Nickel tolerance and accumulation by bacteria from rhizosphere of nickel hyperaccumulators in serpentine soil ecosystem of Andaman, India

Rhizosphere microorganisms harboring nickel hyperaccumulators, Rinorea bengalensis (Wall.) O. K. and Dichapetalum gelonioides ssp. andamanicum (King) Leenh. endemic to serpentine outcrops of Andaman Islands, India, were screened for their tolerance and accumulation of Ni. The rhizosphere soils from both the plants were rich in total and available Ni along with Co, Cr, Fe and Mg but poor in microbial density and were dominated by bacteria. Out of total 123 rhizosphere microorganisms (99 bacteria and 24 fungi), bacteria were more tolerant to Ni than fungi. Viable cells of selected Ni-tolerant bacterial isolates (MIC = 13.6–28.9 mM Ni) belonging to Pseudomonas, Bacillus and Cupriavidus were capable of accumulating nickel (209.5–224.0 μM Ni g⁻¹ protein) from aqueous solution. Cupriavidus pauculus KPS 201 (MTCC 6280), showing highest degree of nickel tolerance (MIC 28.9 mM Ni) and uptake (224.0 μM Ni g⁻¹ protein, 60 min) was used for detailed study. Kinetics of nickel uptake in C. pauculus KPS 201 followed a linearized Lineweaver-Burk plot. The K _m and V _max for nickel uptake by minimal medium grown-cells approximated 1.5 mM Ni and 636.9 μM Ni g⁻¹ protein, respectively. The uptake process was inhibited by Co, Cu, Cd, Mg, Mn and Zn, however, complete inhibition was not achieved even in presence of 500 mM Mg. Metabolic inhibitors, sodium azide (1.0 mM) and carbonyl cyanide m-chlorophenylhydrazone (0.4 mM) strongly inhibited nickel uptake suggesting the process as an energy dependent one. The present study clearly shows that bacteria in the rhizosphere of Ni-hyperaccumulators are capable of tolerating high concentration of Ni and also possesses nickel uptake potential. The Ni-hyperaccumulators in combination with these Ni-resistant bacteria could be an ideal tool for nickel bioremediation.     

Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide

Elevated atmospheric CO₂ increases aboveground plant growth and productivity. However, carbon dioxide-induced alterations in plant growth are also likely to affect belowground processes, including the composition of soil biota. We investigated the influence of increased atmospheric CO₂on bacterial numbers and activity, and on soil microbial community composition in a pasture ecosystem under Free-Air Carbon Dioxide Enrichment (FACE). Composition of the soil microbial communities, in rhizosphere and bulk soil, under two atmospheric CO₂ levels was evaluated by using phospholipid fatty acid analysis (PLFA), and total and respiring bacteria counts were determined by epifluorescence microscopy. While populations increased with elevated atmospheric CO₂ in bulk soil of white clover (Trifolium repens L.), a higher atmospheric CO₂ concentration did not affect total or metabolically active bacteria in bulk soil of perennial ryegrass (Lolium perenne L.). There was no effect of atmospheric CO₂ on total bacteria populations per gram of rhizosphere soil. The combined effect of elevated CO₂ on total root length of each species and the bacterial population in these rhizospheres, however, resulted in an 85% increase in total rhizosphere bacteria and a 170% increase in respiring rhizosphere bacteria for the two plant species, when assessed on a per unit land area basis. Differences in microbial community composition between rhizosphere and bulk soil were evident in samples from white clover, and these communities changed in response to CO₂ enrichment. Results of this study indicate that changes in soil microbial activity, numbers, and community composition are likely to occur under elevated atmospheric CO₂, but the extent of those changes depend on plant species and the distance that microbes are from the immediate vicinity of the plant root surface.     

Nickel distribution in the hyperaccumulator Alyssum serpyllifolium Desf. spp. from the Iberian Peninsula

Abstract

The relative concentration and distribution of nickel (Ni) in vegetative tissues (leaves, stems and trichomes) and reproductive organs (seeds) was studied using energy-dispersive X-ray microanalysis (EDXS) and scanning electron microscopy (SEM) in two previously studied Ni-hyperaccumulator subspecies of Alyssum serpyllifolium Desf. growing naturally in ultramafic soils of the Iberian Peninsula: A. serpyllifolium ssp. lusitanicum Dudley & P. Silva and A. serpyllifolium ssp. malacitanum Rivas Goday ex G. López. Both taxa showed that Ni accumulates preferentially in the leaves, exhibiting a homogeneous distribution on both epidermis surfaces. The highest Ni concentrations were found inside the epidermal cells and at the base of trichome stalks. Ni accumulation in seeds was lower than in the vegetative organs. The location of Ni in these plants allows us to postulate that its accumulation is a protection mechanism against external stress.     

Validation of the H<Subscript>2</Subscript>S method to detect bacteria of fecal origin by cultured and molecular methods

Using biochemical and molecular methods, this research determined whether or not the H₂S test did correctly identify sewage-contaminated waters by being the first to use culturing and molecular methods to identify the types and numbers of fecal indicator organisms, pathogens, and other microbes present in sewage samples with positive H₂S test results. For the culture-based method, samples were analyzed for the presence of fecal bacteria by spread plating the sewage sample onto differential and selective media for Aeromonas spp., Escherichia coli, sulfite-reducing clostridia, H₂S-producing bacteria, and Salmonella/Shigella spp. The isolates were then: (1) tested to determine whether they were H₂S-producing organisms and (2) identified to the genus and species level using biochemical methods. The molecular method used to characterize the microbial populations of select samples was terminal restriction fragment length polymorphisms. These experiments on sewage provided evidence that positive H₂S tests consistently contained fecal bacteria and pathogens. There were strong relationships of agreement between the organisms identified by both methods tested. This study is an important advance in microbial water quality detection since it is focused on the evaluation of a novel, low-cost, water microbiology test that has the potential to provide millions of people worldwide access to water quality detection technology. Of prime consideration in evaluating water quality tests is the determination of the test’s accuracy and specificity, and this article is a fundamental step in providing that information.     

施磷对干旱胁迫下箭竹根际土壤养分及微生物群落的影响

以箭竹及其根际土壤作为研究对象,采用两因素随机区组实验,设置2种水分处理（正常浇水和干旱胁迫）和2种施磷量处理（施磷和不施磷）,探究施磷对干旱胁迫下箭竹根际土壤养分及微生物群落结构和多样性的影响。结果表明：（1）干旱胁迫显著降低了箭竹根际土壤中微生物量碳、可溶性有机氮和有效磷的含量,虽对箭竹根际土壤微生物群落的多样性无显著影响,但显著降低了箭竹根际土壤中总PLFA（phospholipid fatty acid contents）的含量和真菌、细菌、革兰氏阳性菌与革兰氏阴性菌的PLFA含量以及革兰氏阳性菌/革兰氏阴性菌的PLFA比值,显著改变了箭竹根际土壤微生物群落结构,结果显著降低了箭竹的生物量。（2）施磷显著增加了受旱箭竹根际土壤中微生物量碳和有效磷的含量,虽大体上对受旱箭竹根际土壤微生物群落的多样性无显著影响,但显著增加了受旱箭竹根际土壤中总PLFA和真菌PLFA的含量,并在一定程度上增加了细菌、革兰氏阳性菌、革兰氏阴性菌和放线菌的PLFA含量以及革兰氏阳性菌/革兰氏阴性菌和真菌/细菌的PLFA比值,也在一定程度上改善了受旱箭竹根际土壤微生物群落结构,从而改善受旱箭竹的生长。（3）主成分分析表明,干旱对箭竹根际土壤微生物群落结构的影响显著,而施磷的影响不明显。（4）相关分析发现,箭竹根际土壤微生物群落结构与箭竹根际土壤微生物量碳、可溶性有机氮及箭竹生物量呈显著正相关。综上,干旱降低了箭竹根际土壤养分含量和微生物生物量,改变了箭竹根际土壤微生物群落结构,抑制了箭竹的生长;施磷能增加受旱箭竹根际土壤养分含量和微生物生物量,改善受旱箭竹根际土壤微生物群落结构,进而改善受旱箭竹的生长。     

Quantification of the geocarposphere and rhizosphere effect of peanut (Arachis hypogaea L.)

Roots and pods of field-grown peanut (groundnut) (Arachis hypogaea L.) were sampled at the R3, R5, and R7 developmental stages and examined in comparison to root- and pod-free soil for microbial population densities to assess the geocarposphere and rhizosphere effects. G/ S (no. geocarposphere microorganisms/no. soil microorganisms) and R/S (no. rhizosphere microorganisms/no. soil microorganisms) ratios were calculated for total fungi,Asperigillus flavus, spore-forming bacilli, coryneform bacteria, fluorescent pseudomonads, and total bacteria isolated on low- and high-nutrient media. A clear geocarposphere effect was evidenced by increased population densities of bacteria and fungi associated with developing pods compared to soil. G/S and R/S ratios were generally greater than 1.0 for all groups of microorganisms except bacilli. G/S ratios were greater for total bacteria than for total fungi at two of the three sample times, suggesting that bacteria were stimulated more than fungi in the zone around developing pods. In contrast, R/S ratios, were higher for total fungi than for total bacteria at two of three sample times. The preferential association of fungi and bacteria with early developmental stages of the pod indicates that some microorganisms are particularly well adapted for colonization of the peanut geocarposphere. These microorganisms are logical candidates for evaluation as biological control candiates forA. flavus.     

Population variation of invasive <Emphasis Type="Italic">Spartina</Emphasis> <Emphasis Type="Italic">alterniflora</Emphasis> can differentiate bacterial diversity in its rhizosphere

While several studies have documented that invasive plants can change the microbial communities, little is known about how soil microbial communities respond to population variation of invasive plants. Here, nine populations of Spartina alterniflora were selected from the east coast of China along latitudinal gradient to compare bacterial diversity of rhizospheres among these populations. The bacterial diversity in S. alterniflora rhizospheres was valued by denaturing gradient gel electrophoresis (DGGE) analysis. Shannon–Weaver diversity index (H′) and number of DGGE bands showed that rhizosphere bacterial diversity of S. alterniflora populations increased along a latitudinal gradient when all the populations were grown in a common garden. These findings suggest that population variation of S. alterniflora can differentiate the rhizosphere bacterial diversity, and the latitudinal gradient can shape the specific plant–bacterial diversity relationship. Our results adding to the recent literature suggest that invasive plant–soil biota interactions would have clinal variation with environmental gradients and improve our understanding of the mechanisms and processes of plant invasions.     

Influence of an Elevated Atmospheric CO2 Content on Soil and Rhizosphere Bacterial Communities Beneath Lolium perenne and Trifolium repens under Field Conditions

Abstract The increase in atmospheric CO₂ content alters C₃ plant photosynthetic rate, leading to changes in rhizodeposition and other root activities. This may influence the activity, the biomass, and the structure of soil and rhizosphere microbial communities and therefore the nutrient cycling rates and the plant growth. The present paper focuses on bacterial numbers and on community structure. The rhizospheres of two grassland plants, Lolium perenne (ryegrass) and Trifolium repens (white clover), were divided into three fractions: the bulk soil, the rhizospheric soil, and the rhizoplane–endorhizosphere. The elevated atmospheric CO₂ content increased the most probable numbers of heterotrophic bacteria in the rhizosphere of L. perenne. However, this effect lasted only at the beginning of the vegetation period for T. repens. Community structure was assessed after isolation of DNA, PCR amplification, and construction of cloned 16S rDNA libraries. Amplified ribosomal DNA restriction analysis (ARDRA) and colony hybridization with an oligonucleotide probe designed to detect Pseudomonas spp. showed under elevated atmospheric CO₂ content an increased dominance of pseudomonads in the rhizosphere of L. perenne and a decreased dominance in the rhizosphere of T. repens. This work provides evidence for a CO₂-induced alteration in the structure of the rhizosphere bacterial populations, suggesting a possible alteration of the plant-growth-promoting-rhizobacterial (PGPR) effect. Received: 14 December 1998; Accepted: 31 March 1999     

海草根际微生物与海草植株的互作效应

【目的】本文以三亚湾泰来草根际沉积物为主要研究对象,研究室内培养条件下泰来草根际沉积物微生物对于高温处理和海草定殖的响应。【方法】通过对培养过程中水体物理化学参数(如pH、溶解氧、磷酸盐、硝酸盐、亚硝酸盐和铵盐)的监测以分析环境因子的变化;16S rRNA扩增子测序研究微生物群落结构的动态响应;通过荧光定量分析16SrRNA基因丰度变化。【结果】研究表明高温处理组在培养35 d后海水中磷酸盐、硝酸盐、亚硝酸盐和铵盐含量以及pH均要高于模拟原位环境的对照组,高温处理组根际沉积物微生物丰度在培养过程中呈现先上升后降低的趋势,同时,高温处理组根际微生物中初始阶段由厚壁菌门(32.4%)、变形菌门(22.92%)和梭杆菌门(27.21%)占据优势,培养一段时间后,厚壁菌门和梭杆菌门大幅度减少,逐渐被蓝细菌门和放线菌门所替代,最终由变形菌门(51.1%)占据主导地位,其中,属于硫还原细菌的脱硫杆菌科(Desulfobacteraceae)和硫氧化细菌的螺杆菌科(Helicobacteraceae)的细菌丰度不断提高。【结论】揭示了海草的定殖会提高高温处理后沉积物的多样性,并塑造和改善其根际沉积物微生物群落组成。     

Effects of Pseudomonas putida modified to produce phenazine-1-carboxylic acid and 2,4-diacetylphloroglucinol on the microflora of field grown wheat

Pseudomonas putida WCS358r, genetically modified to have improved activity against soil-borne pathogens, was released into the rhizosphere of wheat. Two genetically modified derivatives carried the phzor the phl biosynthetic gene loci and constitutively produced either the antifungal compound phenazine-1-carboxylic acid (PCA) or the antifungal and antibacterial compound 2,4-diacetylphloroglucinol (DAPG). In 1997 and 1998, effects of single introductions of PCA producing derivatives on the indigenous microflora were studied. A transient shift in the composition of the total fungal microflora, determined by amplified ribosomal DNA restiction analysis (ARDRA), was detected. Starting in 1999, effects of repeated introduction of genetically modified microorganisms (GMMs) were studied. Wheat seeds coated with the PCA producer, the DAPG producer, a mixture of the PCA and DAPG producers, or WCS358r, were sown and the densities, composition and activities of the rhizosphere microbial populations were measured. All introduced strains decreased from 10⁷CFU per gram of rhizosphere sample to below the detection limit after harvest of the wheat plants. The phz genes were stably maintained in the PCA producers, and PCA was detected in rhizosphere extracts of plants treated with this strain or with the mixture of the PCA and DAPG producers. The phl genes were also stably maintained in the DAPG producing derivative of WCS358r. Effects of the genetically modified bacteria on the rhizosphere fungi and bacteria were analyzed by using amplified ribosomal DNA restriction analysis. Introduction of the genetically modified bacterial strains caused a transient change in the composition of the rhizosphere microflora. However, introduction of the GMMs did not affect the several soil microbial activities that were investigated in this study. This revised version was published online in August 2006 with corrections to the Cover Date.     

Methanotrophic Bacteria in the Rhizosphere of Trichloroethylene-Degrading Plants

The presence and density of methanotrophic bacteria has been shown to play an important role in the bioremediation of trichloroethylene (TCE). This article describes the methanotrophic bacterial densities in rhizosphere soils from two areas of the Department of Energy's Savannah River Site in Aiken, South Carolina. A direct fluorescent antibody (DFA) technique was evaluated to determine the presence of methanotrophic bacteria in roots and rhizospheres from vascular plants. The first site, the Miscellaneous Chemical Basin (MCB), was contaminated with a mixture of chemicals, including chlorinated solvents. The second site will be potentially affected by outcropping of TCE-contaminated groundwater. Significantly higher numbers of methanotrophic bacteria were observed with DFA in rhizosphere soils and on roots of Lespedeza cuneata and Pinus taeda (that previously showed higher rates of ¹⁴C-TCE mineralization) compared with nonvegetated soils. In addition, viable and heterotrophic microbial counts were consistently higher in rhizosphere soils and on plant roots compared with nonvegetated soils. Therefore, the presence of these plant species may enhance ¹⁴C-TCE mineralization by selectively increasing the microbial population in the root zone. Methanotrophic bacteria were directly observed by DFA in soils, on the surface of root hairs, within plant roots, and in higher densities associated with mycorrhizal fungi. These experiments provide further evidence that specific types of bacterial interactions with vegetation in the rhizosphere may play an important role in remediation of TCE-contaminated soils and groundwater.     

General microflora,arbuscular mycorrhizal colonization and occurrence of endophytes in the rhizosphere of two age groups of <Emphasis Type="Italic">Ginkgo biloba</Emphasis> L.of Indian Central Himalaya

The populations of the general microflora (bacteria, actinomycetes and fungi) in the rhizosphere and their corresponding non-rhizosphere soil samples of Ginkgo biloba L. of two age groups (Group A, <25 years-young trees; Group B, >60 years-old trees) growing under a temperate location of Indian Himalayan Region (IHR) have been determined. Observations were also made for the diversity, distribution and colonization of arbuscular mycorrhizal (AM) fungi and occurrence of endophytes in roots of G. biloba. The population of general microflora was found to be higher in the rhizosphere of Group B trees, more clearly reflected in terms of rhizosphere: soil (R:S) ratios. Contrary to this, per cent colonization and spore densities of AM fungi were higher in the rhizosphere of Group A trees as compared to the rhizosphere of Group B. AM fungal colonization was observed mostly in form of loose coils. All the spores detected, belonged to the genus Glomus with five different types. Presence of endophytes (both bacteria and fungi) was observed in the cortical cells of G. biloba roots, more profound in case of Group B trees. Data suggest that, while the species of Glomus dominated the rhizosphere of G. biloba, an inverse correlation exist between the colonization of general microflora and the colonization of AM fungi including endophytes.     

Carbon and nitrogen cycling during old-field succession: Constraints on plant and microbial biomass

Soil C and N dynamics were studied in a sequence of old fields of increasing age to determine how these biogeochemical cycles change during secondary succession. In addition, three different late-successional forests were studied to represent possible "steady state" conditions. Surface soil samples collected from the fields and forests were analyzed for total C, H₂O-soluble C, total N, potential net N mineralization, potential net nitrification, and microbial biomass. Above-and belowground plant biomass was estimated within each of the old field sites.Temporal changes in soil organic C, total N and total plant biomass were best described by a gamma function [y =at ^b e ^ctd +f] whereas a simple exponential model [y =a(l – e^–bt ) + c] provided the best fit to changes in H₂O-soluble C, C:N ratio, microbial C, and microbial N. Potential N mineralization and nitrification linearly increased with field age; however, rates were variable among the fields. Microbial biomass was highly correlated to soil C and N pools and well correlated to the standing crop of plant biomass. In turn, plant biomass was highly correlated to pools and rates of N cycling.Patterns of C and N cycling within the old field sites were different from those in a northern hardwood forest and a xeric oak forest; however, nutrient dynamics within an oak savanna were similar to those found in a 60-yr old field. Results suggest that patterns in C and N cycling within the old-field chronosequence were predictable and highly correlated to the accrual of plant and microbial biomass.     

The use of phospholipid fatty acids (PL-FA) in the determination of rhizosphere specific microbial communities (RSMC) of two wheat cultivars

To determine differences in microbial community structure, phospholipid fatty acids (PL-FA) from rhizosphere bacteria of two different wheat cultivars Triticum aestivum L. (cv. Bohouth-6 and cv. Salamouni) were extracted and analyzed by gas chromatography. This approach was used to overcome the methodological underestimation of microbial densities obtained with isolation, culture techniques and microscopic observations. Our objective was to verify differences in PL-FA profiles from two wheat cultivars grown under controlled environmental conditions. Principal component analysis (PCA) and cluster analysis were used to detect dissimilarities between rhizosphere microbial communities of the two wheat cultivars and signature fatty acids (FA) were used to determine specific differences in the community structures. PCA of the two cultivars explained 79.18% of the variance on principal component 1 (PC1), which accounted for Bohouth-6 rhizosphere soil. The rhizosphere soil of Salamouni accounted for 11.66% of the variance on principal component 2 (PC2). The results demonstrated repeatedly the clustering of the samples into two distinct groups; each group belonging specifically to one of the two wheat cultivars. Profiles of Bohouth-6 showed higher amounts of cyclopropane acid 19:0cy and Sif 7 (Sum in feature 7) than Salamouni. Those FA are known as signature molecules for Gram-negative bacteria. This was also reflected by the higher bacterial counts (cfu g^–1 fresh root weight) of Gram-negative bacteria from the rhizosphere of the former than the latter. The results indicated that under controlled environmental conditions, wheat cultivars of different genotypes exhibit distinct microbial colonization in their rhizosphere.     

Bacterial diversity in roots of conventional and genetically modified hybrid maize

Cultivated surfaces of genetically modified (GM) crops increased year by year, becoming in 2012 more extensive in developed than in industrialized countries. Furthermore, it has been postulated that the plant is which leads to the selection of the microorganisms on its root exudates, creating specific conditions which in turn regulate the specific microbial structure of each plant. In this study, our main objective was to examine whether the introduction of transgenic maize herbicide-tolerant plants will impact the microbial structures that inhabit at the rhizosphere and rhizoplane with respect to conventional hybrid maize plants. Bacterial populations were determined (CFU/g) using four different semi-selective media. The bacterial genera isolated from the rhizoplane and rhizosphere were identified by sequencing its 16S ribosomal DNA. Although minor differences were found in bacterial populations, our results indicated that there was not a strong change of the microorganisms populations that interact at the rhizosphere of an either conventional hybrid or genetically modified maize. However, we found some bacteria that were only isolated in the either genetically modified [Chryseobacterium sp. (4.39%) and Micrococcus sp. (3.72%)] or conventional maize [Sphingobium sp. (13.17%) and Microbacterium sp. (14.81%)].     

Wheat Cultivar-Specific Selection of 2,4-Diacetylphloroglucinol-Producing Fluorescent <Emphasis Type="Italic">Pseudomonas</Emphasis> Species from Resident Soil Populations

An emerging body of evidence indicates a role for plant genotype as a determinant of the species and genetic composition of the saprophytic microbial community resident to the rhizosphere. In this study, experiments were conducted to determine the capacity of five different wheat cultivars to enhance resident populations and support introduced strains of 2,4-diacetylphloroglucinol (2,4-DAPG)-producing fluorescent pseudomonads, a group of bacteria known to provide biological control of several soilborne diseases. When soils were cropped with three successive 28-day growth cycles of wheat, the 2,4-DAPG-producing strains were consistently recovered from the rhizosphere of the cultivar Lewjain, and commonly were present at populations higher than those recovered from other wheat cultivars. Based on restriction fragment length polymorphism and sequence analyses of phlD, a key gene involved in 2,4-DAPG production, two previously undefined phlD+ genotypes, referred to as genotypes PfZ and PfY, were discovered. Wheat cultivar Lewjain was the primary source of genotype PfY while cultivar Penawawa yielded the majority of genotype PfZ. Based on 16S rDNA sequence analysis, both new phlD genotypes were classified as P. fluorescens. Comparison of the rhizosphere competence of 2,4-DAPG-producing P. fluorescens Q2-87 (genotype B) and P. fluorescens LR3-A28 (genotype PfY) showed that both strains persisted at similar populations in the rhizosphere of all cultivars tested over a 30 day period when introduced as a seed inoculant. However, when strain LR3-A28 was applied as a soil inoculant, this strain was recovered at higher populations from the rhizosphere of wheat cultivar Lewjain than from the rhizospheres of two other cultivars. No cultivar effects were shown for strain Q2-87. Collectively, these results add further to evidence indicating a degree of specificity in interactions between plant cultivars and specific members of the saprophytic microbial community. Furthermore, as 2,4-DAPG-producing fluorescent Pseudomonas spp. have a central role in the spontaneous reduction in severity of take-all disease of wheat in response to continuous wheat monoculture, we postulate that the use of specific cultivars, such as Lewjain, which possess a superior capacity to enhance resident soil populations of these bacteria may have potential to reduce the length of the monoculture period required to induce natural suppressiveness of soils toward this disease.     

Changes of Ni biogeochemistry in the rhizosphere of the hyperaccumulator Thlaspi goesingense

Processes in the rhizosphere of metal hyperaccumulator species are largely unknown. We investigated root-induced changes of Ni biogeochemistry in the rhizosphere of Thlaspi goesingense Hálácsy in a rhizobox experiment and in related soil chemical and Ni uptake studies. In the rhizobox, a root monolayer was separated from rhizosphere soil by a nylon membrane. Rhizosphere soil was then sliced into 0.5 mm layers and analyzed for changes in soluble (water-extractable, Ni _S) and labile (1 M NH ₄NO ₃-extractable, Ni _L) Ni pools. Ni _L in the rhizosphere was depleted due to excessive uptake in T. goesingense. Ni _S in the rhizosphere increased in contrast to expectations based on the experimental Ni desorption isotherm. Mathematical simulations following the Tinker–Nye–Barber approach overestimated the depletion of the Ni _L and predicted a decrease of Ni _S in the rhizosphere. In a hydroponic experiment, we demonstrated that T. goesingense takes up Ni ²⁺ but excludes metal–organic complexes. The model output was then improved in later versions considering this finding. A sensitivity analysis identified I _max and K _m, derived from the Michaelis–Menten uptake kinetics experiment to be the most sensitive of the model parameters. The model was also sensitive to the accuracy of the estimate of the initial Ni concentration (C _Si) in soil solution. The formation of Ni–DOM complexes in solution could not explain the poor fit as in contrast to previous field experiments, the correlation between soluble Ni and dissolved organic carbon (DOC) was weak. Ion competition of Ni with Ca and Mg could be ruled out as explanation of enhanced Ni solubility in the rhizosphere as the molar ratio of Ni/(Ca + Mg) in solution was not affected. However, a decreased Vanselov coefficient Kv near the root plane indicated (an apparent) lower selectivity of the exchange complex for Ni, possibly due to adsorption of oxalate exuded by T. goesingense roots or associated rhizosphere microbes. This conclusion is supported by field data, showing enhanced oxalate concentrations in the rhizosphere of T. goesingense on the same experimental soil. The implications for phytoextraction and bio-available contaminant stripping (BCS) as well as for future modeling and experimental work are discussed.     

黄河三角洲滨海湿地微生物多样性及其驱动因子

微生物在湿地的生物地球化学循环和生态功能调节中发挥着重要作用,对全球气候变化具有重大影响,对维持全球生态系统的健康至关重要。以黄河三角洲滨海湿地为研究对象,通过采集代表性植被群落的土壤表层和部分植物根系,探究土壤微生物群落组成、根际微生物、环境因子及其内在的关联性和影响机制。研究结果表明不同植被覆盖地区微生物多样性存在差异,芦苇区和柽柳区微生物丰度高于泥滩区、碱蓬区和棉田,海漫滩微生物丰度高于河漫滩地和泥滩。土壤微生物菌群结构和多样性显著高于根际：土壤细菌的香农指数约为4-5.5,根际微生物的香农指数约为0-4。土壤细菌主要为厚壁菌门、变形菌门、拟杆菌门和放线菌门,占样品总数的90%以上;而根际细菌主要是蓝藻门、变形菌门和放线菌门,二者在属水平上的菌群结构差异更加明显。环境因子的含量与生境类型有关,SO₄^2-和NO₃^-的相关性最高,植被覆盖区土壤中Mn⁴⁺、Fe³⁺和水解氮的含量低于滩涂裸地。冗余分析（RDA）表明,pH值在小空间尺度上对湿地土壤中细菌群落的影响较小,环境因子在门和属水平的解释率分别为89.7%和86.8%,其中K（23.4%）、NO₂^-（11.8%）、Mn⁴⁺（9.8%）和Na（8.0%）是解释门水平微生物区系结构变化和组成的主要因子。研究为理解湿地微生物多样性与湿地生态系统功能之间的影响机制提供了一个生态学视角,有助于了解黄河三角洲滨海湿地土壤和植物根际的细菌分布特征,对黄河三角洲退化滨海湿地的生物修复具有重要的指导意义。     

Effect of chitin waste-based composts produced by two-phase composting on two oomycete plant pathogens

Biphasic composts were prepared by first mixing peat moss and sawdust with a nitrogen-rich biomass such as chitinous waste or cow manure and composting them until termination of the thermophilic phase. These partially stabilized composts were then amended with shrimp waste inducing a second thermophilic phase. Filter-sterilized water extracts obtained from two mature biphasic composts (SP₂W₂+S and MPW+S) reduced the growth of two oomycete plant pathogens, Phytophthora fragariae var. rubi and Pythium ultimum. Both SP₂W₂+S and MPW+S composts significantly reduce the incidence of cucumber damping-off caused by Pythium ultimum as compared to a commercial brand of compost made from shrimp waste and peat moss. Hydrolysis products of chitin were unlikely to be responsible for growth inhibition since no oligomeric forms of chitin were detected in SP₂W₂+S. The shrimp waste amendment carried out after the first thermophilic phase modified the microbial populations of biphasic composts. Following the amendment, the proportion of branched-chain microbial fatty acids typical of Gram-positive bacteria increased considerably suggesting that this group of bacteria became more prevalent within the total microbial population. These data suggests that the two-phase composting process promotes the proliferation of Gram-positive bacteria antagonistic to oomycete plant pathogens.     

Linking geochemical processes with microbial community analysis: successional dynamics in an arsenic-rich, acid-sulphate-chloride geothermal spring

The source waters of acid‐sulphate‐chloride (ASC) geothermal springs located in Norris Geyser Basin, Yellowstone National Park contain several reduced chemical species, including H₂, H₂S, As(III), and Fe(II), which may serve as electron donors driving chemolithotrophic metabolism. Microorganisms thriving in these environments must also cope with high temperatures, low pH (～3), and high concentrations of sulphide, As(III), and boron. The goal of the current study was to correlate the temporal and spatial distribution of bacterial and archaeal populations with changes in temperature and geochemical energy gradients occurring throughout a newly formed (redirected) outflow channel of an ASC spring. A suite of complimentary analyses including aqueous geochemistry, microscopy, solid phase identification, and 16S rDNA sequence distribution were used to correlate the appearance of specific microbial populations with biogeochemical processes mediating S, Fe, and As cycling and subsequent biomineralization of As(V)‐rich hydrous ferric oxide (HFO) mats. Rapid As(III) oxidation (maximum first order rate constants ranged from 4 to 5 min^?1, t_1/2 = 0.17 ? 0.14 min) was correlated with the appearance of Hydrogenobaculum and Thiomonas–like populations, whereas the biogenesis of As(V)‐rich HFO microbial mats (mole ratios of As:Fe ～0.7) was correlated with the appearance of Metallosphaera, Acidimicrobium, and Thiomonas–like populations. Several 16S sequences detected near the source were closely related to sequences of chemolithotrophic hyperthermophilic populations including Stygiolobus and Hydrogenobaculum organisms that are known H₂ oxidizers. The use of H₂, reduced S(–II,0), Fe(II) and perhaps As(III) by different organisms represented throughout the outflow channel was supported by thermodynamic calculations, confirming highly exergonic redox couples with these electron donors. Results from this work demonstrated that chemical energy gradients play an important role in establishing distinct community structure as a function of distance from geothermal spring discharge.