The detection of leghemoglobin-line sequences in legumes and non-legumes

Summary Leghemoglobin is a major component of the nitrogen-fixing nodules formed by legumes in association with bacterial symbionts of the genusRhizobium. It is thought to be involved in regulating the oxygen tension within nodules. In a series of Southern blot experiments using cloned soybean leghemoglobin cDNAs as hybridization probes, cross-hybridizing sequences have been detected in legumes closely related to soybean (members of the Leguminosae subfamily Papilionoideae), as well as in a distantly related legume not reported to be nodulated (subfamily Caesalpinioideae). With the same probes, the presence of cross-hybridizing sequences has also been detected in plants outside the Leguminosae, including two nitrogen-fixing non-legumes and one species which is not nodulated. These results suggest that the genes for oxygen-binding proteins may be more widely dispersed than previously thought.     

The occurrence of amoeboid plastids in the actinorhizal root nodules of Alnus glutinosa (L.) Gaertn.

Abstract. The invasion of the actinomycete Frankia into the root cells of Alnus glutinosa with subsequent nodule formation effects a number of ultrastructural changes in the host cell cytoplasm. Among other changes the amyloplasts rapidly lose their starch and acquire an amoeboid or pleomorphic form. Such plastids occur predominantly in the mature vesicle-containing, nitrogen-fixing cells of the nodule. They lack starch, have an electron dense stroma and a complex lamellar system. This last would appear to be associated with a distinct membranous reticulum which can be extensive. The flexible form of these plastids is mirrored in their ability to enclose portions of host cytoplasm together with organelles and even other plastids. Their close association with cristate mitochondria suggests an active metabolic role in the nodule symbiosis.     

Leghemoglobin-like sequences in the DNA of four actinorhizal plants

Summary A cloned cDNA partial copy of a soybean leghemoglobin mRNA was used to probe genomic DNA of four species of actinorhizal plants. Southern blot hybridization revealed the presence of sequences with homology to the leghemoglobin probe in DNA from Alnus glutinosa, Casuarina glauca, Ceanothus americanus and Elaeagnus pungens. The hybridization patterns of the restriction fragments revealed some fragment size conservation between the DNA of soybean and the DNA of four actinorhizal plants which are taxonomically unrelated to soybean or to each other. The results presented here indicate that globin gene sequences are much more widely distributed in the plant kingdom than has previously been thought. Furthermore, if sequence conservation is actually as high as the restriction fragment patterns suggest, the evolution of the DNA surrounding the globin sequences has been highly constrained.     

Rhizospheric degradation of phenanthrene is a function of proximity to roots

Rhizodegradation of recalcitrant organic pollutants, such as polycyclic aromatic hydrocarbons (PAH), may benefit from the major role that root exudates have on rhizospheric microbial processes. We investigated the influence of the proximity to ryegrass (Lolium perenneL.) roots on microbial populations and their biodegradation of phenanthrene (PHE) using compartmented pots. PAH degrading bacteria, total heterotrophic bacteria and PHE biodegradation were quantified in three consecutive sections at different distance (0–3, 3–6, 6–9 mm) from a mat of actively exuding roots. A bacterial gradient was observed with higher numbers of heterotrophs and PAH degrading bacteria closest to the roots. In parallel, a PHE biodegradation gradient was evident in the presence of roots. The biodegradation reached 86%, 48% and 36% of initially added PHE, respectively, in the layers 0–3 mm, 3–6 and 6–9 mm from the roots. The biodegradation rate was similar throughout the three layers of the non planted control. The present experimental system seems well suited for spatial and dynamic studies of PAH rhizoremediation.     

Cellulase isoenzyme profiles in Frankia strains belonging to different cross-inoculation groups

Carboxymethyl cellulase activities were evaluated in eight strains of Frankia from diverse host specificity groups and geographical origins. Cellulase activity was detected in culture supernatants of all strains in the absence of CMC (Carboxymethylcellulose) as an inducer using both double-layer plate and reducing sugar assays, indicating a constitutive production of CM-cellulases by Frankia. CM-cellulase isoenzyme profiles were visualized using activity gel electrophoresis of concentrated culture supernatants. Different electrophoretic profiles were observed among the eight strains tested, which correlate with the host specificity and taxonomic grouping of Frankia.     

秸秆还田与施肥对稻田土壤微生物生物量及固氮菌群落结构的影响

利用氯仿熏蒸法和变性梯度凝胶电泳法(PCR-DGGE)研究了秸秆覆盖还田与施肥对灰棕冲积水稻土0—10cm和10—20cm土层土壤微生物生物量碳、氮和固氮菌群落结构的影响。结果表明:土壤微生物量碳、氮和固氮菌多样性从0—10cm土层到10—20cm土层均呈现降低趋势。无秸秆覆盖处理(对照组)的土壤微生物生物量碳(SMB-C)和微生物生物量氮(SMB-N)量最小。在秸秆覆盖还田处理中,低氮和无钾处理的SMB-C和SMB-N都显著低于全量氮磷钾肥处理。虽然无磷处理的SMB-N低于全量氮磷钾处理,但差异不显著。说明秸秆覆盖还田配施充足氮磷钾肥能显著提高土壤微生物生物量碳、氮。由DGGE图谱多样性指数分析得知,配施充足氮磷钾肥的处理土壤的固氮菌多样性最丰富。UPGMA聚类分析显示,10种不同处理的聚类图也不同,对照(无秸秆)处理0—10cm和10—20cm的微生物不同于其它处理单独聚在了一个群里。DGGE条带测序得知,14个条带的近缘种大部分为非培养细菌nifH基因片段,主要优势菌群其归属于变形菌门(Proteobacteria)的β-变形菌纲(Betaproteobacteria)。应用PCR-DGGE技术可以解释灰棕冲积水稻土秸秆覆盖不同肥料用量固氮菌分子群落结构特点。     

PCR-amplified 16S rRNA sequence analysis to confirm nodulation of Datisca cannabina L. by the endophyte of Coriaria nepalensis Wall

Different Frankia strains and crushed nodule suspensions were tested for their ability to nodulate Coriaria nepalensis and Datisca cannabina. Datisca cannabina seedlings were nodulated effectively by both crushed nodule suspension from Coriaria nepalensis and Datisca cannabina. The origin of the endophyte in Datisca nodules induced by crushed nodules of Coriaria was confirmed by comparing partial PCR-amplified 16S rRNA sequences with those of the endophytes of both plants. Coriaria seedlings could only be nodulated by crushed nodule suspensions of Coriaria nepalensis. All pure cultures of Frankia used as a single inoculum source or in combinations with a nodule filtrate, failed to induce nodulation on Coriaria. Two atypical Frankia strains Cn3 and Cn7 isolated from Coriaria nodules showed no acetylene reduction activity and did not induce nodulation on the host seedlings.     

Factors affecting formation of cluster roots in Myrica gale seedlings in water culture

The effect of nutrient deficiency, aeration, phosphorus supply, and nitrogen source on the formation of cluster (proteoid) roots was examined in Myrica gale seedlings growing in water culture. Only the omission of phosphorus resulted in the formation of significant numbers to cluster roots when plants were grown in a number of 1/4 strength Hoagland's solutions, each lacking one mineral nutrient. Aeration shortened the time required for cluster root formation and increased the percentage of plants forming cluster roots. The proportion of the root system comprised of cluster roots decreased as the phosphorus concentration in the solution increased and no cluster roots formed in solutions containing 8 mg P/L. Phosphorus supply also affected total plant biomass, proportion of biomass comprising nitrogen-fixing nodules, shoot:root ratio, phosphorus concentration in the leaves and phosphorus content of the plants. The plants showed luxury consumption of phosphorus and were able to produce large amounts of biomass utilizing only stored phosphorus.Nitrogen source also affected cluster root formation. Urea-fed plants produced cluster roots more quickly and devoted a substantially larger proportion of root growth to cluster roots than did nitrate-fed plants. The longest cluster root axes were produced in nitrate-fed plants supplied with no phosphorus and the shortest were in urea-fed plants at 4 mg P L^–1.Four methods for expressing the extent of cluster root formation were examined and it was concluded that cluster roots as a proportion of total fine root dry weight is preferable in many cases. Formation of cluster roots in response to phosphorus deficiency coupled with previously demonstrated traits allows Myrica gale to adapt to a wide range of soil conditions.     

Formation of cluster roots and mycorrhizal status of Comptonia peregrina and Myrica pensylvanica in Maine, USA

Extent of cluster (proteoid) root formation in the field was examined in relation to availability of P and successional status of the site in two actinorhizal, N₂-fixing shrubs. Comptonia peregrina (L.) Coult. and Myrica pensylvanica Loisel. In C. peregrina cluster roots were present at all 13 sites and comprised between 0.2 and 19% of total fine root dry weight. Cluster root formation was most extensive at recently disturbed sites and was negatively correlated with cover of associated woody species (r =−0.85), litter depth (r =−0.81) and available (extractable) soil P (r =−0.75). In M. pensylvanica cluster roots were present at all 11 sites and comprised between 6 and 20% of total fine root dry weight. On mineral soils (n = 6), extent of cluster root formation was negatively correlated (r =−0.86) with cover of associated woody species and with litter depth (r =−0.78; P = 0.07). Comptonia peregrina and M. pensylvanica lack functional mycorrhizae at these sites because only intracellular infections were found and these lacked arbuscules. None of 22 non-N₂-fixing, dominant woody species associated with C. peregrina and M. pensylvanica formed cluster roots. Cluster roots probably allow C. peregrina and M. pensylvanica to obtain sufficient P from nutrient-poor soils in the absence of functional mycorrhizae. Extensive cluster root formation on disturbed, early successional sites may aid these species in colonizing these sites because they have to form only one symbiosis (with Frankia ) and not two (with Frankia and a mycorrhizal fungus).     

Variation with soil depth,topographic position and host species in the capacity of soils from an Australian locale to nodulateCasuarina andAllocasuarina seedlings

Sandy alluvial soils in a floodplain supporting a native stand ofCasuarina cunninghamiana Miq. produced about three times as many nodulated seedlings and more than twice as many nodules per nodulated seedling on roots of baitedCasuarina spp. than did clay loam red earth soils from the adjacent valley slope. Moist and well-aerated subsurficial alluvial sands had the greatest nodulation capacity of all the soils sampled. For all topographic positions, soil samples from depths greater than 20 cm promoted 76% more nodulated Casuarina seedlings than samples from the surficial 20 cm.Seedlings of three provenances ofC. cunninghamiana, together with seedlings ofC. glauca Sieb. ex Spreng.,C. cristata F. Muell ex Miq. andC. obesa Miq. developed significantly more nodules per pot and nodules per nodulated seedling in soils from this locale than seedlings of twoCasuarina equisetifolia Forst. provenances. Seedlings of two provenances ofAllocasuarina torulosa (Ait.) L. Johnson had fewer than 1% nodulated seedlings, a significantly lower level by far than that ofCasuarina seedlings.A. torulosa provenances also had significantly fewer nodulated seedlings per pot and nodules per nodulated seedling than all Casuarina hosts excepting one poorly-nodulated provenance ofC. equisetifolia.Nodulated seedlings of allCasuarina species had the capacity to fix atmospheric N₂, as indicated by acetylene-reduction capability. The presence of yellow cladodes and low rates of acetylene reduction per plant forC. cristata Miq. suggest that this association was poorly effective.     

Water accessibility to plant roots in different soil structures occurring in the same soil type

The capacity of a soil to supply roots with water and nutrients for crop growth is important when defining sustainable land management which implies maintenance of production and reduction of production risks. Not only the amount of available water is important but also its accessibility, which differs among different soil structures. Different structures within one soil series were associated with three types of management: (i) conventional, temporary grassland (Conv), (ii) biodynamic, temporary grassland (Bio) and (iii) conventional permanent grassland (Perm). Transpiration of barley plants, under identical circumstances, and the associated rooting patterns, were measured in five large undisturbed cores from each of the three soil structures. Management had significantly changed bulk density, organic matter content and porosity. Measured transpiration showed significant differences with highest amounts for Perm followed by Conv and lowest amounts for Bio. Rooting pattern characteristics, defined as the relation between a series of hypothetical extraction zones around each root and the volumes of excluded soil were determined for the three structures. These rooting pattern characteristics were most favourable for Perm, followed by Bio and Conv, respectively. The water supply characteristics, defined as the number of days the soil can satisfy a transpiration demand of 5 mm d^-1 as a function of a hypothetical extraction zone, reflects the capacity of the soil to supply roots with water. These water supply characteristics combined with the rooting pattern characteristics were used to quantify the accessibility of soil water. Accessibility was highest for Perm and Conv with 95% and 94% respectively, followed by Bio with 68%. When used in a simulation model and compared with simulations implicitly assuming total accessibility, measured transpirations were better simulated by introducing the expression for water accessibility.     

A method to separate plant roots from soil and analyze root surface area

Analysis of the effects of soil management practices on crop production requires knowledge of these effects on plant roots. Much time is required to wash plant roots from soil and separate the living plant roots from organic debris and previous years’ roots. We developed a root washer that can accommodate relatively large soil samples for washing. The root washer has a rotary design and will accommodate up to 24 samples (100 mm diam. by 240 mm long) at one time. We used a flat-bed scanner to digitize an image of the roots from each sample and used a grid system with commercially-available image analysis software to analyze each sample for root surface area. Sensitivity analysis and subsequent comparisons of ‘dirty’ samples containing the roots and all the organic debris contained in the sample and ‘clean’ samples where the organic debris was manually removed from each sample showed that up to 15% of the projected image could be coveredwith debris without affecting accuracy and precision of root surface area measurements. Samples containing a large amount of debris may need to be partitioned into more than one scanning tray to allow accurate measurements of the root surface area. Sample processing time was reduced from 20 h, when hand separation of roots from debris was used, to about 0.5 h, when analyzing the image from an uncleaned sample. The method minimizes the need for preprocessing steps such as dying the roots to get better image contrast for image analysis. Some information, such as root length, root diameter classes and root weights, is not obtained when using this technique. Root length measurements, if needed, could be made by hand on the digital images. Root weight measurement would require sample cleaning and the advantage of less processing time per sample with this method would be lost. The significance of the tradeoff between information not obtained using this technique and the ability to process a greater number of samples with the time and personnel resources available must be determined by the individual researcher and research objectives.     

A study of the tensile force required to pull wheat roots from soil

Experiments were carried out to determine the tensile properties of mature wheat roots and the force necessary to pull roots from undisturbed soils at a range of moisture contents using an Instron materials testing rig. Roots decreased in cross sectional area from 1.5 to 0.1 mm²and in tensile strength from 7.0 to 2.3 Newtons (N) along the first 12 cm of their length. Breaking strain was constant along the root but the breaking stress increased. Increased seeding rate decreased root diameter and tensile strength but plant growth regulators and fertiliser nitrogen level did not affect the tensile properties. Roots were pulled from mesh tubes of soil (25 mm ± 75 mm) into which they had grown. The peak loads for sandy clay loam and sandy loam soils were 4.8 and 3.9 N respectively and increasing the soil moisture from 17% to 26% reduced the peak load from 5.2 N to 3.5 N. With the drier soil the inner stele pulled free leaving the outer periderm in the soil in a higher proportion of the roots indicating a stronger root/soil bond than in the wetter soil. The load us displacement relationship when pulling roots from soil resembled that for a fibre reinforced composite material. The presence of branch roots resulted in an uneven trace in which there were a number of sub-peaks as branch roots gave way. It is suggested that soil wetting could contribute to lodging of wheat by reducing the resistance of roots to slippage and breaking.     

Effects of roots and litter on mineralization processes in forest soil

Summary Leaf litter breakdown and fine root production, including exudation, are two major influences upon carbon and nitrogen mineralization rates in forest soil. Sieving and root removal experiments were used to examine their effects. Although carbon mineralization rates declined in smaller particle size fractions of forest litter, this trend largely disappeared when results were calculated on an ash-free basis. Nitrogen mineralization by contrast, was greatest in smaller fractions.Much of the variation in carbon mineralization rates appeared to be associated with fine roots. A rapid initial exponential decay phase noted in laboratory respiration studies was probably associated with disappearance of available carbon in the form of root exudates and/or the microorganisms dependent on them. Clear cutting caused a marked reduction in the size of available carbon pools, reflecting decreased root exudation and rhizosphere activity. A model of mineralization is proposed which represents the available and humified carbon pools.Deceased     

薇甘菊根际可培养固氮菌和氨化细菌的分离鉴定与促生作用

【目的】固氮菌和氨化细菌是氮循环产生生物有效氮的关键起始环节,直接影响了外来入侵植物的生长速度和扩散进程。然而,关于典型入侵植物薇甘菊根际可培养固氮菌和氨化细菌的研究尚未见报道,这在很大程度上制约了我们对薇甘菊根际高效的氮素转化机制的深刻理解。【方法】采用传统平板涂布培养法对野外采集的薇甘菊根际土壤中的可培养固氮菌和氨化细菌进行了分离鉴定,并进行了接种验证实验。【结果】结果表明,入侵植物薇甘菊根际土壤中的固氮菌和氨化细菌的菌群密度显著高于两个本地伴生植物(火炭母和鸡屎藤),其固氮效率及有机氮矿化效率也优于2个本地种;系统发育分析表明：薇甘菊根际的固氮菌菌株归类于5个属,分别为伯克霍尔德氏菌属(Burkholderia)、肠杆菌属(Enterobacter)、植物杆菌属(Phytobacter)、新肠杆菌属(Kosakonia)和根瘤菌属(Rhizobium);氨化细菌归类于7个属,分别为沙雷氏菌属(Serratia)、不动杆菌属(Acinetobacter)、假单胞菌属(Pseudomonas)、博德特氏菌属(Bordetella)、寡养单胞菌属(Stenotrophomonas)、苍...     

普洱地区茶叶内生细菌与根际土壤细菌群落结构分析

[目的]茶叶内生细菌、根际土壤细菌在普洱茶的发酵中起着重要的作用,还可以促进茶树生长,诱导茶树抗病性.研究其群落结构组成及相互关系可为微生物资源开发利用提供理论依据.[方法]本研究以普洱地区茶树叶片和根际土壤为材料,采用高通量测序技术,对茶叶及根际土壤细菌的16S核糖体RNA基因(16S rRNA)进行测序,比较分析茶...     

Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo

We investigated ammonia-oxidizing bacteria in activated sludge collected from 12 sewage treatment systems, whose ammonia removal and treatment processes differed, during three different seasons. We used real-time PCR quantification to reveal total bacterial numbers and total ammonia oxidizer numbers, and used specific PCR followed by denaturing gel gradient electrophoresis, cloning, and sequencing of 16S rRNA genes to analyze ammonia-oxidizing bacterial communities. Total bacterial numbers and total ammonia oxidizer numbers were in the range of 1.6 x 10(12) - 2.4 x 10(13) and 1.0 x 10(9) - 9.2 x 10(10)cellsl(-1), respectively. Seasonal variation was observed in the total ammonia oxidizer numbers, but not in the ammonia-oxidizing bacterial communities. Members of the Nitrosomonas oligotropha cluster were found in all samples, and most sequences within this cluster grouped within two of the four sequence types identified. Members of the clusters of Nitrosomonas europaea-Nitrosococcus mobilis, Nitrosomonas cryotolerans, and unknown Nitrosomonas, occurred solely in one anaerobic/anoxic/aerobic (A2O) system. Members of the Nitrosomonas communis cluster occurred almost exclusively in association with A2O and anaerobic/aerobic systems. Solid residence time mainly influenced the total numbers of ammonia-oxidizing bacteria, whereas dissolved oxygen concentration primarily affected the ammonia-oxidizing activity per ammonia oxidizer cell.     

The Phylogeny of Acetic Acid Bacteria Based on the Partial Sequences of 16S Ribosomal RNA: The Elevation of the Subgenus Gluconoacetobacter to the Generic Level

Thirty-six strains of acetic acid bacteria classified in the genera Acetobacter, Gluconobacter, and Acidomonas were examined for their partial base sequences in positions 1220 through 1375, 156 bases, of 16S rRNA. The strains of the Q₁₀-equipped Gluconobacter species examined were divided into two subgroups, which included the type strains of Gluconobacter oxydans, the type species of the genus Gluconobacter, and of a second species, Gluconobacter cerinus, respectively. The base differences numbered four between the two type strains. The strains of the Q₉-equipped species examined classified in the type subgenus Acetobacter of the genus Acetobacter were not very distant phylogenetically from those of the genus Gluconobacter. The calculated number of base differences was 9–6 between the type strains of G. oxydans and G. cerinus and the type strains of Acetobacter aceti and Acetobacter pasteurianus. In contrast, the strains of the Q₁₀-equipped species examined classified in the subgenus Gluconoacetobacter of the genus Acetobacter were very distant phylogenetically from those of the Acetobacter and Gluconobacter species mentioned above. The number of base differences was calculated to be 14-8. Furthermore, the strains of the methanol-assimilating, Q₁₀-equipped species of the genus Acidomonas examined were located in phylogenetically isolated positions. The type strain of Acidomonas methanolica (≡ Acetobacter methanolicus), the type species of the genus Acidomonas, had 16–9 base differences. The data obtained here indicated that the members of the subgenus Gluconoacetobacter of the genus Acetobacter can be distinguished at the generic level. The new genus Gluconoacetobacter was proposed with the type species, Gluconoacetobacter liquefaciens, in recognition of the genus Acidomonas along with the genera Acetobacter and Gluconobacter in the classification of the acetic acid bacteria.     

基于高通量测序的稀释平板计数细菌群落变化研究

【目的】明确平板计数法中不同稀释梯度对土壤细菌数量和组成的影响规律,比较稀释平板计数法和高通量测序研究土地利用方式变化下土壤细菌群落的差异。【方法】针对不同土地利用方式下的4种土壤(次生林、健康蕉园、发病蕉园和水稻土),设置5个土壤悬液10^-1-10^-5稀释梯度开展平板计数,获得平板上可培养细菌富集物并提取总DNA;同时直接提取原位土壤微生物总DNA,高通量测序细菌富集物DNA和土壤总DNA中的16S rRNA基因,研究不同土壤悬液稀释梯度下的可培养细菌群落和背景土壤细菌多样性,明确可培养细菌占土壤总细菌的比例以及多样性差异。【结果】次生林垦殖为蕉园土壤后土壤呼吸增幅最高,细菌数量降幅最高,稀释平板计数与实时荧光定量PCR (real-time fluorescent quantitative PCR)结果一致,但其他土地利用方式变化的稀释平板计数与实时荧光定量细菌数量的结果并不完全一致。连续稀释显著降低了可培养细菌多样性。与原位土壤总细菌相比,土壤可培养细菌群落Chao 1指数降幅高达86%-98%。与土壤悬液稀释10倍(10^-1...