecture. As a consequence, beech mid-term regeneration and development may be facilitated under birch as compared with pine.     

Microscale fumigation-extraction and substrate-induced respiration methods for measuring microbial biomass in barley rhizosphere

Changes in microbial biomass in the rhizosphere of young barley seedlings was studied. A fumigation-extraction (FE) method with measurement of ninhydrin-reactive nitrogen (NR-N) and a substrate-induced respiration (SIR) method were applied on a microscale to rhizosphere soil samples of approximately 0.1 g. Rhizosphere soil was defined as the soil adhering to the roots when they were carefully separated from the bulk soil. The rhizosphere soil was gently washed off the roots with either distilled water (FE) or with glucose solution (SIR). Shaking and mild sonication was used to disperse the soil without disrupting the roots. Fumigation was carried out by direct addition of liquid chloroform to the isolated soil. These techniques were proven to give reliable results under the experimental conditions of this investigation. Rhizosphere soil was isolated from segments of the roots representing different distances to the seed different root ages. In the rhizosphere of young barley seedlings, biomass NR-N increased significantly compared to the bulk soil from day 6 after sowing (average increases of 33–97%), especially where adventitious roots had developed. From this time, SIR rates were also significantly higher in the rhizosphere than in bulk soil (average increases 72–170%). The average ratio of SIR rate to biomass NR-N was found to be approximately 50% higher in the rhizosphere than in the bulk soil, which may indicate that a larger fraction of the microbial community is potentially active in the rhizosphere as compared to the bulk soil.     

杨树人工林品种更替连作与非更替连作根际效应的比较

采用空间位移法对杨树人工林更替连作和非更替连作两种经营模式下土壤养分、土壤酶活性和土壤微生物的根际效应进行了比较研究,以期探明不同连作经营模式对杨树人工林土壤生态环境的影响,探讨品种更替对杨树人工林地力维持的生态效果。研究结果表明,更替连作和非更替连作均导致杨树人工林土壤发生不同程度的衰退,非更替连作导致的林地土壤衰退现象更为严重。杨树根际和非根际土壤养分在非更替连作中下降最为显著,土壤有机质的根际效应显著大于更替连作,而土壤速效N、P、K的根际效应在更替连作中显著增大。非更替连作导致根际和非根际土壤中过氧化氢酶、脲酶和碱性磷酸酶活性发生较大幅度的下降,而多酚氧化酶和过氧化物酶活性较大幅度的上升;更替连作也导致土壤酶活性有类似的变化趋势,但下降(上升)幅度远小于非更替连作,土壤酶活性的根际效应总体呈现非更替连作变化幅度强于品种更替连作的趋势。两种连作模式下土壤中可培养土壤微生物的数量变化大致呈现一致趋势,连作将导致根际和非根际土壤微生物数量整体下降,其中土壤细菌比例有所降低,真菌比例上升,土壤呈现从细菌型向真菌型转化的特点,非更替连作对土壤微生物的根际效应明显大于更替连作。更替连作和非更替连作根际效应的差异可能由不同杨树品种根系分泌物的差异所导致。     

自然林下与田间根腐三七根际微生物群落特征及比较分析

【背景】三七根际微生物群落特征与其土传根腐病害密切相关,而针对自然林下根腐三七的相关研究鲜见报道。【目的】比较分析自然林下与田间根腐三七根际土壤微生物群落的组成特征,结合土壤理化性质与酶活性分析,为三七根腐病害防治与仿野生栽培提供科学依据。【方法】采集自然林下与田间根腐三七根际土壤,利用高通量测序技术,分析土壤细菌与真菌群落的物种组成与多样性,并测定土壤理化性质和酶活性。【结果】自然林下与田间根腐三七根际土壤中细菌和真菌群落组成具有明显差异,自然林下根腐三七根际土壤中担子菌门(Basidiomycota)、酸杆菌门(Acidobacteria)和疣微菌门(Verrucomicrobia)的相对丰度较高,而田间根腐三七根际土壤中子囊菌门(Ascomycota)、变形菌门(Proteobacteria)和绿弯菌门(Chloroflexi)的相对丰度较高。在属分类水平,镰刀菌属(Fusarium)是自然林下根腐三七根际土壤中的优势菌群,相对丰度为17.30%,而癣囊腔菌属(Plectosphaerella)是田间根腐三七根际土壤中的优势菌群,相对丰度为22.55%;Candidatus Ba...     

Real-time PCR detection of Holophagae (Acidobacteria) and Verrucomicrobia subdivision 1 groups in bulk and leek (Allium porrum) rhizosphere soils

In the light of the poor culturability of Acidobacteria and Verrucomicrobia species, group-specific real-time (qPCR) systems were developed based on the 16S rRNA gene sequences from culturable representatives of both groups. The number of DNA targets from three different groups, i.e. Holophagae (Acidobacteria group 8) and Luteolibacter/Prosthecobacter and unclassified Verrucomicrobiaceae subdivision 1, was determined in DNA extracts from different leek (Allium porrum) rhizosphere soil compartments and from bulk soil with the aim to determine the distribution of the three bacterial groups in the plant-soil ecosystem. The specificity of the designed primers was evaluated in three steps. First, in silico tests were performed which demonstrated that all designed primers 100% matched with database sequences of their respective groups, whereas lower matches with other non-target bacterial groups were found. Second, PCR amplification with the different primer sets was performed on genomic DNA extracts from target and from non-target bacteria. This test demonstrated specificity of the designed primers for the target groups, as single amplicons of expected sizes were found only for the target bacteria. Third, the qPCR systems were tested for specific amplifications from soil DNA extracts and 48 amplicons from each primer system were sequenced. All sequences were > 97% similar to database sequences of the respective target groups. Estimated cell numbers based on Holophagae-, Luteolibacter/Prosthecobacter- and unclassified Verrucomicrobiaceae subdivision 1-specific qPCRs from leek rhizosphere compartments and bulk soils demonstrated higher preference for one or both rhizosphere compartments above bulk soil for all three bacterial groups.     

生姜根系不同生态位细菌群落多样性特征、组成及结构差异

生姜作为常见的调味品和传统中药材,是我国重要的经济作物之一。作为取食部分的生姜块茎与根系直接相连,其产量、品质与根相关细菌群落密切相关。然而,关于生姜根系微环境中细菌群落的特点仍鲜有报道,土壤环境能否衍生出宿主特异性内生菌群落尚不清楚。以生姜根系不同生态位细菌群落为研究对象,采用高通量测序技术,对非根际、根际及根内细菌进行16S rRNA基因测序。结果表明,不同生态位细菌群落多样性存在显著差异,其中非根际及根际细菌群落多样性(Shannon index, Observed species, Faith′s PD)显著高于内生菌群落。同时,各生态位共现网络稳定性和复杂度表现为非根际>根际>根内细菌群落。而在组成上,细菌群落在不同生态位差异显著(R²=0.57,P=0.001)。其中变形菌门(Proteobacteria)是根内的优势门,该门类下假单胞菌属(Pseudomonas)、短波单胞菌属(Brevundimonas)、寡养单胞菌属(Stenotrophomonas)及泛菌属(Pantoea)在根内显著富集。在根际细菌中,拟杆菌门(Bacteroid...     

沙地樟子松人工林土壤磷素转化的根际效应

对大青沟自然保护区内不同年龄樟子松人工林根际和非根际土壤中不同形态磷素含量和酸性磷酸单酯酶（AP）活性进行了比较.结果表明,樟子松根系活动显著地提高了根际土壤有机碳含量及有机质的C/P比,增强了土壤微生物活动和AP活性,促进了有机磷的可利用性与矿化;显著地降低了土壤pH值,促进了Ca-P的溶解;从而提高了土壤磷素的有效性,促进了有机磷和Ca-P向Fe-P、Al-P的转化.与AP活性的根际效应相反,随林龄增加,樟子松对各形态磷素的根际效应逐渐增强,根际和非根际土壤中各形态磷素的变化趋势基本一致,土壤全磷和有机磷含量逐渐下降,而活性磷含量升高.为了保持土壤有机磷库和磷素的持续供应,必须对地被物予以保护.     

水仙根围细菌群落组成

【目的】探究水仙(Narcissus tazetta var.chinensis roem)土壤根围微生物组成及其与水仙生长特性的相关性。【方法】分别采集崇明水仙及漳州水仙健康植株根围土壤,抽提根围土壤中细菌总DNA并纯化,扩增16S r RNA基因并进行高通量测序分析比较不同产地植株根围细菌的组成与多样性。【结果】崇明水仙和漳州水仙根围微生物组成的主要细菌门类相同,均为12种,其中,优势菌为Proteobacteria、Chloroflexi、Bacteroidetes和Acidobacteria。根围微生物OTUs(Operational taxonomic units)分布及主成分分析(PCA)表明崇明水仙和漳州水仙根围微生物组成有较大差异,且Planctomycetales和Xanthomonadales在崇明水仙根围分布显著多于漳州水仙,而Chloroflexales和Chlorobiales在漳州水仙根围的丰度较高。【结论】根围微生物的组成,如厌氧氨氧化细菌、机会致病菌和光合细菌的多样性与丰度可能与水仙生长特性有密切的关系。     

Comparison of Rhizosphere Bacterial Communities in Arabidopsis thaliana Mutants for Systemic Acquired Resistance

Systemic acquired resistance (SAR) is an inducible systemic plant defense against a broad spectrum of plant pathogens, with the potential to secrete antimicrobial compounds into the soil. However, its impact on rhizosphere bacteria is not known. In this study, we examined fingerprints of bacterial communities in the rhizosphere of the model plant Arabidopsis thaliana to determine the effect of SAR on bacterial community structure and diversity. We compared Arabidopsis mutants that are constitutive and non-inducible for SAR and verified SAR activation by measuring pathogenesis-related protein activity via a β-glucoronidase (GUS) reporter construct driven by the β-1-3 glucanase promoter. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of MspI- and HaeIII-digested 16S rDNA to estimate bacterial rhizosphere community diversity, with Lactobacillus sp. added as internal controls. T-RFLP analysis showed a clear rhizosphere effect on community structure, and diversity analysis of both rhizosphere and bulk soil operational taxonomic units (as defined by terminal restriction fragments) using richness, Shannon–Weiner, and Simpson’s diversity indices and evenness confirmed that the presence of Arabidopsis roots significantly altered bacterial communities. This effect of altered soil microbial community structure by plants was also seen upon multivariate cluster analysis of the terminal restriction fragments. We also found visible differences in the rhizosphere community fingerprints of different Arabidopsis SAR mutants; however, there was no clear decrease of rhizosphere diversity because of constitutive SAR expression. Our study suggests that SAR can alter rhizosphere bacterial communities, opening the door to further understanding and application of inducible plant defense as a driving force in structuring soil bacterial assemblages.     

Survival of black alder (Alnus glutinosa L.), silver birch (Betula pendula Roth.) and Scots pine (Pinus sylvestris L.) seedlings in a reclaimed oil shale mining area

Early survival and growth of black alder, silver birch and Scots pine were investigated on reclaimed extremely stony and heterogeneous calcareous (pH 8) opencast oil shale mining areas (OOSMAs). Biomass allocation, production, leaf and root adaptations, and mineral nutrition in relation to tree species and soil heterogeneity were analysed. The adaptive strategies of tree species in first-year plantations on OOSMA were different. Scots pine allocated 1.5–2 times more biomass into leaves and fine roots than deciduous trees. The lower leaf/fine root biomass ratio was in proportion to the better survival (%) of seedlings, decreasing in the following order: black alder (93%) ≥ Scots pine (83%) > silver birch (64%). Deciduous trees improved mineral nutrition more by fine-root morphological adaptations than Scots pine; e.g. the mean specific root length (SRL, m g^?1) of short roots increased in the following order: Scots pine (62) < black alder (172) < silver birch (314). The effect of soil heterogeneity on growth and adaptations was minor. All studied species suffered from P and N, and deciduous species also from K deficiency. In the first year after planting, black alder was best adapted to the harsh conditions of the post-mining substrate. The approaches of this study can be used for other regions where wastelands require reclamation.     

Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed

The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands.