Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.     

武汉市蔬菜重金属污染现状的调查与评价

通过对武汉市6种蔬菜的供食部位及所对应的土壤中重金属Hg(汞)、Cu(铜)、Pb(铅)、Cd(镉)、Cr(铬)、Zn(锌)、As(砷)含量及分布特征进行了检测,结果表明:Pb、Cr是武汉市蔬菜中主要的污染元素;Hg、Cd只在个别叶菜类上超标;Zn、Cu、As无超标样。在所时应的土样中,普遍存在污染的是Cd,其它6种重金属元素均未超标。     

Phytoremediation of potentially toxic elements in a polluted industrial soil using Poinsettia

Potentially toxic elements (PTEs) pollution has become a serious environmental threat, particularly in developing countries such as China. In response, there is a growing interest in phytoremediation studies to identify plant species as designated hyperaccumulators of PTEs in polluted soils. Poinsettia was selected as a candidate species for phytoremediation of six PTEs (Zn, Pb, Hg, Cr, As, Cu) in this study. A pot cultivation experiment (randomized incomplete block experimental design with 5 treatments and 4 blocks) was conducted using contaminated soils gathered from an industrial area in southcentral China. The bioaccumulation factor (BAF), translocation factor (TF), and bioconcentration factor were analyzed to determine the phytoremediation potential of poinsettia potted in different ratios of polluted soils. One-way ANOVA with post-hoc Tukey’s test showed that poinsettia had significant uptake of Zn, Pb, Cu (BAF < 1 and TF < 1, p < 0.05) and Hg (BAF < 1 and TF > 1, p < 0.05). Poinsettias can therefore effectively accumulate Zn, Pb, and Cu in their lateral roots while extracting and transferring Hg into their leaves. Moreover, poinsettia exhibited tolerance towards As and Cr. Interestingly, it was also observed that PTEs can inhibit the height of potted poinsettia at a certain concentration.     

四川甘洛铅锌矿区优势植物的重金属含量

通过野外调查采样,分析了四川凉山州甘洛县铅锌矿区土壤的重金属含量,以及矿区生长的13种优势植物对Pb、Zn、Cd、Cr、Cu的吸收与富集能力及其富集特性.结果表明,矿区土壤受Pb、Zn、Cd 3种重金属污染严重,13种植物体内的Pb含量均高于普通植物10倍以上,具有修复矿区土壤铅污染的潜力,其中植物1的转运系数和富集系数都大于1,满足Pb超富集植物的基本特征.Zn在凤尾蕨、细风轮菜、大火草、蔗茅、小飞蓬和牛茄子中含量较高.小飞蓬和紫茎泽兰的Cd含量较一般植物高出17～61倍,其中,紫茎泽兰的转运系数与富集系数均大于1,其对Cd的吸收特性值得进一步研究.     

Ectomycorrhizal fungal communities associated with Masson pine (Pinus massoniana Lamb.) in Pb–Zn mine sites of central south China

To advance our understanding of ectomycorrhizal fungal communities in mining areas, the diversity and composition of ectomycorrhizal fungi associated with Masson pine (Pinus massoniana Lamb.) and soil chemistry were investigated in Taolin lead–zinc (Pb–Zn) mine tailings (TLT), two fragmented forest patches in a Huayuan Pb–Zn mineland (HY1 and HY2), and a non-polluted forest in Taolin in central south China. Ectomycorrhizal fungal species were identified by morphotyping and sequence analyses of the internally transcribed spacer regions of ribosomal DNA. The two study sites in the Huayuan mineland (HY1 and HY2) were significantly different in soil Pb, Zn, and cadmium (Cd) concentrations, but no significant difference was observed in ectomycorrhizal colonization, ectomycorrhizal fungal richness, diversity, or rank–abundance. In addition, the similarity of ectomycorrhizal fungal communities between HY1 and HY2 was quite high (S?rensen similarity index?=?0.47). Thus, the concentration of heavy metals may not be determining factors in the structure of these communities. In the tailings, however, significantly lower ectomycorrhizal colonization and ectomycorrhizal fungal richness were observed. The amounts of Pb and Zn in the tailing sand were higher than the non-polluted forest but far lower than in HY1. Thus, these heavy metals did not account for the reduced colonization and ectomycorrhizal fungal richness in TLT. The ectomycorrhizal fungal community in TLT was dominated by four pioneer species (Rhizopogon buenoi, Tomentella ellisii, Inocybe curvipes, and Suillus granulatus), which collectively accounted for 93.2?% of root tip colonization. The immature soil conditions in tailing (low N and P, sand texture, and lack of organic matter) may only allow certain pioneer ectomycorrhizal fungal species to colonize the site. When soil samples from four sites were combined, we found that the occurrences of major ectomycorrhizal fungal taxa were not clearly related to the concentrations of Pb, Zn, and Cd. In conclusion, our results suggest that ectomycorrhizal fungal communities in mining areas are not necessarily affected by heavy metals themselves but could be largely determined by soil maturity.     

Phytoremediation Potential of Weeds in Heavy Metal Contaminated Soils of the Bassa Industrial Zone of Douala,Cameroon

Phytoremediation is a promising option for reclaiming soils contaminated with toxic metals, using plants with high potentials for extraction, stabilization and hyperaccumulation. This study was conducted in Cameroon, at the Bassa Industrial Zone of Douala in 2011, to assess the total content of 19 heavy metals and 5 other elements in soils and phytoremediation potential of 12 weeds. Partial extraction was carried out in soil, plant root and shoot samples. Phytoremediation potential was evaluated in terms of the Biological Concentration Factor, Translocation Factor and Biological Accumulation Coefficient. The detectable content of the heavy metals in soils was Cu:70–179, Pb:8–130, Zn:200–971, Ni:74–296, Co:31–90, Mn:1983–4139, V:165–383, Cr:42–1054, Ba:26–239, Sc:21–56, Al:6.11–9.84, Th:7–22, Sr:30–190, La:52–115, Zr:111–341, Y:10–49, Nb:90–172 in mg kg^?1, and Ti:2.73–4.09 and Fe:12–16.24 in wt%. The contamination index revealed that the soils were slightly to heavily contaminated while the geoaccumulation index showed that the soils ranged from unpolluted to highly polluted. The concentration of heavy metals was ranked as Zn > Ni > Cu > V > Mn > Sc > Co > Pb and Cr in the roots and Mn > Zn > Ni > Cu > Sc > Co > V > Pb > Cr > Fe in the shoots. Dissotis rotundifolia and Kyllinga erecta had phytoextraction potentials for Pb and Paspalum orbiculare for Fe. Eleusine indica and K. erecta had phytostabilisation potential for soils contaminated with Cu and Pb, respectively.     

南京城市土壤重金属含量及其影响因素

研究了南京城市土壤重金属含量、来源及其与土壤性质的关系。结果表明,南京城市土壤中,Fe、Ni、Co、V污染不明显,但受到了不同程度的Mn、Cr、Cu、Zn、Pb污染,其中：Pb污染非常严重;重金属在土壤剖面分布没有规律性;Fe、Ni、Co、V元素主要来源于原土壤物质,Cu、Zn、Pb、Cr元素主要来源于人为输入,Mn可能在不同的土壤中来源不同;Fe、Cr、Ni、Co、V元素含量之间均呈极显著正相关,Cu、Zn、Pb、Cr元素含量之间均呈极显著正相关。Fe、Co、V、Ni含量与粘粒含量、CEC呈极显著正相关;Cu、Zn、Pb含量与粘粒含量呈极显著负相关;Cu、Zn、Pb、Cr含量与有机碳呈极显著正相关,Pb含量与pH呈极显著正相关。     

Toward a census of bacteria in soil

For more than a century, microbiologists have sought to determine the species richness of bacteria in soil, but the extreme complexity and unknown structure of soil microbial communities have obscured the answer. We developed a statistical model that makes the problem of estimating richness statistically accessible by evaluating the characteristics of samples drawn from simulated communities with parametric community distributions. We identified simulated communities with rank-abundance distributions that followed a truncated lognormal distribution whose samples resembled the structure of 16S rRNA gene sequence collections made using Alaskan and Minnesotan soils. The simulated communities constructed based on the distribution of 16S rRNA gene sequences sampled from the Alaskan and Minnesotan soils had a richness of 5,000 and 2,000 operational taxonomic units (OTUs), respectively, where an OTU represents a collection of sequences not more than 3% distant from each other. To sample each of these OTUs in the Alaskan 16S rRNA gene library at least twice, 480,000 sequences would be required; however, to estimate the richness of the simulated communities using nonparametric richness estimators would require only 18,000 sequences. Quantifying the richness of complex environments such as soil is an important step in building an ecological framework. We have shown that generating sufficient sequence data to do so requires less sequencing effort than completely sequencing a bacterial genome.     

Rhizosphere bacterial populations of metallophyte plants in heavy metal-contaminated soils from mining areas in semiarid climate

Rhizosphere bacterial populations associated with four metallophyte plants in one of major polymetallic (Pb–Zn–Cu) semiarid Moroccan Hercynian province (Draâ Sfar, Marrakech, Morocco) presenting long-term contamination mainly with Zn and Pb were analysed and compared to selected control soils. In the highly Zn-, Cu-, Pb- and Cd- contaminated soils, the total number of culturable heterotrophic bacteria were found in low proportions (< 2.6 × 10² – 1.6 × 10⁴ g^–1soil). This bacterial content was slightly similar to that found in moderately polluted and controls soils (6.7 × 10⁴ – 5.8 × 10⁶). However, the bacterial diversity and the rhizosphere/soil ratio, which compares the bacterial content (or bacterial charge) around the metallophyte plants with that in non-rhizosphere soil, were the bacteriological parameters mostly affected by heavy metal contamination. The chronic Zinc-stress results in an increase of tolerance to this metal of both the rhizosphere and non-rhizosphere bacterial communities. However, in general, the rhizosphere bacterial populations exhibited less tolerance to Zn toxicity than the bacterial population of non-rhizosphere soils. This result suggests that toxic effects of Zn decrease in the rhizosphere soils of the metallophyte plants.     

Environmental Risk Assessment Studies of Heavy Metal Contamination in the Industrial Area of Kattedan,India—A Case Study

Kattedan is an industrial area near Hyderabad, Andhra Pradesh, India, contaminated with high concentrations of metals attributed to industrial sources (battery manufacturing, metal plating, textile and pharmaceuticals production and others). Twelve different locations in the Kattedan industrial area were assessed for concentrations of metals (Zn, Cr, Cu, Ni, Co, Pb, Hg, Cd, and As) in soils, waters, and vegetation. Application of sequential extraction technique for the soils revealed relatively high percentages of Zn, Cu, and Cr associated with mobile fractions, and correspondingly high concentrations of Zn, Cr, Cu, and Pb in forage grass samples and a high degree of bioavailability to humans. Human exposure assessment revealed high concentrations of Pb, Zn, and Cr in blood and urine samples from the residents of the study area showing a direct pathway and a potential for toxicological hazard due to heavy metal pollution.     

Relationships among site characteristics,taxonomical structure and functional trait distribution of arthropods in forest,urban and agricultural soils of Southern Italy

Urbanization and agriculture cause alterations in soil biodiversity. As arthropods quickly respond to soil changes, they have been recognized as good indicators of soil quality. This study aimed to evaluate if (1) soil physico-chemical properties act as environmental filters of the functional trait distribution of soil arthropod community; (2) the abundance of certain functional traits is linked to different land uses; (3) the taxonomical and functional approaches provide complementary information about the evaluation of biological soil quality. The study was performed at forest, agricultural and urban sites in downtown and surroundings of Naples. The soils were characterized for texture, pH, organic matter content, water content, total Cd, Cr, Cu, Ni, Pb and Zn concentrations. The forest soils showed the highest organic matter and water contents, and the lowest metal concentrations; the agricultural soils showed the lowest organic matter and water contents and high Cd and Cu concentrations, whereas the urban soils showed high Pb and Zn concentrations. The forest soils showed the highest arthropod density, taxa richness and diversity. The distribution of the functional traits in the arthropod communities of the different land uses highlighted similarity only for the preference to occupy soil and for the percentage contribution of detritivores. The abundance of arthropods living above litter and omnivores were positively correlated to Pb and Zn concentrations, whereas predators were positively correlated to Cu concentrations. The findings suggest that the arthropod identification at order level could be enough to detect differences in functional traits among forest, urban, and agricultural soils.     

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon–Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed.     

交通要道重金属污染对农田土壤动物群落结构及空间分布的影响

为了解交通要道重金属对路边农田土壤动物群落结构及空间分布的影响,分季节分层次对104国道浙江上虞段周围农田5条样带及1条对照样带进行取样调查,共获得土壤动物4046个,计50个类群,隶属于4门7纲,弹尾目、前气门亚目、甲螨亚目为优势类群,其余为常见类群和稀有类群。同时测定了采样带土壤理化性质和重金属含量,结合类群特征指数,研究农田土壤动物群落结构特征以及土壤动物对土壤重金属污染的响应。结果表明,6条样带土壤理化指标全磷和pH、重金属各因子差异显著(P0.05),公路周围重金属含量明显高于对照和土壤背景值,随着采样距104国道的距离的减小,土壤动物的类群数和个体数呈现减少的趋势,在土层垂直分布上,并呈现表聚性减弱的现象。灰色关联分析表明,在调查样带中全磷对土壤动物的影响最大,土壤pH次之,其次是铅、铬的影响,锌的影响最小。土壤理化指标全磷和pH对农田土壤动物的影响大于土壤重金属,但重金属对污染样带土壤动物群落结构的影响已不能忽视。     

PCR-DGGE Comparison of Bacterial Community Structure in Fresh and Archived Soils Sampled along a Chihuahuan Desert Elevational Gradient

The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.     

郑汴路路旁土壤-小麦系统重金属积累及其健康风险评价

按离路基不同距离采集土壤、麦苗和籽粒样品, 在测定样品重金属 (Pb、Cd、Zn、Cr和Cu) 的基础上, 开展了路旁土壤-小麦系统重金属分布、积累和污染状况分析, 并对膳食小麦 (Triticumaestivum) 引起的健康风险进行了评价。结果表明:1) 土壤-小麦系统重金属含量随着离开路基距离的增加呈先增加后减少的趋势, 土壤重金属含量>麦苗重金属含量>籽粒重金属含量。2) 麦苗和小麦籽粒对土壤重金属富集能力的大小顺序均为Cu>Cd>Zn>Pb>Cr, 麦苗对重金属的富集能力大于小麦籽粒。3) 膳食小麦所致的Cd个人健康风险较大。     

Spatial Patterns and Risk Assessment of Heavy Metals in Soils in a Resource-Exhausted City,Northeast China

Northeast China is an intensive area of resource-exhausted city, which is facing the challenges of industry conversion and sustainable development. In order to evaluate the soil environmental quality influenced by mining activities over decades, the concentration and spatial distribution of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), and Zinc (Zn) in surface soils (0-20cm) of a typical resource-exhausted city were investigated by analyzing 306 soil samples. The results showed that the average concentrations in the samples were 6.17 mg/kg for As, 0.19 mg/kg for Cd, 51.08 mg/kg for Cr, 23.27 mg/kg for Cu, 31.15 mg/kg for Ni, 22.17 mg/kg for Pb, and 54.21 mg/kg for Zn. Metals distribution maps produced by using the inverse distance weighted interpolation method and results revealed that all investigated metals showed distinct geographical patterns, and the concentrations were higher in urban and industrial areas than in farmland. Pearson correlation and principal component analysis showed that there were significant positive correlations (p<0.05) between all of the metals, and As, Cd, Cr, Mn, Ni, Pb, and Zn were closely associated with the first principal component (PC1), which explained 39.81% of the total variance. Cu and As were mainly associated with the second component (PC2). Based on the calculated Nemerow pollution index, percentage for slightly polluted (1<P ≤ 2) surface soils were reached 57.33%, while 42.65% topsoil samples are moderate polluted (2<P≤ 3). According to the results above-mentioned, different soil environmental function areas were classified and proper soil environmental management policy was proposed to decrease the environmental risks in the process of industrial city transformation.     

兰州市某交通干道土壤重金属分布特征及其对绿化植物的影响

为研究交通运输造成的重金属污染特征及潜在生态风险,选取兰州市某交通干道,利用原子吸收分光光度计检测了金属元素的含量,并利用单因子指数法和潜在生态风险指数法评价了土壤污染程度和潜在生态风险,进而分析了土壤重金属污染对绿化植物叶绿素和Ca含量的影响。结果表明: 城市交通导致土壤重金属Cr、Mn、Zn、Cu和Ni的含量均显著增高,且Cr、Pb和Cu达到了中度污染,潜在生态风险排序为Cu＞Pb＞Cr＞Ni＞Zn＞Mn;槐树、月季、紫叶李和冬青卫矛对交通源重金属Pb、Mn、Zn、Ni等表现出不同程度的积聚作用;落叶植物槐树、月季和紫叶李叶片中叶绿素含量表现为路侧采样点＞对照点,而常绿植物冬青卫矛和侧柏的叶绿素含量为对照点＞路侧采样点,所有绿化植物叶片中Ca含量表现为路侧采样点＞对照点,高的叶绿素和Ca含量可能有利于绿化植物在土壤重金属污染环境中生存。交通运输导致研究区域土壤中重金属Cr、Mn、Zn、Cu和Ni等的积累;槐树、月季、紫叶李和冬青卫矛等对Pb、Mn、Zn和Ni具有不同程度的积聚作用,可推荐为相应重金属污染土壤绿化植物。     

Contamination features and health risk of heavy metals in suburban vegetable soils,Yanbian, Northeast China

In recent years, heavy metal contamination in suburban vegetable soils calls for significant concerns due to the rapid urbanization and industrialization. In present study, 110 suburban vegetable soil samples from Yanbian, Northeast China, were collected. Concentration characteristics, pollution level, health risk, and source identification were evaluated by using different quantitative indices. Concentrations of Pb, Cr, Cu, Ni, Zn, Cd, and As in suburban soils were measured. Mean concentrations of Pb, Cr, Cu, Ni, Zn Cd, and As were 34.9 ± 10.5, 73.5 ± 44.4, 29.6 ± 19.4, 23.4 ± 12.0, 88.5 ± 26.7, 0.16 ± 0.16, and 9.24 ± 3.79 mg/kg, which were showed significantly higher than corresponding background values of Jilin province, respectively. The soils were moderately heavy polluted by Cu and Cd based on the results of geo-accumulated index and pollution indices. The pollution load index indicated that almost all of the study area were middle or heavy polluted, especially in Antu County and Helong City. Children in Yanbian may pose non-carcinogenic and carcinogenic risks with the major exposure pathway of ingestion. Principle component analysis results suggested that Pb, Cu, Zn, and Cd were mainly associated with agricultural activities, Ni and Cr were defined as combined source (lithogenic and anthropogenic), and As was tended to be from excessive application of pesticides and industrial activities.     

The distribution of Minuartia verna and Thlaspi alpestre in the British Isles in relation to 13 soil metals

The plant-communities from habitats of the metallophyte species Minuartia verna and Thlaspi alpestre (T. caerulescens) at sites disturbed and undisturbed by mining are described. Four communities were delineated by cluster and principal component analysis. Group 1 comprised species-poor communities on disturbed non-calcareous soils; group 2, relatively species-rich communities on disturbed calcareous soils; group 3, species-rich communities in the main on undisturbed calcareous soils. Group 4 consisted of species-rich communities with an alpine element, in damp habitats on base-rich soils derived from igneous rocks. Total and exchangeable elements As, Ba, Ca, Cd, Co, Cr, Cu, Fe, Mg, Mn, Ni, Pb and Zn were determined for the soils of these sites. Levels of soil Ca, Cd, Pb and Zn accounted for most of the variation along the first axis of the PCA and soil nutrient levels were probably the main predictor along the second.Abbreviations PCA Principal Component Analysis