KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

In addition to the often-cited advantages of using Arabidopsis thaliana as a model system in plant biological research (1), Arabidopsis has many additional characteristics that make it an attractive experimental organism for studying lea d (Pb) accumulation and tolerance in plants. These include its fortuitous familial relationship to many known metal hyperaccumulators (Brassicaceae), as well as similar Pbaccumulation patterns to most other plants. Using nutrient-agar plates, hydroponic culture, and Pb-contaminated soils as growth media, we found significant variation in Arabidopsis thaliana ecotypes in accumulation and tolerance of Pb. In addition, we have found that Pb accumulation is not obligatorily linked with Pb tolerance, suggesti ng that different genetic factors control these two processes. We also screened ethyl methanesulfonate-mutagenized M2 populations and identified several Pb-accumulating mutants. Current characterization of these mutants indicates that their phenotypes are likely due to alteration of general metal ion uptake or translocation processes since these mutants also accumulate many other metals in shoots. We expect that further characterization of the ecotypes and mutants will shed light on the basic genetic and physiological underpinnings of plant-based Pb remediation. 7. Aromatic nitroreduction of acifluorfen in soils, rhizospheres, and pure cultures of rhizobacteria. Zablotowicz, R. M., Locke, M. A., and Hoagland, R. E. Phytoremediation of soil and water contaminants. Washington, DC : American Chemical Society, 1997. p. 38-53. NAL Call #: QD1.A45-no.664 Abstract: Reduction of nitroaromatic compounds to their corresponding amino derivatives is one of several pathways in the degradation of nitroxenobiotics. Our studies with the nitrodiphenyl ether herbicide acifluorfen showed rapid metabolism to am inoacifluorfen followed by incorporation into unextractable soil components in both soil and rhizosphere suspensions. Aminoacifluorfen was formed more rapidly in rhizospheres compared to soil, which can be attributed to higher microbial populations, espec ially of Gram-negative bacteria. We identified several strains of Pseudomonas fluorescens that possess nitroreductase activity capable of converting acifluorfen to aminoacifluorfen. Factors affecting acifluorfen nitroreductase activity in pure cultures an d cell-free extracts, and other catabolic transformations of acifluorfen, ether bond cleavage, are discussed. Plant rhizospheres should be conducive for aromatic nitroreduction. Nitroreduction by rhizobacteria is an important catabolic pathway for the ini tial degradation of various nitroherbicides and other nitroaromatic compounds in soils under Reduction of nitroaromatic compounds to their corresponding amino derivatives is one of several pathways in the degradation of nitroxenobiotics. Our studies with the nitrodiphenyl ether herbicide acifluorfen showed rapid metabolism to am inoacifluorfen followed by incorporation into unextractable soil components in both soil and rhizosphere suspensions. Aminoacifluorfen was formed more rapidly in rhizospheres compared to soil, which can be attributed to higher microbial populations, espec ially of Gram-negative bacteria. We identified several strains of Pseudomonas fluorescens that possess nitroreductase activity capable of converting acifluorfen to aminoacifluorfen. Factors affecting acifluorfen nitroreductase activity in pure cultures an d cell-free extracts, and other catabolic transformations of acifluorfen, ether bond cleavage, are discussed. Plant rhizospheres should be conducive for aromatic nitroreduction. Nitroreduction by rhizobacteria is an important catabolic pathway for the ini tial degradation of various nitroherbicides and other nitroaromatic compounds in soils under phytoremediation management. 8. Ascorbate: a biomarker of herbicide stress in wetland plants. Lytle, T. F. and Lytle, J. S. Phytoremediation of soil and water contaminants. Washington, DC : American Chemical Society, 1997. p. 106-113. NAL Call #: QD1.A45-no.664 Abstract: In laboratory exposures of wetland plants to low herbicide levels (<0.1 micrograms/mL), some plants showed increased total ascorbic acid suggesting a stimulatory effect on ascorbic acid synthesis occurred; at higher herbicide conce ntrations (greater than or equal to 0.1 micrograms/mL) a notable decline in total ascorbic acid and increase in the oxidized form, dehydroascorbic acid occurred. Vigna luteola and Sesbania vesicaria were exposed for 7 and 21 days respectively to atrazine (0.05 to 1 microgram/mL); Spartina alterniflora 28 days at 0.1 micrograms/mL trifluralin; Hibiscus moscheutos 14 days at 0.1 and 1 microgram/mL metolachlor in fresh and brackish water. The greatest increase following low dosage occurred with S. alterniflo ra, increasing from <600 micrograms/g wet wt. total ascorbic acid to >1000 micrograms/g. Ascorbic acid may be a promising biomarker of estuarine plants exposed to herbicide runoff; stimulation of ascorbic acid synthesis may enable some wetland plant s used in phytoremediation to cope with low levels of these compounds. In laboratory exposures of wetland plants to low herbicide levels (<0.1 micrograms/mL), some plants showed increased total ascorbic acid suggesting a stimulatory effect on ascorbic acid synthesis occurred; at higher herbicide conce ntrations (greater than or equal to 0.1 micrograms/mL) a notable decline in total ascorbic acid and increase in the oxidized form, dehydroascorbic acid occurred. Vigna luteola and Sesbania vesicaria were exposed for 7 and 21 days respectively to atrazine (0.05 to 1 microgram/mL); Spartina alterniflora 28 days at 0.1 micrograms/mL trifluralin; Hibiscus moscheutos 14 days at 0.1 and 1 microgram/mL metolachlor in fresh and brackish water. The greatest increase following low dosage occurred with S. alterniflo ra, increasing from <600 micrograms/g wet wt. total ascorbic acid to >1000 micrograms/g. Ascorbic acid may be a promising biomarker of estuarine plants exposed to herbicide runoff; stimulation of ascorbic acid synthesis may enable some wetland plant s used in phytoremediation to cope with low levels of these compounds. 9. Atmospheric nitrogenous compounds and ozone--is NO(x) fixation by plants a possible solution. Wellburn, A. R. New phytol. 139: 1 pp. 5-9. (May 1998). NAL Call #: 450-N42 Descriptors: ozoneair-pollution nitrogen-dioxide nitric-oxide air-quality tolerancebioremediationacclimatizationnutrient-sources nutrient-uptake plantscultivarsgenetic-variation literature-reviews 10. Atrazine degradation in pesticide-contaminated soils: phytoremediation potential. Kruger, E. L., Anhalt, J. C., Sorenson, D., Nelson, B., Chouhy, A. L., Anderson, T. A., and Coats, J. R. Phytoremediation of soil and water contaminants. Washington, DC : American Chemical Society, 1997. p. 54-64. NAL Call #: QD1.A45-no. 664 Abstract: Studies were conducted in the laboratory to determine the fate of atrazine in pesticide-contaminated soils from agrochemical dealer sites. No significant differences in atrazine concentrations occurred in soils treated with atrazine i ndividually or combinations with metolachlor and trifluralin. In a screening study carried out in soils from four agrochemical dealer sites, rapid mineralization of atrazine occurred in three out of eight soils tested, with the greatest amount occurring i n Bravo rhizosphere soil (35% of the applied atrazine after 9 weeks). Suppression of atrazine mineralization in the Bravo rhizosphere soil did not occur with the addition of high concentrations of herbicide mixtures, but instead was increased. Plants had a positive impact on dissipation of aged Studies were conducted in the laboratory to determine the fate of atrazine in pesticide-contaminated soils from agrochemical dealer sites. No significant differences in atrazine concentrations occurred in soils treated with atrazine i ndividually or combinations with metolachlor and trifluralin. In a screening study carried out in soils from four agrochemical dealer sites, rapid mineralization of atrazine occurred in three out of eight soils tested, with the greatest amount occurring i n Bravo rhizosphere soil (35% of the applied atrazine after 9 weeks). Suppression of atrazine mineralization in the Bravo rhizosphere soil did not occur with the addition of high concentrations of herbicide mixtures, but instead was increased. Plants had a positive impact on dissipation of aged atrazine in soil, with significantly less atrazine extractable from Kochia-vegetated soils than from nonvegetated soils. 11. Bacterial inoculants of forage grasses that enhance degradation of 2-chlorobenzoic acid in soil. Siciliano, S. D. and Germida, J. J. Environ toxicol chem. 16: 6 pp. 1098-1104. (June 1997). NAL Call #: QH545.A1E58 Descriptors: polluted-soils bioremediationAbstract: Biological remediation of contaminated soil is an effective method of reducing risk to human and ecosystem health. Bacteria and plants might be used to enhance remediation of soil pollutants in situ. This study assessed the potential of bacteria (12 isolates), plants (16 forage grasses), and plant-bacteria associations (selected pairings) to remediate 2-chlorobenzoic acid (2CBA)-contaminated soil. Initially, grass viability was assessed in 2CBA-contaminated soil. Soil was contaminated wi th 2CBA, forage grasses were grown under growth chamber conditions for 42 or 60 d, and the 2CBA concentration in soil was determined by gas chromatography. Only five of 16 forage grasses grew in 2CBA-treated (816 mg/kg) soil. Growth of Bromus inermis had no effect on 2CBA concentration, whereas Agropyron intermedium, B. biebersteinii, A. riparum, and Elymus dauricus decreased 2CBA relative to nonplanted control soil by 32 to 42%. The 12 bacteria isolates were screened for their ability to promote the germ ination of the five grasses in 2CBA-contaminated soil. Inoculation of A. riparum with Pseudomonas aeruginos

Phytoremediation : 植物による環境/土壌浄化

Microbial functioning refers to microbial activity because only the active microorganisms drive biogeochemical processes. Despite the importance of active microorganisms, most methods focus on estimating total microbial biomass and fail to evaluate its active fraction. At first, we have described the differences among the active , potentially active , and dormant microbial states in soil and suggested threshold values of parameters for their identification. Secondly, we critically reviewed the ability of a broad range of approaches to estimate and characterize the active and the potentially active microorganisms in soil. Following approaches were evaluated: plate count and microbial cultures; direct microscopy combined with cell staining; ATP, PLFA, DNA and RNA content; microarray analyses; PCR-based approaches; stable isotope probing; soil proteomics, enzymes activity; and various approaches based on respiration and substrate utilization. The “static” approaches, mainly based on the single-stage determination of cell components (ATP, DNA, RNA, and molecular biomarkers), detect well the presence of microorganisms and total biomass, but they fail to evaluate the active part and consequently the functions. In contrast, the dynamic approaches, estimating the changes of these parameters during microbial growth and based on process rates: substrate utilization and product formation, e.g., respiration, help to evaluate active microbial biomass and relate it to specific process rates. Based on a comparison of all approaches for their universality (possibility to analyze active, potentially active and dormant microorganisms), we concluded that 1) direct microscopy with complementary stains, 2) a combination of RNA-based FISH with staining of total microbial biomass, and 3) approaches based on microbial growth were the most advantageous and allowed simultaneous quantitative estimation of active , potentially active, and dormant microorganisms in soil. The active microorganisms compose only about 0.1–2% of the total microbial biomass and very seldom exceed 5% in soils without input of easily available substrates. Nonetheless, the fraction of potentially active microorganisms (ready to start utilization of available substrates within few hours) is much higher, contributing between 10 and 40% (up to 60%) of the total microbial biomass. Therefore, we emphasize the role of potentially active microorganisms with quick response to fluctuating substrate input in soil microhabitats and hotspots. The transition from the potentially active to the active state occurs in minutes to hours, but the shift from dormant to active state takes anywhere from hours to days. Despite very fast activation, the reverse process – fading to the potentially active and dormant stage – requires a much longer period and is very different for individual criteria: ATP, DNA, RNA, enzyme production, respiration rates. This leads to further difficulties in the estimation of the active part of microbial community by methods based on these parameters. Consequently, the standardization, further elaboration, and broad application of approaches focused on the portion of active microorganisms in soil and their functions are urgently needed. We conclude that because active microorganisms are the solely microbial drivers of main biogeochemical processes, analyses of the active and potentially active fractions are necessary in studies focused on soil functions.

Active microorganisms in soil: Critical review of estimation criteria and approaches

Heavy metal accumulation in soil has been rapidly increased due to various natural processes and anthropogenic (industrial) activities. As heavy metals are non-biodegradable, they persist in the environment, have potential to enter the food chain through crop plants, and eventually may accumulate in the human body through biomagnification. Owing to their toxic nature, heavy metal contamination has posed a serious threat to human health and the ecosystem. Therefore, remediation of land contamination is of paramount importance. Phytoremediation is an eco-friendly approach that could be a successful mitigation measure to revegetate heavy metal-polluted soil in a cost-effective way. To improve the efficiency of phytoremediation, a better understanding of the mechanisms underlying heavy metal accumulation and tolerance in plant is indispensable. In this review, we describe the mechanisms of how heavy metals are taken up, translocated, and detoxified in plants. We focus on the strategies applied to improve the efficiency of phytostabilization and phytoextraction, including the application of genetic engineering, microbe-assisted and chelate-assisted approaches.

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Phytoremediation: A Promising Approach for Revegetation of Heavy Metal-Polluted Land

Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.

Mycobiome diversity: high-throughput sequencing and identification of fungi.

Since the emergence of phytoremediation, much research has focused on its development for (i) the removal of metals from soil and/or (ii) the reduction of metal bioavailability, mobility, and ecotoxicity in soil. Here, we review the lights and shades of the two main strategies (i.e., phytoextraction and phytostabilization) currently used for the phytoremediation of metal contaminated soils, irrespective of the level of such contamination. Both strategies face limitations to become successful at commercial scale and, then, often generate skepticism regarding their usefulness. Recent innovative approaches and paradigms are gradually establishing these phytoremediation strategies as suitable options for the management of metal contaminated soils. The combination of these phytotechnologies with a sustainable and profitable site use (a strategy called phytomanagement) grants value to the many benefits that can be obtained during the phytoremediation of metal contaminated sites, such as, for instance, the restoration of important ecosystem services, e.g. nutrient cycling, carbon storage, water flow regulation, erosion control, water purification, fertility maintenance, etc.

From phytoremediation of soil contaminants to phytomanagement of ecosystem services in metal contaminated sites.

Effects of chelates on plants and soil microbial community: comparison of EDTA and EDDS for lead phytoextraction.

Impact of repeated single-metal and multi-metal pollution events on soil quality

Functional diversity as indicator of the recovery of soil health derived from Thlaspi caerulescens growth and metal phytoextraction

Soil pollution with heavy metals is a worldwide environmental problem. Phytoremediation through phytoextraction and phytostabilization appears to be a promising technology for the remediation of polluted soils. It is important to strongly emphasize that the ultimate goal of a heavy metal remediation process must be not only to remove the heavy metals from the soil (or instead to reduce their bioavailability and mobility) but also to restore soil quality. Soil quality is defined as the capacity of a given soil to perform its functions. Soil microbial properties are increasingly being used as biological indicators of soil quality due to their quick response, high sensitivity, and, above all, capacity to provide information that integrates many environmental factors. Indeed, microbial properties are among the most ecologically relevant indicators of soil quality. Consequently, microbial monitoring of the recovery of soil quality is often carried out during heavy metal phytoremediation processes. However, soil microbial properties are highly context dependent and difficult to interpret. For a better interpretation of microbial properties as indicators of soil quality, they may be grouped within categories of higher ecological relevance, such as soil functions, ecosystem health attributes, and ecosystem services.

Lur Epelde

Papers

From phytoremediation of soil contaminants to phytomanagement of ecosystem services in metal contaminated sites.

Effects of chelates on plants and soil microbial community: comparison of EDTA and EDDS for lead phytoextraction.

Impact of repeated single-metal and multi-metal pollution events on soil quality

Functional diversity as indicator of the recovery of soil health derived from Thlaspi caerulescens growth and metal phytoextraction

Microbial Monitoring of the Recovery of Soil Quality During Heavy Metal Phytoremediation