The microbial DNA cycle in soil.

Upon microbial cell death and lysis in soil, the free or naked DNA is exposed to the dynamic environment of the soil. The DNA can be enzymatically degraded by nucleases (DNases), bind to soil components, genetically transform competent bacterial cells and be a nutrient for other microorganisms. In this article we discuss the dual role of DNA as genetic material and as a nutrient source in the soil environment.     

微生物强化修复石油污染土壤的研究进展

微生物修复被认为是去除石油污染物和修复石油污染土壤的一种经济、高效且无二次污染的绿色清洁技术。受土壤环境条件和石油污染物性质等因素制约,土壤中土著石油降解微生物常存在数量不足、活性偏低、生长缓慢等问题,导致修复效果不佳、修复周期偏长。微生物强化修复技术可有效提高微生物降解效能,通过投加具有降解效能的功能菌株或菌剂、营养物质、表面活性剂、生长基质及固定化微生物等手段,可改善提升土著微生物对石油污染土壤的修复效果。文中梳理了已报道的石油降解微生物的种类,总结了微生物修复石油污染土壤的主要影响因素,阐述了微生物强化修复石油土壤的多种有效策略,提出了微生物强化修复石油污染的未来发展方向。     

Characterization of Heavy Metals in Soil by High Gradient Magnetic Separation

In recent years forecasting soil cleaning efficiencies of polluted soil, especially those contaminated with heavy metals, has become an important issue. Failure of the methods to predict the right efficiency has resulted in financial losses and penalties. This article describes an addition to the traditional characterization methods for soils contaminated by heavy metals, improving the quality of the basic decisions to be made. The method is based on magnetic separation using a Frantz Isodynamic Separator (FIS) for this study. The FIS isolates soil particles containing heavy metals so that these particles, which are relevant for soil cleaning, can be studied in more detail. Four contaminated soils were tested, for example, soils that were a problem for the soil-cleaning industry. The experiments indicate that each soil has its own magnetic properties that should be regarded as a fingerprint. Density measurements of two soils show that densities approach the quartz density separated at moderate and high magnetic fields suggesting that some of the heavy metals cannot be removed by density separation techniques. A pilot plant scale test supports this conclusion. It also shows that a part of the heavy metals are found in particles lighter than quartz. Based on the results, a qualitative model is proposed to account for the presence of the heavy metals in soil.     

Nocardia brasiliensis: from microbe to human and experimental infections

Nocardia brasiliensis is a Gram-positive bacterium that lives as a saprophyte in soil. In this article the physical properties, chemical composition and taxonomic position of this species is reviewed. Human infections and an experimental model of actinomycetoma in BALB/c mice as well as the host-immune response is described.     

NMR-based metabolomics using earthworms as potential indicators for soil health

Soil health is key for sustainable productivity and adaptation to climate change. Agricultural practice can significantly impact on soil health. The aim of this study was to examine the effect of two land management regimes on organisms (earthworms) that may be used as indicators for soil health via NMR metabolomics. Earthworms are important in the soil decomposition process and viewed as a sentinel species in soil. The presence/absence of earthworm species and their relative abundances provide a gross indication of the health of the soil and it is expected that land use would affect earthworm metabolism as the populations rose or declined in response to changing soil health parameters. In order to test this hypothesis metabolomics approaches were employed to determine if biological indicators of soil change can be detected. Two species of earthworms, an unidentified native species and the European species Aporrectodea caliginosa, were collected from properties in Victoria, Australia where the land was treated with either biological (organic) or conventional (chemical) treatment regimes. Both lipid and aqueous NMR metabolomics for earthworms was employed, demonstrating that class classifications can be achieved with both datasets and provide orthogonal, complementary, chemical information. The study indicates that land-use has a measurable effect on the biochemistry of worm populations. Potential biomarkers of land use and worm stress were found, including elevated levels of glucose, maltose, alanine and triacylglycerides. This study demonstrates the utility of NMR metabolomics approaches in detecting biomarkers related to land treatment regimes and potentially soil health attributes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Contribution of arbuscular mycorrhizal symbiosis to plant growth under different types of soil stress

The development of symbioses between soil fungi, arbuscular mycorrhizae (AM), and most terrestrial plants can be very beneficial to both partners and hence to the ecosystem. Among such beneficial effects, the alleviation of soil stresses by AM is of especial significance. It has been found that AM fungi can alleviate the unfavourable effects on plant growth of stresses such as heavy metals, soil compaction, salinity and drought. In this article, such mechanisms are reviewed, in the hope that this may result in more efficient use of AM under different stress conditions.     

Nutrient uptake as a contributing explanation for deep rooting in arid and semi-arid ecosystems

Explanations for the occurrence of deep-rooted plants in arid and semi-arid ecosystems have traditionally emphasized the uptake of relatively deep soil water. However, recent hydrologic data from arid systems show that soil water potentials at depth fluctuate little over long time periods, suggesting this water may be rarely utilized or replenished. In this study, we examine the distributions of root biomass, soil moisture and nutrient contents to 10-m depths at five semi-arid and arid sites across southwestern USA. We couple these depth distributions with strontium (Sr) isotope data that show deep (>1 m) nutrient uptake is prevalent at four of the five sites. At all of the sites, the highest abundance of one or more of the measured nutrients occurred deep within the soil profile, particularly for P, Ca²⁺ and Mg²⁺. Phosphate contents were greater at depth than in the top meter of soil at three of five sites. At Jornada, for example, the 2–3 m depth increment had twice the extractable P as the top meter of soil, despite the highest concentrations of P occurring at the surface. The prevalence of such deep resource pools, and our evidence for cation uptake from them, suggest nutrient uptake as a complementary explanation for the occurrence of deep-rooted plants in arid and semi-arid systems. We propose that hydraulic redistribution of shallow surface water to deep soil layers by roots may be the mechanism through which deep soil nutrients are mobilized and taken up by plants.Electronic Supplementary Material Supplementary material is available for this article at     

Release Of Petroleum Hydrocarbons From Bioremediated Soils

This article presents a qualitative evaluation of the extent to which the bioavailability (release) of a chemical is related to the biodegradation of hydrocarbons in a field bioremediation unit. The objectives of this research were to (1) quantify the rate of release of petroleum hydrocarbons from two soils that were bioremediated, (2) explore hydrocarbon release as a process affecting bioremediation; and (3) investigate the impact of bioremediation on chemical release in the two soils. An experimental protocol was used to quantify the rate of release of these hydrocarbons from two soils that had been bioremediated in a field-scale prepared bed land treatment unit. One soil showed little change in hydrocarbon concentration during 55 weeks of prepared bed bioremediation. The field study results indicated that, prior to the bioremediation, this soil had reached an environmentally acceptable endpoint. The second soil showed considerable hydrocarbon loss as a result of the bioremediation. The rate of hydrocarbon release was determined for the first soil and for the second soil at time zero and after 1, 2, and 7 months of prepared bed bioremediation. The results indicated: (1) the fraction (F) of the specific hydrocarbons that were released rapidly from the soil and the rates of release (k₂) of the residual hydrocarbons that were released slowly, (2) that the mass of each chemical of concern that was released from the first soil was very low; and (3) that the hydrocarbon released rapidly from the second soil decreased as treatment progressed. The experiments also verified, qualitatively, that some portion of each chemical evaluated was not able to be released, and thus was unavailable for bioremediation in the prepared bed land treatment unit.     

Standardisation of methods in soil microbiology: progress and challenges

A plethora of methods have been developed over the few last decades to enable a better understanding of the ecology of soil microbial communities and their roles in soil functioning. However, there is generally considerable variation (both subtle and more extensive) in the actual realisation of these methods, and limited efforts have been devoted to their standardisation, despite this being crucial to underpin data comparison and integration. Ensuring comparable data across studies through standardisation is arguably best-practice, as well as necessary to effectively meet the objectives of various schemas, which require assessment of the consequences of the global change and intensification of human activities on the functioning of the soil ecosystem and its biological diversity. This article presents an overview of the existing and forthcoming ISO standards in soil microbiology and highlights possible future research efforts to be undertaken for developing new standards. We also discuss some practical and theoretical bottlenecks and hurdles that have limited standardisation in soil microbiology up to now.     

甲烷氧化细菌氧化活性影响因素的研究

分别对土壤含水量、温度、施肥措施、土壤中CO_2和O_2含量等几个影响甲烷氧化细菌氧化活性的因素作一综述,分析其原因,为今后进一步研究奠定基础。     

Trophic relationships in the soil microfood-web: predicting the responses to a changing global environment

In this article, we evaluate how global environmental change may affect microfood-webs and trophic interactions in the soil, and the implications of this at the ecosystem level. First we outline how bottom-up (resource control) and top-down (predation-control) forces regulate food-web components. Food-web components can respond either positively or negatively to shifts in NPP resulting from global change, thus creating difficulties in developing general principles about the response of soil biota to global change phenomena. We also demonstrate that top-down effects can be important in soil food-webs, creating negative feed-backs which may partially counter bottom-up effects. Secondly, we determine how soil food-webs and the processes they regulate respond to various global change phenomena. Enhanced atmospheric CO₂ levels can have two main effects on plants which are relevant for the soil food-web, i.e. enhanced NPP (often positive) and diminished organic matter quality (with negative effects, at least in the short term). Climate change effects resulting from elevated CO₂ levels may be mainly secondary through alteration of vegetation, as shown by examples. Intensification of land management is usually associated with greater disturbance, which alters soil food-web composition and key processes; this is particularly apparent in comparisons of conventionally tilled and nontilled agroecosystems. Global change involves shifts in plant species composition and diversity, possibly affecting soil food-webs; we interpret this in terms of theories relating biodiversity to ecosystem function. We conclude that a more detailed understanding of interactions between NPP, soil organic matter and components of the soil food-web, as well as their regulation of biogeochemical processes and ultimately ecosystem-level properties, is essential in better understanding long-term aspects of global change phenomena.     

阿特拉津降解菌ATR3的分离鉴定与土壤修复

阿特拉津因效率高、价格低廉,是我国玉米田施用最广泛的除草剂之一,但其结构稳定,残留时间长,因此对生态环境和人类健康造成了一定的危害。从长期受阿特拉津污染的玉米田土壤中筛选并鉴定阿特拉津降解菌,明确其在不同类型土壤中的去除能力。对分离出的阿特拉津降解菌ATR3进行生理生化分析和16S rRNA序列鉴定,确定菌株ATR3为节杆菌属（Arthrobacter sp.）。该菌株以阿特拉津为唯一氮源,培养48 h后对1 000 mg/L阿特拉津的去除率达到97%以上。敏感作物盆栽试验结果表明,阿特拉津在棕壤上去除最快,褐土次之,黑土最慢,说明阿特拉津在土壤中的去除过程与土壤本身的理化性质呈相关关系。同时,该菌株处理14 d后,能明显恢复玉米的各项生物学指标,说明该菌株对阿特拉津污染土壤具有良好的修复能力。为阿特拉津降解菌剂的推广利用提供参考。     

土壤重金属生物毒性研究进展

世界范围内土壤重金属污染不断加重,由污染所带来的问题以及如何治理污染已经受到人们越来越多的关注.土壤重金属将对土壤生物产生影响,而土壤生物在重金属的胁迫下也会产生不同的响应.综述了国内外近年来土壤重金属生物毒性的研究进展,介绍了土壤重金属污染对陆地生态系统中植物、动物和微生物生长的影响;土壤重金属生物毒性的影响因素;土壤重金属生物毒性的研究方法;土壤重金属生物毒性的预测模型,最后提出了问题和展望.     

一种同时提取水稻土壤中细胞外和细胞内形态DNA的方法

采用灭菌的水稻田土壤为基质,分别投加细菌基因组DNA和细菌活体,应用该方法提取细胞内和细胞外DNA。结果表明,DNA提取效率平均在75.4%-82.3%,DNA纯度OD260/280在1.75-1.85之间。用细菌16S rDNA通用引物PCR表明,DNA纯度能满足PCR要求,细胞内DNA与细胞外DNA互不污染。     

Improvements of Polymerase Chain Reaction and Capillary Electrophoresis Single-Strand Conformation Polymorphism Methods in Microbial Ecology: Toward a High-throughput Method for Microbial Diversity Studies in Soil

The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE–SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE–SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE–SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE–SSCP. Studies on PCR and CE–SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE–SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.     

A Study of Vadose Zone Transport Model VLEACH

Application of vadose zone transport models has been hampered by lack of model validation. Difficulties to validate vadose zone models using field data not only come from model assumptions that are uncertain to the subsurface transport processes but also from the uncertainties associated with soil contaminants’ release time and quantity, soil sampling, sample transport, and analytical procedures. This article first conducts a test of a popularly used vadose zone transport VLEACH by comparing model results with a set of laboratory soil column infiltration and volatilization study data. The comparison shows a close agreement between the VLEACH model results and the laboratory data. Second, the sorption coefficient K_d calculated in VLEACH is compared with field data. The comparison indicates that VLEACH may overestimate the mass leached from soil to groundwater. The article also discusses the selection of the model simulation timestep, the vertical dimension increment, the Courant criterion, and the lower boundary condition using the sensitivity analysis method based on a case study of soil remediation for trichloroethylene. The procedures presented in this paper are important to practical model application and modification. This level of work should be routinely conducted for any new or modified version of vadose zone models.     

Diversity of The Chlorite Dismutase Gene in Low and High Organic Carbon Rhizosphere Soil Colonized by Perchlorate-Reducing Bacteria

Chlorite dismutase (cld) is an essential enzyme in the biodegradation of perchlorate. The objective of this study was to determine the change in sequence diversity of the cld gene, and universal bacterial 16S rRNA genes, in soil samples under varying conditions of organic carbon, bioaugmentation, and plant influence. The cld gene diversity was not different between high organic carbon (HOC) and low organic carbon (LOC) soil. Combining results from HOC and LOC soil, diversity of the cld gene was decreased in soil that had been bioaugmented or planted. However, with both bioaugmentation and planting the cld diversity was not decreased. These observations were repeated when focusing on LOC soil. However, in HOC soil the cld diversity was not affected by reactor treatment. General bacterial diversity as measured with 16S rRNA was significantly greater in HOC soil than in LOC soil, but no significant difference was observed between reference soil and planted or bioaugmented soil. Different sequences of the cld gene occur in different species of microorganisms. In LOC soil, combining bioaugmentation and planting results in a highly diverse population of perchlorate degraders. This diverse population will be more resilient and is desirable where perchlorate reduction is a critical remediation process.

Supplemental materials are available for this article. Go to the publisher's online edition of International Journal of Phytoremediation to view the supplemental file.     

Plant-Uptake of Uranium: Hydroponic and Soil System Studies

Limited information is available on screening and selection of terrestrial plants for uptake and translocation of uranium from soil. This article evaluates the removal of uranium from water and soil by selected plants, comparing plant performance in hydroponic systems with that in two soil systems (a sandy-loam soil and an organic-rich soil). Plants selected for this study were Sunflower (Helianthus giganteus), Spring Vetch (Vicia sativa), Hairy Vetch (Vicia villosa), Juniper (Juniperus monosperma), Indian Mustard (Brassica juncea), and Bush Bean (Phaseolus nanus).

Plant performance was evaluated both in terms of the percent uranium extracted from the three systems, as well as the biological absorption coefficient (BAC) that normalized uranium uptake to plant biomass. Study results indicate that uranium extraction efficiency decreased sharply across hydroponic, sandy and organic soil systems, indicating that soil organic matter sequestered uranium, rendering it largely unavailable for plant uptake. These results indicate that site-specific soils must be used to screen plants for uranium extraction capability; plant behavior in hydroponic systems does not correlate well with that in soil systems. One plant species, Juniper, exhibited consistent uranium extraction efficiencies and BACs in both sandy and organic soils, suggesting unique uranium extraction capabilities.     

Long-distance ABA Signaling and Its Relation to Other Signaling Pathways in the Detection of Soil Drying and the Mediation of the Plant’s Response to Drought

In this article we review evidence for a variety of long-distance signaling pathways involving hormones and nutrient ions moving in the xylem sap. We argue that ABA has a central role to play, at least in root-to-shoot drought stress signaling and the regulation of functioning, growth, and development of plants in drying soil. We also stress the importance of changes in the pH of the leaf cell apoplast as influenced both by edaphic and climatic variation, as a regulator of shoot growth and functioning, and we show how changes in xylem and apoplastic pH can affect the way in which ABA regulates stomatal behavior and growth. The sensitivity to drought of the pH/ABA sensing and signaling mechanism is emphasized. This allows regulation of plant growth, development and functioning, and particularly shoot water status, as distinct from stress lesions in growth and other processes as a reaction to perturbations such as soil drying.