Structure and activity of bacterial community inhabiting rice roots and the rhizosphere

Root-derived carbon provides a major source for microbial production and emission of CH4 from rice field soils. Therefore, we characterized the structure and activity of the bacterial community inhabiting rice roots and the rhizosphere. In the first experiment, DNA retrieved from rice roots was analysed for bacterial 16S rRNA genes using cloning, sequencing and in situ hybridization. In the second experiment, rice plants were pulse-labelled with 13CO2 (99% of atom 13C) for 7 days, and the bacterial RNA was isolated from rhizosphere soil and subjected to density gradient centrifugation. RNA samples from density fractions were analysed by terminal restriction fragment length polymorphism fingerprinting, cloning and sequencing. The experiments showed that the dominant bacteria inhabiting rice roots and the rhizosphere particularly belonged to the Alphaproteobacteria, Betaproteobacteria and Firmicutes. The RNA stable isotope probing revealed that the bacteria actively assimilating C derived from the pulse-labelled rice plants were Azospirillum spp. (Alphaproteobacteria) and members of Burkholderiaceae (Betaproteobacteria). Both anaerobic (e.g. Clostridia) and aerobic (e.g. Comamonas) degraders were present at high abundance, indicating that root environments and degradation processes were highly heterogeneous. The relative importance of iron and sulfate reducers suggested that cycling of iron and sulfur is active in the rhizosphere.     

Expression of serotonin derivative synthetic genes on a single self-processing polypeptide and the production of serotonin derivatives in microbes

Soils are rich in organics, particularly those that support growth of plants. These organics are possible sources of sustainable energy, and a microbial fuel cell (MFC) system can potentially be used for this purpose. Here, we report the application of an MFC system to electricity generation in a rice paddy field. In our system, graphite felt electrodes were used; an anode was set in the rice rhizosphere, and a cathode was in the flooded water above the rhizosphere. It was observed that electricity generation (as high as 6 mW/m², normalized to the anode projection area) was sunlight dependent and exhibited circadian oscillation. Artificial shading of rice plants in the daytime inhibited the electricity generation. In the rhizosphere, rice roots penetrated the anode graphite felt where specific bacterial populations occurred. Supplementation to the anode region with acetate (one of the major root-exhausted organic compounds) enhanced the electricity generation in the dark. These results suggest that the paddy-field electricity-generation system was an ecological solar cell in which the plant photosynthesis was coupled to the microbial conversion of organics to electricity.     

New Insights into How Increases in Fertility Improve the Growth of Rice at the Seedling Stage in Red Soil Regions of Subtropical China

The differences in rhizosphere nitrification activities between high- and low- fertility soils appear to be related to differences in dissolved oxygen concentrations in the soil, implying a relationship to differences in the radial oxygen loss (ROL) of rice roots in these soils. A miniaturised Clark-type oxygen microelectrode system was used to determine rice root ROL and the rhizosphere oxygen profile, and rhizosphere nitrification activity was studied using a short-term nitrification activity assay. Rice planting significantly altered the oxygen cycling in the water-soil system due to rice root ROL. Although the oxygen content in control high-fertility soil (without rice plants) was lower than that in control low-fertility soil, high rice root ROL significantly improved the rhizosphere oxygen concentration in the high-fertility soil. High soil fertility improved the rice root growth and root porosity as well as rice root ROL, resulting in enhanced rhizosphere nitrification. High fertility also increased the content of nitrification-induced nitrate in the rhizosphere, resulting in enhanced ammonium uptake and assimilation in the rice. Although high ammonium pools in the high-fertility soil increased rhizosphere nitrification, rice root ROL might also contribute to rhizosphere nitrification improvement. This study provides new insights into the reasons that an increase in soil fertility may enhance the growth of rice. Our results suggest that an amendment of the fertiliser used in nutrient- and nitrification-poor paddy soils in the red soil regions of China may significantly promote rice growth and rice N nutrition.     

Isolation of Sphingomonas Strains from Ears of Rice and Other Plants of Family Gramineae

Sphingomonas strains were isolated in high frequency from ears of rice (Oryza sativa), Echinochloa crus-galli, and Setaria viridis. Isolates were identified by the rapid method of cellular fatty acid analysis. Isolated Sphingomonas strains have 2-hydroxymyristate as a sole hydroxy fatty acid, ubiquinone Q-10, and glycosphingolipid. This study demonstrated that sphingomonads are members of a natural flora of microorganisms in ears of rice and taxonomically related plants.     

New evidence for Neolithic rice cultivation and Holocene environmental change in the Fuzhou Basin,southeast China

A stratified profile of the Zhuangbianshan (ZBS) archaeological site (Fuzhou Basin, Fujian) was studied to investigate Neolithic era anthropogenic influence and associated environmental changes. Analysis of the archaeological sediments focused on phytoliths, palynomorphs and microcharcoal. Until now, a lack of direct evidence for agriculture has made it difficult to know if Neolithic cultures of this area relied on the exploitation of wild plants such as nuts and sago palm, or a combination of farming and foraging. Three types of rice phytoliths were found in ZBS archaeological deposits, providing robust evidence for rice farming as part of a broad-spectrum Neolithic subsistence economy centered on fishing and hunting. Chronologies based on AMS ¹⁴C dates and artifact typology place the earliest rice during the Tanshishan (TSS) Period (5,000–4,300 cal bp) followed by a shift to economic dependency on rice in the Huangguashan (HGS) Period (4,300–3,500 cal bp). The ZBS phytolith assemblage contains high frequencies of rice husk (peaked-shape glume cells) phytoliths, with far fewer leaf and stem types. This indicates late stage processing activities such as dehusking, implying a focus on consumption rather than rice production. High concentrations of charcoal in the Neolithic ZBS deposits indicate local human settlement and peaks in fire use. The ZBS pollen record also reflects human settlement and peaks in local forest clearance during the Neolithic. Forest cover was renewed when the site was temporarily abandoned following the Neolithic. Rapid formation of the Min River floodplain began ~2,000 cal bp in association with retreating sea level and intensifying anthropogenic influence. Prior to that, rice farming in the Fuzhou Basin was limited by the scarcity of wetlands suitable for agriculture.     

Bacterial Biosynthesis of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase and Indole-3-Acetic Acid (IAA) as Endophytic Preferential Selection Traits by Rice Plant Seedlings

In this study, bacteria were isolated from the rhizosphere and inside the roots and nodules of berseem clover plants grown in the field in Iran. Two hundred isolates were obtained from the rhizosphere (120 isolates), interior roots (57 isolates), and nodules (23 isolates) of clover plants grown in rotation with rice plants. Production of chitinase, pectinase, cellulase, siderophore, salicylic acid, hydrogen cyanide, indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, solubilization of phosphate, antifungal activity against various rice plant pathogen fungi, N₂ fixation, and colonization assay on rice seedlings by these strains was evaluated and compared (endophytic isolates vs. rhizosphere bacteria). The results showed both the number and the ability of plant growth-promoting (PGP) traits were different between endophytic and rhizosphere isolates. A higher percentage of endophytic isolates were positive for production of IAA, ACC deaminase, and siderophore than rhizosphere isolates. Therefore, it is suggested that clover plant may shape its own associated microbial community and act as filters for endophyte communities, and rhizosphere isolates with different (PGP) traits. We also studied the PGP effect of the most promising endophytic and rhizosphere isolates on rice seedlings. A significant relationship among IAA and ACC deaminase production, the size of root colonization, and plant growth (root elongation) in comparison with siderophore production and phosphate solubilization for the isolates was observed. The best bacterial isolates (one endophytic isolate and one rhizosphere isolate), based on their ability to promote rice growth and colonize rice roots, were identified. Based on 16S rDNA sequence analysis, the endophytic isolate CEN7 and the rhizosphere isolate CEN8 were closely related to Pseudomonas putida and Pseudomonas fluorescens, respectively. It seems that PGP trait production (such as IAA, ACC deaminase) may be required for endophytic and rhizosphere competence as compared to other PGP traits in rice seedlings under constant flooded conditions. The study also shows that the presence of diverse rhizobacteria with effective growth-promoting traits associated with clover plants may be used for sustainable crop management under field conditions.     

Are drought-resistance promoting bacteria cross-compatible with different plant models?

The association between plant and plant growth promoting bacteria (PGPB) contributes to the successful thriving of plants in extreme environments featured by water shortage. We have recently shown that, with respect to the non-cultivated desert soil, the rhizosphere of pepper plants cultivated under desert farming hosts PGPB communities that are endowed with a large portfolio of PGP traits. Pepper plants exposed to bacterial isolates from plants cultivated under desert farming exhibited a higher tolerance to water shortage, compared with untreated control. This promotion was mediated by a larger root system (up to 40%), stimulated by the bacteria, that enhanced plant ability to uptake water from dry soil. We provide initial evidence that the nature of the interaction can have a limited level of specificity and that PGPB isolates may determine resistance to water stress in plants others than the one of the original isolation. It is apparent that, in relation to plant resistance to water stress, a feature of primary evolutionary importance for all plants, a cross-compatibility between PGPB and different plant models exists at least on a short-term.     

Soil acidification and adaptations of plants and microorganisms in Bornean tropical forests

In tropical forest ecosystems, a paradoxical relationship is commonly observed between massive biomass production and low soil fertility (low pH). The loss and deficiency of soil phosphorus (P) and bases generally constrain biomass production; however, high productivity on nutrient-deficient soils of Bornean tropical forests is hypothesized to be maintained by plant and microorganism adaptation to an acidic soil environment. Proton budgets in the plant–soil system indicated that plants and microorganisms promote acidification to acquire bases, even in highly acidic tropical soils. The nitric and organic acids they produce contribute to the mobilization of basic cations and their uptake by plants. In response to soil P deficiency and the recalcitrance of lignin-rich organic matter, specific trees and fungi can release organic acids and enzymes for nutrient acquisition. Organic acids exuded by roots and rhizosphere microorganisms can promote the solubilization of P bonded to aluminum and iron oxides and its uptake by plants from P-poor soils. Lignin degradation, a rate-limiting step in organic matter decomposition, is specifically enhanced in acidic organic layers by lignin peroxidase, produced by white-rot fungi, which may solubilize recalcitrant lignin and release soluble aromatic substances into the soil solution. This dissolved organic matter functions in the transport of nitrogen, P, and basic cations in acidic soils without increasing leaching loss. In Bornean tropical forests, soil acidification is promoted by plants and microorganisms as a nutrient acquisition strategy, while plant roots and fungi can develop rhizosphere and enzymatic processes that promote tolerance of low pH.     

An overview of rhizosphere processes related with plant nutrition in major cropping systems in China

Rhizosphere processes of individual plants have been widely investigated since 1904 when the term “rhizosphere” was first put forward. However, little attention has been paid to rhizosphere effects at an agro-ecosystem level. This paper presents recent research on the rhizosphere processes in relation to plant nutrition in main cropping systems in China. In the peanut (Arachis hypogaea L.)/maize (Zea mays L.) intercropping system, maize was found to improve the Fe nutrition of peanut through influencing its rhizosphere processes, suggesting an important role of phytosiderophores released from Fe-deficient maize. Intercropping between maize and faba bean (Vicia faba L.) was found to improve nitrogen and phosphorus uptake in the two crops compared with corresponding sole crop. There was a higher land equivalent ratio (LER) in the intercropping system of maize and faba bean than the treatment of no root interactions between the two crops. The increased yield of maize intercropped with faba bean resulted from an interspecific facilitation in nutrient uptake, depending on interspecific root interactions of the two crops. In the rotation system of rice (Oryza sativa L.)-wheat (Triticum aestivum L.) crops, Mn deficiency in wheat was caused by excessive Mn uptake by rice and Mn leaching from topsoil to subsoil due to periodic cycles of flooding and drying. However, wheat genotypes tolerant to Mn deficiency tended to distribute more roots to deeper soil layer and thus expand their rhizosphere zones in the Mn-deficient soils and utilize Mn from the subsoil. Deep ploughing also helped root penetration into subsoil and was propitious to correcting Mn deficiency in wheat rotated with rice. In comparison, oilseed rape (Brassica napus L.) took up more Mn than wheat through mobilizing sparingly soluble soil Mn due to acidification and reduction processes in the rhizosphere. Thus, oilseed rape was tolerant to the Mn-deficient conditions in the rice-oilseed rape rotation. Oxidation reactions on root surface of rice also resulted in the formation of Fe plaque in the rice rhizosphere. Large amounts of Zn were accumulated on the Fe plaque. Zinc uptake by rice plants increased as Fe plaque formed, but decreased at high amounts of Fe plaque. It is suggested that to fine-tune cropping patterns and optimize nutrient management based on a better understanding of rhizosphere processes at an agro-ecosystem level is crucial for increasing nutrient use efficiency and developing sustainable agriculture in China.     

基于Ecopath评估蟹-稻复合生态系统营养结构和能量流动

蟹-稻综合种养模式为我国水产养殖以及农业从单一经营转变为复合经营提供了一种新模式,为了促进蟹-稻共作模式的推广和普及,应用Ecopath生态通道模型对该系统进行了营养结构和能量流动的分析。研究结果表明蟹-稻共作生态系统的最高营养级(3.140)高于稻田单作系统的最高营养级(2.676),生态系统的能量流动主要有两条途径,即以沉水植物和其他维管束植物为起点的牧食链及以碎屑为起点的腐质链;蟹-稻共作农田生态系统在6月和10月的Finn′s循环指数(Finn′s cycling index,FCI,0.55和1)和Finn′s循环平均能流路径长度(Finn′s cycling mean path length,FCL,2.066和2.077),稻田单作农田生态系统在6月和10月的FCI(1.14和0.81)和FCL(2.089和2.137),说明蟹-稻共作模式可以形成一个稳定的生态系统,中华绒螯蟹的加入可以促进该完整的生态系统的能量流动,且随着螃蟹的成长,系统成熟度有所提高,只是较单作系统的成熟度低,共作系统有更大的成熟空间;蟹-稻共作农田生态系统在6月和10月的连接指数(Connectance index,CI)分别为0.135和0.135,稻田单作系统在6月和10月的CI为0.188和0.161,共作系统的各功能组之间的连接强度较单作系统弱,稳定程度相对较低,蟹-稻共作农田生态系统的初级生产力显著高于单作农田生态系统,且蟹-稻共作农田生态系统的发育良好。     

Soil and crop management strategies to prevent iron deficiency in crops

Plants and humans cannot easily acquire iron from their nutrient sources although it is abundant in nature. Thus, iron deficiency is one of the major limiting factors affecting crop yields, food quality and human nutrition. Therefore, approaches need to be developed to increase Fe uptake by roots, transfer to edible plant portions and absorption by humans from plant food sources. Integrated strategies for soil and crop management are attractive not only for improving growing conditions for crops but also for exploiting a plant??s potential for Fe mobilization and utilization. Recent research progress in soil and crop management has provided the means to resolve complex plant Fe nutritional problems through manipulating the rhizosphere (e.g., rhizosphere fertilization and water regulation), and crop management (includes managing cropping systems and screening for Fe efficient species and varieties). Some simple and effective soil management practices, termed ??rhizosphere fertilization?? (such as root feeding and bag fertilization) have been developed and widely used by local farmers in China to improve the Fe nutrition of fruit plants. Production practices for rice cultivation are shifting from paddy-rice to aerobic rice to make more efficient use of irrigation water. This shift has brought about increases in Fe deficiency in rice, a new challenge depressing iron availability in rice and reducing Fe supplies to humans. Current crop management strategies addressing Fe deficiency include Fe foliar application, trunk injection, plant breeding for enriched Fe crop species and varieties, and selection of cropping systems. Managing cropping systems, such as intercropping strategies may have numerous advantages in terms of increasing Fe availability to plants. Studies of intercropping systems on peanut/maize, wheat/chickpea and guava/sorghum or -maize increased Fe content of crops and their seed, which suggests that a reasonable intercropping system of iron-efficient species could prevent or mitigate Fe deficiency in Fe-inefficient plants. This review provides a comprehensive comparison of the strategies that have been developed to address Fe deficiency and discusses the most recent advance in soil and crop management to improve the Fe nutrition of crops. These proofs of concept studies will serve as the basis for future Fe research and for integrated and optimized management strategies to alleviate Fe deficiency in farmers?? fields.     

Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution

The genus Burkholderia comprises 19 species, including Burkholderia vietnamiensis which is the only known N(2)-fixing species of this bacterial genus. The first isolates of B. vietnamiensis were recovered from the rhizosphere of rice plants grown in a phytotron, but its existence in natural environments and its geographic distribution were not reported. In the present study, most N(2)-fixing isolates recovered from the environment of field-grown maize and coffee plants cultivated in widely separated regions of Mexico were phenotypically identified as B. cepacia using the API 20NE system. Nevertheless, a number of these isolates recovered from inside of maize roots, as well as from the rhizosphere and rhizoplane of maize and coffee plants, showed similar or identical features to those of B. vietnamiensis TVV75(T). These features include nitrogenase activity with 10 different carbon sources, identical or very similar nifHDK hybridization patterns, very similar protein electrophoregrams, identical amplified 16S rDNA restriction (ARDRA) profiles, and levels of DNA-DNA reassociation higher than 70% with total DNA from strain TVV75(T). Although the ability to fix N(2) is not reported to be a common feature among the known species of the genus Burkholderia, the results obtained show that many diazotrophic Burkholderia isolates analyzed showed phenotypic and genotypic features different from those of the known N(2)-fixing species B. vietnamiensis as well as from those of B. kururiensis, a bacterium identified in the present study as a diazotrophic species. DNA-DNA reassociation assays confirmed the existence of N(2)-fixing Burkholderia species different from B. vietnamiensis. In addition, this study shows the wide geographic distribution and substantial capability of N(2)-fixing Burkholderia spp. for colonizing diverse host plants in distantly separated environments.     

Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plants

Despite their importance for rhizosphere functioning, rhizobacterial Pseudomonas spp. have been mainly studied in a cultivation-based manner. In this study a cultivation-independent method was used to determine to what extent the factors plant species, sampling site and year-to-year variation influence Pseudomonas community structure in bulk soil and in the rhizosphere of two Verticillium dahliae host plants, oilseed rape and strawberry. Community DNA was extracted from bulk and rhizosphere soil samples of flowering plants collected at three different sites in Germany in two consecutive years. Pseudomonas community structure and diversity were assessed using a polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) system to fingerprint Pseudomonas-specific 16S rRNA gene fragments amplified from community DNA. Dominant and differentiating DGGE bands were excised from the gels, cloned and sequenced. The factors sampling site, plant species and year-to-year variation were shown to significantly influence the community structure of Pseudomonas in rhizosphere soils. The composition of Pseudomonas 16S rRNA gene fragments in the rhizosphere differed from that in the adjacent bulk soil and the rhizosphere effect tended to be plant-specific. The clone sequences of most dominant bands analysed belonged to the Pseudomonas fluorescens lineage and showed closest similarity to culturable Pseudomonas known for displaying antifungal properties. This report provides a better understanding of how different factors drive Pseudomonas community structure and diversity in bulk and rhizosphere soils.     

Rhizosphere pH as a result of nitrogen levels and NH4/NO3 ratio and its effect on zinc availability and on growth of rice flower (Ozothamnus diosmifolius)

The effect of modification of the rhizosphere pH, via solution-N concentration and source, on rice flower (Ozothamnus diosmifolius, Astraceae) growth was investigated in two different experiments. In order to simulate a wide range of pHs easily, the plants were grown in an inert artificial substrate (perlite). In the first the rhizosphere pH was modified through variation of N concentrations and the NH₄/NO₃-N ratio in the irrigation water. In the second the rhizosphere pH was modified solely by altering the NH₄/NO₃-N ratio while irrigation-N concentration was held at the level found to be optimal in the first experiment. Cultivation of rice flower, a new crop in Israel, is hampered by lack of knowledge on its Zn nutrition. Because availability of soil Zn largely depends on pH we investigated in the second experiment the effect of Zn foliar application. The growth of rice flower plants under low-N fertilization or low NH₄/NO₃-N ratio was poor and the plants exhibited growth disorders such as tipburn, severe chlorosis and necrosis. These growth disorders could not be ascribed to any direct effect of N nutrition therefore it was suggested that the indirect effect of the treatments, e.g., the rhizosphere pH dominates rice flower growth through its effect on nutrient availability. The only nutrient that was significantly correlated with pH and yield parameters in both experiments was Zn. All irrigation-nutrients concentrations were within the recommended range for hydroponically grown plants; however, the leaf-Mn concentration of plants grown in pH above 7.5 was in the toxic range while that of Zn was deficient. The high preferential uptake of Mn over Zn by rice flower plants and the question of whether high Mn uptake induced Zn deficiency remain open.     

稻、麦根系H~ 的分泌与介质磷水平的关系

水稻、小麦根系H~ 的分泌量随供磷水平的降低而增加,并存在明显的昼夜变化。在自然光照下H~ 分泌量随光强度增加而增多,同时强光比黑暗时H~ 分泌对磷供应水平更为敏感。磷供应不足还诱导水稻根系柠檬酸分泌量增加,而苹果酸则差异不明显。难溶性磷的溶解率与根系H~ 和柠檬酸分泌所导致的根际pH下降有密切联系。因此,在有效磷不足的条件下可明显提高稻、麦根际土壤中难溶性磷的利用率,其中丰产型小麦和粳稻品种对土壤中磷利用的根际效应更为显著。     

稻鸭共作对水稻条纹叶枯病发生规律的影响

由灰飞虱传毒危害的水稻条纹叶枯病是近年来在我国部分稻作区严重发生的病毒病害.作为稻作生产生态实践模式之一的稻鸭共作技术对稻田病虫草具有显著的控制效应,然而目前还没有关于稻鸭共作对灰飞虱和条纹叶枯病影响的报道.因此,于2004～2005年在南京农业大学东台试验场进行了田间实验,共设计了4个处理,分别为常规稻作区（不养鸭、施药）、稻鸭共作区（养鸭、不施药）和秧田期覆盖防虫网、栽后大田稻鸭共作区（秧田覆盖防虫网、栽后稻田养鸭、不施药）和对照区（不养鸭、不施药）.结果表明：稻鸭共作以及秧田期覆盖防虫网、栽后大田稻鸭共作处理对灰飞虱有显著的控制效应,因此也显著降低了两处理在水稻整个生长期间条纹叶枯病的发病率;稻鸭共作处理对条纹叶枯病的综合防效为79.44﹪,略高于常规稻作78.82﹪的防效,而秧田期覆盖防虫网、栽后大田稻鸭共作处理对稻田灰飞虱和条纹叶枯病的防治效果最好,对条纹叶枯病的防效超过94.01﹪.总之,通过以上试验结果可知,稻鸭共作尤其是秧田期覆盖防虫网、栽后稻鸭共作处理为防治条纹叶枯病提供了一条安全高效的生态控制途径.     

Anaerobic consumers of monosaccharides in a moderately acidic fen

16S rRNA-based stable isotope probing identified active xylose- and glucose-fermenting Bacteria and active Archaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH(4)-emitting fen. Xylose and glucose were converted to fatty acids, CO(2), H(2), and CH(4) under moderately acidic, anoxic conditions, indicating that the fen harbors moderately acid-tolerant xylose- and glucose-using fermenters, as well as moderately acid-tolerant methanogens. Organisms of the families Acidaminococcaceae, Aeromonadaceae, Clostridiaceae, Enterobacteriaceae, and Pseudomonadaceae and the order Actinomycetales, including hitherto unknown organisms, utilized xylose- or glucose-derived carbon, suggesting that highly diverse facultative aerobes and obligate anaerobes contribute to the flow of carbon in the fen under anoxic conditions. Uncultured Euryarchaeota (i.e., Methanosarcinaceae and Methanobacteriaceae) and Crenarchaeota species were identified by 16S rRNA analysis of anoxic slurries, demonstrating that the acidic fen harbors novel methanogens and Crenarchaeota organisms capable of anaerobiosis. Fermentation-derived molecules are conceived to be the primary drivers of methanogenesis when electron acceptors other than CO(2) are absent, and the collective findings of this study indicate that fen soils harbor diverse, acid-tolerant, and novel xylose-utilizing as well as glucose-utilizing facultative aerobes and obligate anaerobes that form trophic links to novel moderately acid-tolerant methanogens.     

Copper bioavailability and rhizosphere pH changes as affected by nitrogen supply for tomato and oilseed rape cropped on an acidic and a calcareous soil

Vineyard soils have been contaminated by long-term applications of copper salts as fungicides against mildew, raising the question of the bioavailability (and toxicity) of such accumulated Cu to cultivated plants which can replace vines. The aim of this study was to assess, in an acidic and a calcareous Cu-contaminated soil, how the extractability and bioavailability of soil Cu was affected by pH changes in the rhizosphere of two plant species (oilseed rape and tomato), in response to various forms of nitrogen supply (nitrate only or both nitrate and ammonium). Besides shoot analysis, the experimental approach used in the present work provided an easy access to both roots and rhizosphere soil. Roots of tomato and rape induced a systematic acidification in the calcareous soil while root-induced alkalinization occurred in the acidic soil. Whilst few differences were found between treatments in the calcareous soil, oilseed rape took up more Cu and also alkalinized its rhizosphere more strongly than tomato in the acidic soil. The growth of tomato roots was restricted in the acidic soil, while that of oilseed rape was not, suggesting that tomato was either more sensitive to soil acidity and/or Cu toxicity. A major finding was that, in the acidic soil, Cu bioavailability increased with increasing rhizosphere pH. This was largely due to the enhanced accumulation of Cu in the root compartment of both species with increasing rhizosphere pH. The hypothetical explanation proposed here is that Cu binding to root cell walls played a major role in the accumulation of Cu into the plant. Apoplasmic Cu (Cu bound to cell walls) would indeed be expected to increase with increasing pH as a consequence of the pH-dependency of the charges of cell wall constituents.     

Selection of mixed inoculants exhibiting growth-promoting activity in rice plants from undefined consortia obtained by continuous enrichment

Aims

The main objective of this study was to test the hypothesis that isolating and characterizing bacterial suspensions (undefined consortia) from the root/rhizosphere of rice will contribute to the selection of mixtures of rhizobacteria with better growth-promoting activity of rice plants.

Methods

Bacterial consortia were obtained from roots/rhizosphere soil samples of rice plants grown under upland and irrigated production systems. Those undefined consortia were subjected to five consecutive passes every 7 days in NFb (N-free broth) semisolid medium. Thereafter, strains of each growth-promoting consortia were isolated by plating on three different culture media. Then, undefined consortia, as well as mix and single bacterial strains, were characterized in terms of indoleacetic acid production, nitrogen fixation capacity, and growth promotion of rice plants.

Results

Of the 72 consortia analyzed, 41.7 % and 50.0 % increased nitrogenase activity and the production of indolic compounds, respectively, after 5 continuous passes in NFB medium. Three undefined consortia, 11 single strains and 5 strain mixtures, exhibited plant growth promotion in rice plants under greenhouse conditions.

Conclusions

Continuous enrichment in Nfb medium of undefined consortia from root/rhizosphere soil is a good strategy for the selection of plant growth-promoting bacteria for rice plants.     

Microbial Communities of Continuously Cropped, Irrigated Rice Fields

In continuously cropped, irrigated rice fields, soil microbial biomass as measured by total phospholipid fatty acid concentrations declined during the second half of the crop cycle. This decline was also observed in other components of the microbial community assessed by viable counts, including denitrifiers and sporeformers. Simultaneous with total biomass decline was the increase in potential indicators of nutrient stress--such as ratios of cyclopropanol ((Sigma)[cy/(omega)7c]) and trans ((Sigma)[(omega)7t/(omega)7c]) phospholipid fatty acids--in plain crop soil but not in the rhizosphere. Polyhydroxyalkanoate levels were enhanced in the root environment of mature rice. Polyunsaturated eukaryotic biomarkers accounted for only 13 to 16 mol% of the total phospholipids, including 2 mol% of 18:2(omega)6, which is considered a fungal biomarker. Single biomarkers for defined physiological groups of bacteria did not follow the declining trend of total microbial biomass. Signature compounds for gram-positive and gram-negative fermenters (plasmalogen phospholipids), methanogenic bacteria (diether lipids), and methanotrophs (18:1(omega)8c) increased as the crop approached maturity. Methanotrophs were not particularly enriched in the rhizosphere. Methanogenic biomarkers were, however, most abundant in root extracts from mature rice plants. Assuming that soil microbial biomass plays a significant role as a passive nutrient pool, its reduction during the second half of the cropping season suggests a mechanism that may ultimately contribute to declining productivity in irrigated, continuous rice cropping systems.