The "Plant Root" is taking off. It is fitting that we should commemorate the birth of our new journal for a moment. It is certainly an honor to have a chance to send a message for the inaugural issue. Here I would like to describe the background of launching this journal and our hopes for its destination. I think it is good to capture and write down the atmosphere now, I believe, that is shared by the people who are involved in the launching of this journal.

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The effects of field application of liquid pig (Sus scrofa) slurry (PS) on the root system of maize (Zea mays L.) were assessed during two successive cropping seasons in a tropical environment. Root development was monitored on a plot treated with pig slurry, corresponding to a total nitrogen input of 265 kg N ha^-1 the first year and 185 kg N ha^-1 the second year, in comparison to that recorded in an unfertilized control plot (C plot). In both treatments, the root system was determined at four phenological stages by the trench-profile method and using a model that calculates root length density from counts of numbers of living roots. The results showed that PS had a positive effect on maize aboveground biomass until harvest. Its effect on root development was very positive during the first third of the cycle (+130% for the root length density), but this beneficial impact quickly vanished. At the grain maturation stage, the root length was 18% lower on the PS plot as compared to the C plot, despite the much higher shoot biomass (+50%). It was concluded that one factor began having an adverse effect on root growth in the surface soil layer during the maize growth cycle. This factor was not fully identified, but several elements suggest that it involved soil acidification associated with the nitrification of ammonium nitrogen in PS in this already relatively acid soil. This could lead to a rhizotoxicity problem.

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Bacteria in the rhizosphere influence plant growth and interact with plant roots. Microscopy and culture method have been used for studies of microorganisms of the rhizosphere, but these methods are insufficient for evaluation because most rhizosphere bacteria are viable but non-culturable (VBNC). Bacteria in the rhizosphere of rice cultivated in Andosol lowland and upland fields were analyzed in this study using PCR-DGGE and FISH, in combination with modified pretreatments. Results show that the two methods with the pretreatments, more than conventional methods, provided a rapid and simple analysis of rhizosphere bacteria. The 16S rDNA band pattern of bacteria in the rhizosphere obtained using PCR-DGGE indicated different species composition of bacterial community in the two ecosystems and greater diversity of bacteria in the rhizosphere in upland field. Sequencing of major 16S rDNA bands identified Bacterium A35 and Clostridium bifermentans as dominant bacteria in the rhizosphere of rice in lowland fields and Klebsiella planticola and Bacillus fusiformis in upland fields. Furthermore, FISH observation indicated the predominance of gram-positive low GC bacteria in both rhizospheres and a higher proportion of Clostridium spp. in lowland fields, which is consistent with results of PCR-DGGE analysis. The results suggest that the bacteria in the rice rhizosphere can be changed depending on aerobic and anaerobic conditions of fields. It is expected to apply the PCR-DGGE and FISH to agricultural field experiments as reliable methods to evaluate the rhizosphere bacteria.

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We evaluated variation in nodal root angle in the genus Zea and performed quantitative trait locus (QTL) mapping for the trait. Angle (in degrees) of roots emerging from the second (2nd-root angle) and third (3rd-root angle) nodes from the bottom of shoot showed wide variation in nine accessions; relatively high repeatability was obtained. QTL analyses controlling root angle were performed in the two sets of F₂ populations (127 individuals in Trial A and 123 in Trial B) developed from different crossings of maize ‘B73’ (deep-rooting) × teosinte ‘Zea luxurians’ (shallow-rooting). In Trial A, we used an SSR-based map with 107 markers, covering 1,329 cM throughout all ten chromosomes. By composite interval mapping analysis, four QTLs were identified, two on chromosome 10 for 2nd-root angle and one each on chromosomes 2 and 7 for 3rd-root angle. In Trial B, using a 1,397 cM SSR-based map with 92 markers, one QTL was located on chromosome 4 and two on chromosome 7 for 2nd-root angle and one each on chromosomes 2, 4 and 7 for 3rd-root angle. The QTL on chromosome 7 (identified as Qra2nd3rd7.04) was consistently found across the trials. A potential role of the Qra2nd3rd7.04 in controlling angles of nodal roots and thus flooding tolerance was discussed.

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Plant associated endophytic Acremonium species are capable of interacting with the host plant and altering its response towards pathogens and pests. Specialized root-colonizing Acremonium spp. can achieve biocontrol effects based on induced disease resistance in whole plant assays. However, these fungi are hard to detect and to study in root tissue by classical methods of light microscopy or microbiology. To enable further progress in investigations of induced mechanisms of defence in the plant, better visualization of the endophytic symbiont Acremonium strictum was attempted by use of autofluorescent GFP-transformants. Subcultures of three stable transformed A. strictum-isolates were used in agar plate assays with sterilized flax seedlings to document root colonization and infection with confocal laser scanning microscopy. In greenhouse tests the fitness of the transformants was proved in comparison to the wild type A. strictum for bioprotection against Fusarium-wilt. In these trials the endophyte trait to reduce disease incidence and symptom severity was verified in all three transformants as well as in the wild type of A. strictum. The suitability of these transformants for further research scopes and microscopy methods are indicated.

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Fine-root turnover is an important component of forest carbon dynamics. We detail the characteristics of the minirhizotron method of measuring fine-root turnover and discuss its methodological implications. Minirhizotron data are relative values proportional to the data taken from the bulk, in situ soil, since they are taken at the soil-tube interface, so we propose several ways to validate minirhizotron data. Most short-term studies show fine-root production to be higher than fine-root mortality, suggesting that disturbance resulting from minirhizotron installation continues for several years. Initial-years results tend to lead to overestimates of fine-root dynamics, although these results define the maximal limits of fine-root production and mortality. We compare the definitions of fine-root turnover and methods of calculation used in different studies. We find that values of fine-root turnover depend on the definition of fine roots, methods of measurement, definition of turnover, and methods of calculation, so these factors must be taken into account when turnover values are discussed. In addition, soil depth is a key factor in the study of fine-root turnover, as is variation in the physical qualities, form and function, of the fine roots. Further long-term research into these key factors in relation to biotic and abiotic parameters will improve our knowledge of forest carbon dynamics.

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The root systems of higher plant consist of primary, lateral, and adventitious roots. There is a current hypothesis, named ‘root apical dominance’, that root-derived suppressor negatively regulates the formation of adventitious and lateral roots. According to this hypothesis, we have studied the mechanisms involved in the regulation of adventitious and lateral root forma-tion. trans-zeatin riboside (ZR), one of cytokinin species, was identified in squash root xylem sap as a main suppressor of adventitious root formation in cucumber, suggesting that ZR transported from root via xylem sap acts as an endogenous suppressor of hypocotyl adventi-tious root formation in planta. Moreover, we isolated Arabidopsis mutant, wooden leg-3 (wol-3), for stimulated adventitious root formation in intact plants. Analyses of wol-3 mutant have revealed that cytokinin receptors are necessary for the primary and lateral root formation via the formation of auxin-transporting vascular tissues in the hypocotyl, but not for adventitious roots. In this review, we discuss the relationship between cytokinin and adventitious and lateral root formation.

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Aquaporins (water channels) are membrane proteins which facilitate the transport of water and low molecular weight compounds across biological membranes. The author and collaborators identified barley aquaporins and investigated the level of transcripts in roots, water transport activity, tissue localization, expression reduction by salt stress, and diurnal changes in the expression of a particular aquaporin. Over-expression of a barley aquaporin, HvPIP2;1, increased the shoot/root ratio and raised salt sensitivity in transgenic rice plants. Aquaporin research is providing significant insights into the water relations of plant roots.

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Flooding or waterlogging is a major factor in reducing crop yields. In order to increase crop productivity in temporarily flooded soils, development of flooding-tolerant lines is required. Three primary factors affecting flooding tolerance in plants have been reported: (1) the ability to grow adventitious roots at the soil surface during flooding; (2) the capacity to form root aeren-chyma; and (3) tolerance to toxins (e.g., Fe²⁺, H₂S) under reducing soil conditions. By analyzing these components separately, it could be possible to perform selections for genotypes exhibiting varying degrees of flooding tolerance. In quantitative trait locus (QTL) analyses for flooding tolerance, using teosinte as a germ-plasm resource, we have identified several QTLs associated to flooding traits. Based on the DNA marker information linked to flooding tolerance-related QTLs, the potential transfer of QTLs conferring flooding tolerance from teosinte to maize and pyramiding these QTLs into selected maize lines are now possible.

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The Arabidopsis root is a model system for studying root growth, development, and response to environmental stresses. Due to its small size, many Arabidopsis seedlings can be cultured in a single nutrient-containing agar plate. Two of the common parameters used to evaluate root growth are the root length and the elongation rate. Various methods including manual measurement and digital image analysis can be used to measure the root length. In this paper, we report the development of a simple color image analysis program, RootLM, in combination with a modified marking technique of root growth on the surface of a Petri dish, for length measurement of primary roots. Our method provides an alternative tool to quickly generate accurate and reproducible root growth measurement with a minimum equipment requirement. In addition, the program is free for public download.

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The aim of this study is to evaluate the effects of plant root on soil organisms. The response of soil organisms (microbes, nematodes, and microarthropods) to root and fertilization (four inorganic fertilization regimes and organic fertilization) was studied in a wheat field in Japan. Microbial substrate-induced respiration (SIR) and the population densities of nematodes and microarthropods in the rhizosphere and interrow soil were measured from April to June in 2004 and 2005. Application of inorganic NPK fertilizer had positive effects on the population densities of all three types of soil organism. Microbial SIR and the population density of bacterivorous nematodes were high in plots to which high levels of inorganic NPK fertilizer and/or ammonium nitrate for top dressing were applied. Application of ammonium nitrate increased the population density of microarthropods in 2005. Whereas organic fertilization regime had lower population density of nematodes and microarthropods than other inorganic fertilization regime having similar root biomass. Soil organisms in the rhizosphere and the interrow soil responded similarly to fertilization and, consequently, the rhizosphere/interrow ratio, defined by the ratio of the number of organisms per gram in rhizosphere soil to the number in interrow soil, was hardly affected by the fertilization regimes studied. The ratio indicated how much soil organisms were influenced by root. It was high for microarthropods population density and low for nematodes population density. Root biomass was strongly correlated with microbial SIR but it was not correlated with nematodes population density. With the results from the rhizosphere/interrow ratio and the correlations between soil organisms and root biomass, we suggested that fertilization affected microbial SIR and microarthropods population density through root. But the effect of root was not obvious to nematodes population density.

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