Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Rice roots provide a specific habitat for microorganisms in the rhizosphere of a submerged field through supply of oxygen and organic matter. Many studies have focused on the microbial community in the rice rhizosphere, but less is still known about the microeukaryotic community structure of rice rhizosphere. This study explored the microeukaryotic community structure of a rice rhizosphere through denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA gene. The rice roots and the rhizosphere soil samples, which were collected from a field under rice-wheat rotation system, were separately analyzed. To characterize the rice rhizosphere-specific community, the bulk soil of rice field and the wheat rhizosphere samples were also examined. DGGE fingerprints showed that the microeukaryotic community of rice roots were distinct from the community of the bulk soil and showed a temporal shift with the growth stage. The rhizosphere soil community was distinct from the root and bulk soil communities, but this could be explained by that the root and bulk soil communities were shared in the rhizosphere. The rice rhizosphere community was also distinct from those in the wheat rhizosphere. Microeukaryotes that characterized the rice rhizosphere (roots and the rhizosphere soil) community could be affiliated to Polymyxa, flagellates, and oomycetes, which suggested that microeukaryotes with various ecological roles, e.g., parasites, bacterial grazers, and decomposers, inhabit the rice rhizosphere. The results showed that the rice root and its growth stages are key factors shaping the microeukaryotic community structure in the rhizosphere.     

Fungi associated with roots of continuously cropped upland rice

Fungi on and in roots of continuously cropped upland rice were examined. Dominant fungi on the root surfaces were found to be composed of limited genera: Fusarium, Penicillium, and Pyrenochaeta. Among them, only Pyrenochaeta sp. was remarkable in regard to continuous cropping of upland rice. The results showed that Pyrenochaeta sp. penetrated into and multiplied in root tissues of aged plants and could survive during the winter on infected root residues left in the field, and in the next spring colonized the root surfaces of new seedlings, and then penetrate into root tissues and thus be accumulated on and in roots by the continuous cropping of upland rice. Pyrenochaeta sp. was also found to have a considerable specific affinity for roots of upland rice, compared with the roots of several other plants.     

Growth of hydrogenotrophic and acetoclastic methanogens on substrate from rice plant callus cells in anaerobic soil: an estimation to the role of slough-off root cap cells to their growth

Flooded paddy fields are the major anthropogenic sources of methane (CH₄) emission, and organic materials of rice plant origin were estimated to be important as its source. This study used rice (Oryza sativa L. cv, Yukihikari) callus cells as a model material for slough-off root cap cells, and carbon-13 (¹³C)-labelled callus cells were subjected to decomposition in aerobic and anaerobic soil microcosms for 56 days. DNA was extracted from a soil incubated with carbon-12 (¹²C)- and ¹³C-callus cells and subjected to buoyant density gradient centrifugation to identify methanogenic archaeal species that assimilated carbon from the callus cells. ¹³C-labelled 16S rRNA gene (16S rDNA) fragments from methanogenic archaea were not polymerase chain reaction (PCR)-amplified in heavy fractions under aerobic soil conditions, while they were successfully done from day 3 onwards under anaerobic soil conditions. Eighty-four denaturing gradient gel electrophoresis (DGGE) bands in heavy fractions were sequenced, revealing that they were members of Methanosarcina spp. (20 clones), Methanosaeta spp. (18 clones), Methanocella spp. (25 clones), Methanomicrobiales (10 clones), Methanobacterium spp. (7 clones) and Cluster ZC-I (2 clones). They included hydrogenotrophic and acetoclastic methanogens and were phylogenetically different from those residing in rice roots and, presumably, from those assimilating root exudate and mucilage-derived carbon. This study indicates that carbon of slough-off root cap cells propagates specific methanogenic species in rice rhizosphere under anaerobic soil conditions and thus augments the diversity of the total rhizospheric methanogenic community.     

Effect of Free-Air CO2 Enrichment (FACE) on Methanogenic Archaeal Communities Inhabiting Rice Roots in a Japanese Rice Field

The effect of free-air CO₂ enrichment (FACE) on the methanogenic archaeal communities inhabiting rice roots was studied in a Japanese rice field by separately collecting rice roots three times (at mid-tillering, panicle initiation, and heading stages) according to their nodal number, extracting DNA from the roots and subjecting it to polymerase-chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and sequence analyses. Appearance of roots indicated that aging and senescence occurred faster under the FACE conditions than under the ambient conditions. The number of DGGE bands of methanogenic archaeal communities tended to increase with the growth stages. Cluster analysis showed that the succession of methanogenic archaeal communities in the ambient plot preceded that in the FACE plot, while the trend of the appearance of rice roots was opposite. All the closest relatives associated with the DGGE bands belonged to Methanomicrobiales and Rice cluster I, and FACE did not affect the phylogenetic position of the closest relatives associated with the characteristic DGGE bands. Faster succession of methanogenic archaeal communities in the ambient plot and similar phylogenetic members between the plots were observed in rice roots in years with both warmer (1999) and cooler (2003) weather during the rice cultivation period than in average years.     

Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach

Although root cap cells are an important substrate for microorganisms in the rhizosphere, little attention has been paid to the decomposition of sloughed root cap cells by microorganisms. This study used rice plant callus cells grown on medium containing ¹³C-labelled glucose as a model material for rice plant root cap cells. Harvested ¹³C-labelled callus cells (78 atom % ¹³C) were subjected to decomposition in an aerobic soil microcosm for 56 days. The low cellulose and lignin levels and the disaggregated nature of the callus cells indicated that these cells were an appropriate model material for root cap cells. DNA was extracted from a soil incubated with ¹²C- and ¹³C-callus cells and subjected to buoyant density gradient centrifugation to identify bacterial species that assimilated carbon from the callus cells. The stability of the total bacterial communities during the incubation was estimated. Many DGGE bands in light fractions of soil incubated with ¹³C-callus cells were weaker in intensity than those from soil incubated with ¹²C-callus cells, and those bands were shifted to heavier fractions after ¹³C-callus treatment. ¹³C-labelled DNA was detected from Day 3 onwards, and the DGGE bands in the heavy fractions were most numerous on Day 21. DGGE bands from heavy and light fractions were sequenced, revealing more than 70% of callus- C incorporating bacteria were Gram-negative, predominantly α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Sphingobacteria and Actinobacteria. These species were phylogenetically distinct from the bacteria reported to be present during plant residue decomposition and resident in rice roots. This study indicates that root cap cells are decomposed by specific bacterial species in the rhizosphere, and that these species augment the diversity of rhizospheric bacterial communities.     

黄土区不同龄期灌木柠条锦鸡儿根系的分布特征及其固土护坡效果

为定量评价西宁盆地黄土区优势灌木柠条锦鸡儿根系固土护坡效果,该研究以区内生长期为幼龄期（<6 a）、中龄期（6～14 a）和老龄期（>14 a）3个龄期的柠条锦鸡儿为研究对象,通过原位挖掘法与原位拉拔试验相结合的方式,调查不同龄期柠条锦鸡儿根系形态学指标和根系分布特征,并通过单根拉伸试验获得单根抗拉强度。以此为基础,利用WWM模型对不同龄期柠条锦鸡儿根系附加黏聚力进行计算,评价不同龄期柠条锦鸡儿根系对土体抗剪强度的增强效果。结合有限元数值模拟分析,定量评价不同龄期柠条锦鸡儿根系加筋和锚固作用对黄土边坡稳定性的贡献。结果表明：随着龄期的增加,柠条锦鸡儿根系埋深、根系总根长、主根根径和主根根长均逐渐增加;各龄期柠条锦鸡儿根系主要分布在0～0.6 m土层深度范围内,随着土层深度增加,幼龄期和老龄期根系根长和根数呈逐渐减少趋势;中龄期根系则呈先增大后减小趋势,根长和根数的最大值出现在0.3～0.6 m的土层深度内。幼龄期和老龄期柠条锦鸡儿根面积比和根系附加黏聚力均随着土层深度增加而逐渐减少,中龄期柠条锦鸡儿则呈先增大后减小变化趋势,且该龄期根系增强土体抗剪强度的效果相对最为显著。不...     

Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis

Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem was evaluated by the denaturing gradient gel electrophoresis (DGGE) after PCR amplification of the 16S rRNA genes (16S rDNAs), sequencing analysis and data evaluation by principal component analysis. Data were obtained from samples collected from the plowed soil layer, rice roots, rice straws incorporated in soil, plant residues (mixture of weeds, rice litters, rice roots, and rice stubbles) in soil, and composing rice straw. The number of bands of DGGE profiles ranged from 12 to 26 with the highest numbers in rice roots and rice straws incorporated in soil. However, the diversity indices based on both the numbers and intensity of bands indicated that the community of the plowed soil layer was the most diverse, even, and stable. Sequencing of the main DGGE bands showed the presence of Methanomicrobiales, Methanosarcinales, Methanobacteriaceae, and Methanocellales. The plowed soil layer included all phylogenetic groups of the methanogenic archaea of the other studied habitats, with prevalence of the members of Methanomicrobiales and Methanocellales. The phylogenetic diversity was compared with that of paddy soils collected in Italy, China, and the Philippines and that of 12 anaerobic environments (fen, waste, coast, permafrost, natural gas field, bovine rumen, riparian soil, termite, ciliate endosymboints, lake sediment, landfill, and seep rumen). The phylogenetic diversity was more similar among paddy soils than with the other anaerobic environments. Probably, the methanogenic archaeal communities of the paddy field soils were characterized by indigenous members and some of the members of the community of the plowed soil layer colonized rice roots, rice straws, and plant residues.     

氮肥对稻田土壤反硝化细菌群落结构和丰度的影响

以氮肥田间定位试验为研究对象,利用PCR-DGGE(聚合酶链反应变性梯度凝胶电泳)和荧光定量PCR(real-time PCR)技术,通过对反硝化细菌nirS基因的检测,分析了定位试验第2年稻田反硝化细菌群落结构和丰度的变化。DGGE图谱及依据其条带位置和亮度数字化数值进行的主成分分析(PCA)结果均显示:在氮肥定位试验第2年,与不施肥对照(CK)比较,在水稻各个生育期(分蘖期、齐穗期和成熟期)内,施用氮肥[150kg(N)·hm-2]的稻田根层土或表土中的反硝化细菌群落结构均无明显变化;且稻田根层土或表土中的反硝化细菌群落结构在水稻各个生育期间也均无明显差异。荧光定量PCR结果显示,在水稻生长发育过程中,施用氮肥的稻田根层土或表土中的反硝化细菌nirS基因拷贝数始终显著(P<0.05)高于其对应的不施肥对照。此外,无论施用氮肥与否,根层土中的反硝化细菌nirS基因拷贝数在水稻成熟期时都会显著(P<0.05)降低;但表土中的nirS基因拷贝数在水稻各生育期间无明显变化;且水稻成熟期时施用氮肥和不施肥的稻田表土中nirS基因拷贝数都显著(P<0.05)高于根层土。同时,与对照比较施用氮肥可促进水稻增产44%。研究表明,短期定位试验中施用氮肥能够显著提高稻田土壤反硝化细菌的丰度,但对其群落结构没有明显影响。     

Molecular identification of methane oxidizing bacteria in a Japanese rice field soil

By using cultivation-independent techniques, community changes of methane-oxidizing bacteria (MOB) in rice bulk soils were investigated under field conditions in a Japanese rice field. The representative soil samples were collected during the typical rice growing season and nonrice growing period all year round. Statistical characterization of denaturing gradient gel electrophoresis (DGGE) community patterns of MOB pmoA/amoA functional gene fragments showed that MOB community structures in the rice bulk soils remained largely unchanged throughout the investigated period. The total intensity of six common DGGE bands that appeared consistently throughout the investigated period accounted for 64% of the total intensity of all 18 different DGGE bands detected. The low squared distance of the Ward cluster analysis of the DGGE pattern and the high Sorensen similarity coefficient (81%) also implied the high similarity of the MOB community structures. The stable MOB community structure did not couple well with the wide variation of soil water contents all year round. Sequencing analysis of the nine characteristic bands including six common bands revealed the presence of Type I, Type II methanotrophs, and β-proteobacterial ammonia oxidizers in rice bulk soils. In comparison with MOB type species, three DGGE bands showed a wide variation of the highly conserved amino acid residues, implying the presence of novel MOB bacteria inhabiting the rice bulk soil. The high diversity of MOB composition suggested that rice bulk soils might serve as an ideal reservoir for the dynamic changes of MOB in a rice field ecosystem in response to environment changes.     

Response of alfalfa (Medicago sativa L.) to single and mixed inoculation with phosphate-solubilizing bacteria and Sinorhizobium meliloti

The objectives of this work were to phenotypically and genetically characterize alfalfa rhizosphere bacteria and to evaluate the effect of single or mixed inoculation upon nodulation and biological nitrogen fixation. Thirty-two strains showed tricalcium phosphate solubilization ability, and two of them caused bigger or equal solubilization halos than the control strain P. putida SP22. The comparison of the 16S ribosomal DNA sequences indicated that these strains are phylogenetically related to Bacillus spp. and Pseudomonas spp. A beneficial effect of both isolates on alfalfa growth was observed in coinoculation assays. Pseudomonas sp. FM7d caused a significant increase in root and shoot dry weight, length, and surface area of roots, number, and symbiotic properties of alfalfa plants. The plants coinoculated with Sinorhizobium meliloti B399 and the Bacillus sp. M7c showed significant increases in the measured parameters. Our results indicating that strains Pseudomonas sp. FM7d and Bacillus sp. M7c can be considered for the formulation of new inoculants.     

Dual inoculation of pretransplant stage Oryza sativa L. plants with indigenous vesicular-arbuscular mycorrhizal fungi and fluorescent Pseudomonas spp.

Summary This study examined the response of rice (Oryza sativa L.) plants at the pretransplant/nursery stage to inoculation with vesicular-arbuscular mycorrhizal (VAM) fungi and fluorescent Pseudomonas spp., singly or in combination. The VAM fungi and fluorescent Pseudomonas spp. were isolated from the rhizosphere of rice plants. In the plants grown in soil inoculated with fluorescent Pseudomonas spp. alone, I found increases in shoot growth, and in root length and fine roots, and decreases in root growth, and P and N concentrations. In contrast, in the plants colonized by VAM fungi alone, the results were the reverse of those of the pseudomonad treatment. Dual inoculation of soil with VAM fungi and fluorescent Pseudomonas spp. yielded plants with the highest biomass and nutrient acquisition. In contrast, the plants of the control treatment had the lowest biomass and nutrient levels. The dual-inoculated plants had intermediate root and specific root lengths. The precentages of mycorrhizal colonization and colonized root lengths were significantly lower in the dual-inoculated treatment than the VAM fungal treatment. Inoculation of plants with fluorescent Pseudomonas spp. suppressed VAM fungal colonization and apparently reduced photosynthate loss to the mycorrhizal associates, which led to greater biomass and nutrient levels in dual-inoculated plants compared with plants inoculated with VAM fungi alone. Dual inoculation of seedlings with fluorescent Pseudomonas spp. and VAM fungi may be preferable to inoculation with VAM alone and may contribute to the successful establishment of these plants in the field.     

Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field

Abstract

Methane-oxidizing bacteria (MOB) are crucial to the reduction of CH₄ emitted to the atmosphere. However, it is unclear how MOB in rice straw are affected by straw decomposition processes. In a Japanese rice field, a year-round experiment was set up to study the effects of agricultural practice (rice cultivation/winter fallow), straw parts (leaf sheath/blade) and the site of straw placement (plow layer/soil surface) on MOB communities in rice straw using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing analyses of key MOB functional genes (pmoA and amoA). Thirty-eight different DGGE bands were observed over the entire investigation period. Principal component analysis of DGGE pattern suggested that agricultural practice is the key factor regulating the MOB communities. Sequencing of dominant DGGE bands showed that: (1) during the rice cultivation period, methanotrophs (particularly type I methanotrophs) dominated the MOB community, (2) during the winter fallow season both type I and type II methanotrophs were dominant in sheath segments placed both on the soil surface and in the plow layer, whereas ammonia oxidizers seemed to dominate blade segments placed in the plow layer. Alignment of diagnostic amino acid sequences of MOB suggested the presence of novel ammonia oxidizers in rice straw in rice fields.     

Interaction among free-living N-fixing bacteria isolated from Drosera villosa var. villosa and AM fungi (Glomus clarum) in rice (Oryza sativa)

Rice is usually grown in N-deficient soils, demanding that the element be supplied to the field by commercially available N fertilizers. Unfortunately, a substantial amount of the urea-N or NO₃-N applied as fertilizers is lost through different mechanisms, causing environmental pollution problems. Utilization of biological N₂ fixation (BNF) technology can decrease the application of N fertilizers, reducing environmental risks. This study evaluated the effects of four free-living N-fixing bacterial species, isolated from oligotrophic soil conditions, as single inoculants or combined with arbuscular mycorrhizal fungi (Glomus clarum), on the development of rice plants grown as flooded or upland rice, in the greenhouse. Upland rice roots were inoculated with Methylobacterium sp., Burkholderia sp. and Sphingomonas sp., whereas the species Burkholderia sp., Pseudomonas sp. and Sphingomonas sp., were inoculated on flooded rice. Inoculants consisted of individual bacterial species or their mixtures, with or without G. clarum. Controls included non-bacteria/non-AM fungi, and AM fungi alone. Experiments were carried out in five replicates. The presence of G. clarum decreased or did not significantly affect plant growth under the different culture conditions. The presence of AM fungi stimulated the N-fixing bacterial population of upland rice. Bacterial species had different effects, under both culture conditions, and some genera of N-fixing bacteria increased root and shoot growth at different plant growth stages. The level of mycorrhiza colonization had no influence on plant growth     

Isolation,partial identification and application of diazotrophic rhizobacteria from traditional Indian rice cultivars

A diversity of N₂-fixing (diazotrophic) bacteria was isolated from two traditional rice cultivars, Sataria and Kartiki, from the rice growing area of Mithila region of North Bihar, India, where low levels of nitrogen fertilizers are applied. Nitrogen-free semisolid media NFb, JMV and LGI with different carbon sources and pH-values were used for enrichment and isolation of root-associated diazotrophs. The colonization density of roots by diazotrophs, as estimated from positive pellicle formation at highest dilution in nitrogen-free enrichment media, was 10⁶–10⁸ diazotrophic bacteria per g fresh root weight. Roots of the cultivar Kartiki were found to be more densely colonized endophytically by diazotrophs as detected after chloramine T (1%) surface disinfection. To ascertain the phylogenetic affiliation of the isolates, phylogenetic oligonucleotide probes and the Fluorescent in situ Hybridization (FISH) technique were applied. Using group-specific rRNA directed oligonucleotide probes, the majority of the isolates could be identified as alpha-, beta-, or gamma-proteobacteria. Using 16S and 23S rRNA-directed genus- or species-specific probes, Herbaspirillum seropedicae, Azospirillum amazonense, Burkholderia cepacia/vietnamiensis, Rhizobia and Pseudomonas spp. were found to be the most prominent root associated culturable diazotrophs. Diazotrophic Gluconacetobacter spp. were also demonstrated as colonizers of rice roots. Burkholderia cenocepacia, Pseudomonas sp. and three diazotrophic PGPR reference strains were used for the inoculation of axenically grown rice seedlings to determine the plant growth promoting potential. Significant increases in the shoot length (up to 60%), shoot dry weight (up to 33%) and the grain yield (up to 26%) per plant were observed in non-axenic pot and field trials. Using semisolid enrichment media after surface sterilization of field grown inoculated rice roots and oligonucleotide probing of the diazotrophic enrichment cultures, a sustainable colonization with the inoculated bacteria could be demonstrated.     

Uptake and Accumulation Characteristics of Arsenic and Iron Plaque in Rice at Different Growth Stages

Arsenic (As) uptake by rice plants and its toxicity to human beings have caused worldwide concerns. Investigating the characteristics of As accumulation in rice in relation to root surface iron plaque during the whole growth of rice would provide important information for devising measures to mitigate rice As uptake in As-polluted areas. Uptake and accumulation characteristics of As in rice at different growth stages as well as iron plaque on rice root surfaces were investigated in a pot culture experiment in a greenhouse. The results showed that As concentrations in roots, stems, and leaves increased with rice growth, while As concentration in spikelets decreased with grain development: 53.63% of As content in leaves, 61.51% in spikelets, and 82.09% in stems were found at both the jointing and booting stages, which suggested that the two stages were the key stages of As uptake. Root surface iron plaque at different growth stages was extracted by DCB (dithionite-citrate-bicarbonate). DCB-extractable iron (Fe) and DCB-extractable As were significantly increased with rice growth (P < 0.001), and there was a significant positive correlation between DCB-extractable Fe and As (P < 0.001), indicating that iron plaque was very important to sequester As on rice root surfaces.     

Effect of fungi associated with roots on the growth of continuously cropped upland rice

Pyrenochaeta sp. enriched on and in roots of upland rice through its continuous cropping, was shown to have an ability to inhibit the growth of upland rice in quartz or partially sterilized soil. It was established that the microorganism produced some substance inhibiting the growth of seedlings of upland rice or/in roots of the plant. The results suggested that Pyrenochaeta sp. produced this inhibitor even on/in roots of upland rice continuously cropped on the field, and may play a role in the appearance of upland rice soil sickness.     

The flavonoid naringenin enhances intercellular colonization of rice roots by<Emphasis Type="Italic"> Azorhizobium caulinodans</Emphasis>

The intercellular colonization of rice roots by Azorhizobium caulinodans and other diazotrophic bacteria has been studied using strains marked with the lacZ reporter gene. A. caulinodans were able to enter the roots of rice at emerging lateral roots (lateral root cracks) by crack entry and this was observed by light microscopy. After colonization of lateral roots, bacteria moved into intercellular space within the cortical cell layer of roots. Naringenin at 1×10^-5 and 5×10^-5 M concentration significantly enhanced root colonization. The role of nodABC and regulatory nodD genes was also studied; lateral root crack (LRC) colonization of rice was shown to be Nod factor and NodD independent. Lateral root crack colonization of rice was also observed with similar frequency following inoculation with Azospirillum brasilense and the colonization by A. brasilense was stimulated by naringenin and other flavonoid molecules.     

抗真菌转基因水稻根际土壤真菌群落结构的动态变化

以非转基因水稻"七丝软粘"为对照,采用传统平板计数法和变性梯度凝胶电泳技术,研究了抗真菌转基因水稻"转品1"和"转品8"生长周期内对根际土壤中可培养真菌数和真菌群落结构的影响。结果显示,相同生育期转基因水稻根际土壤可培养真菌数量与其非转基因对照水稻相比较无显著性差异,表明转基因水稻的种植没有对根际土壤真菌数量产生明显影响;18S rRNA真菌群落DGGE图谱分析显示,相同生育期转基因水稻与其非转基因对照水稻的根际土壤真菌DGGE条带数量和条带位置均无显著性差异,表明转基因水稻的种植没有对根际土壤真菌群落结构产生明显影响。进一步分析相同生育期转基因水稻与其非转基因对照水稻的根际土壤真菌群落香农多样性指数(Shannon diversity index)和均匀度指数(Evenness index)的动态变化,发现两者均没有显著性差异。以上研究结果表明,外源抗真菌基因的导入对水稻根际土壤中真菌群落数量和群落结构均没有明显影响。此外,将不同位置的真菌DGGE条带切胶回收,克隆、测序后,进行系统进化树分析,结果表明根际土壤真菌群落主要归属为子囊菌门(Ascomycota)、担子菌门(Basidiomycota)、壶菌门(Chytridiomycota)、接合菌门(Zygomycota)和未知真菌(unknown fungi)5个类群。     

Effect of root exudates on growth of newly isolated nitrifying bacteria from barley rhizoplane

An ammonia-oxidizing bacterium, strain PJA1, and nitrite-oxidizing bacterium, strain PJN1, were newly isolated from the rhizoplane of barley. The cells of strain PJA1 were lobate, compartmentalized, and showed characteristics of the genus Nitrosolobus. The similarity of the 16S rRNA gene to Nitrosolobus multiformis ATCC25196 was 99.04%. The cells of strain PJN1 were rod-shaped. The similarity of the 16S rRNA gene to Nitrobacter agilis ATCC14123 was 98.57%. These newly isolated bacteria were identified as Nitrosolobus sp. PJA1 and Nitrobacter sp. PJN1, respectively. The exudates prepared from barley roots of both the pre-heading and post-heading stages promoted the growth of strain PJA1 (15–20% increase). The growth of the non-rhizoplane strains like Nitrosomonas europaea ATCC25978 was remarkably inhibited by the exudates. The growth of strain PJN1 was also remarkably promoted by the root exudates at the pre-heading stage (6 time increase), and by the root exudates at the post-heading stage (2.5 time increase). The root exudates did not effect the growth of Nitrobacter winogradskyi IFO14297, isolated from the non-rhizoplane.     

Bacterial communities in manganese nodules in rice field subsoils: Estimation using PCR-DGGE and sequencing analyses

Abstract

The phylogenetic positions of bacterial communities in manganese (Mn) nodules from subsoils of two Japanese rice fields were estimated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by sequencing of 16S rDNA. The DGGE band patterns and sequencing analysis of characteristic DGGE bands revealed that the bacterial communities in Mn nodules were markedly different from those in the plow layer and subsoils. Three out of four common bands found in Mn nodules from two sites corresponded to Deltaproteobacteria and were characterized as sulfate-reducing and iron-reducing bacteria. The other DGGE bands of Mn nodules corresponded to sulfate and iron reducers (Deltaproteobacteria), methane-oxidizing bacteria (Gamma and Alphaproteobacteria), nitrite-oxidizing bacteria (Nitrospirae) and Actinobacteria. In addition, some DGGE bands of Mn nodules showed no clear affiliation to any known bacteria. The present study indicates that members involved in the reduction of Mn nodules dominate the bacterial communities in Mn nodules in rice field subsoils.