Modified pretreatment method for total microbial DNA extraction from contaminated river sediment

Extraction of high-quality microbial DNA from contaminated environmental samples is an essential step in microbial ecological study. Based on previously published methods for soil and sediment samples, a modified pretreatment method was developed for extracting microbial DNA from heavily contaminated river sediment samples via selection of optimal pretreatment parameters (i.e., reagent solution, reaction duration, and temperature). The pretreatment procedure involves washing the river sediment sample for three times with a solution containing 0.1 mol·L^-1 ethylene diamine tetraacetic acid (EDTA), 0.1 mol·L^-1 Tris (pH 8.0), 1.5 mol·L^-1 NaCl, 0.1 mol·L^-1 NaH₂PO₄, and Na₂HPO₄ at 65°C with 180 r·min^-1 for 15 min to remove humic materials and heavy metals prior to the employment of standard DNA extraction procedures. We compared the results of standard procedure DNA extraction following pretreatment, without pretreatment, and with using a commercial PowerSoil^TM DNA Isolation Kit. The results indicated that the pretreatment significantly improved the DNA quality based on DNA yield, DNA fragment length, and determination of prokaryotic diversity. Prokaryotic diversity exhibited in the DNA with the pretreatment was also considerably higher than that extracted with the PowerSoil^TM DNA Isolation Kit only. The pretreatment method worked well even with a small amount of sediment sample (0.25 g or even lower). The method provides a novel, simple, cost-effective tool for DNA extraction for microbial community analysis in environmental monitoring and remediation processes.     

Microbial RNA and DNA synthesis in marine sediments

A technique for measuring rates of RNA and DNA synthesis in sedimentary microbial communities has been adapted from methods developed for marine and freshwater microplankton research. The procedure measures the uptake, incorporation and turnover of exogenous [2, ³H]-adenine by benthic microbial populations. With minor modification, it is applicable to a wide range of sediment types. Measurement of nucleic acid synthesis rates are reported from selected benthic marine environments, including coral reef sediments (Kaneohe Bay, Oahu, Hawaii), intertidal beach sands (Oahu and southern California) and California borderland basin sediment (San Pedro Basin), and comparisons are made to selected water-column microbial communities. Biomass-specific rates of nucleic acid synthesis in sediment microbial communities were comparable to those observed in water-column assemblages (i.e., 0.02 to 2.0 pmol deoxyadenine incorporated into DNA [ng ATP]^-1 h^-1 and 0.2 to 8.9 pmol adenine incorporated into RNA [ng ATP]^-1 h^-1). DNA synthesis rates were used to calculate carbon production estimates ranging from 2 g C cm^-3 h^-1 in San Pedro Basin sediment (880 m water depth) to 807 g C cm^-3 h^-1 in coral reef sediment from the Kaneohe Bay. Microbial community specific growth rate, (d^-1), estimated from DNA synthesis rates in surface sediments ranged from 0.1 in San Pedro Basin to 4.2 in Scripps Beach (La Jolla, California) intertidal sand.     

Chromium in intertidal sediments of the Clyde,UK: potential for remobilisation and bioaccumulation

Detailed surveys of intertidal sediments have been performed along the north and south shores of the Inner Clyde estuary, UK. Surface sediment data reveal significant spatial variation in Cr content and an association with major sediment characteristics and location within the estuary. Depth variation for Cr and other heavy metals cannot be explained by variation in major geochemical controls such as grain size and organic matter and highlights the impact of historical contamination on sediment quality. These elevated levels at depth may still have environmental impact through redox-reactivity, in association with iron and manganese. Sequential extraction of sediments and pore water analysis of Cr(VI) and Cr(III) provide detailed information on release potential from the sediments. The implication of Cr mobility for biota in the estuary has been assessed by the analysis of a common marine bivalve, Mytilus edulis (Blue Mussel) and a burrowing polychaete, Nereis diversicolor (rag worm) from a number of survey sites. Bioconcentration factors for Mytilus indicate that the weakly held portion of sediment Cr is available for uptake and in the case of Nereis, bioaccumulation appears to be inhibited by sediment organic matter.     

“生物有效性测量”与“全沉积物毒性识别评估(TIE)”联用有效识别出沉积物中主要致毒污染物

沉积物中污染物种类繁多,准确判断其中产生生物毒性的主要来源是个难点,本文作者先采用TIE法初步判断出主要致毒污染物为有机物和重金属(毒性描述阶段(相I)),传统的毒性单位分析结果显示Cr、Cu、Ni、Pb和Zn主要致毒重金属,而为氯氰菊酯、氯氟氰菊酯、溴氰菊酯和氟虫腈为主要致毒有机物中(毒性鉴定阶段(相II))。采用4步分级提取法和Tenax提取法分析了重金属和有机物的生物有效性。生物有效性毒性单位分析更加准确地锁定了毒性主要贡献重金属为Zn、Ni和Pb,毒性主要贡献有机物为氯氰菊酯、氯氟氰菊酯和氟虫腈。沉积物的稀释降低了重金属的毒性并使其毒性贡献鉴定变得复杂,生物有效性测量可以有效地提高TIE结果的准确性。
精选自Xiaoyi Yi, Huizhen Li, Ping Ma and Jing You. Identifying the causes of sediment-associated toxicity in urban waterways in South China: Incorporating bioavailabillity-based measurements into whole-sediment toxicity identification evaluation. Environmental Toxicology and Chemistry: Volume 34, Issue 8, pages 1744–1750, August 2015. DOI: 10.1002/etc.2970
详情请见http://onlinelibrary.wiley.com/doi/10.1002/etc.2970/full     

“生物有效性测量”与“全沉积物毒性识别评估(TIE)”联用有效识别出沉积物中主要致毒污染物

沉积物中污染物种类繁多,准确判断其中产生生物毒性的主要来源是个难点,本文作者先采用TIE法初步判断出主要致毒污染物为有机物和重金属(毒性描述阶段(相I)),传统的毒性单位分析结果显示Cr、Cu、Ni、Pb和Zn主要致毒重金属,而为氯氰菊酯、氯氟氰菊酯、溴氰菊酯和氟虫腈为主要致毒有机物中(毒性鉴定阶段(相II))。采用4步分级提取法和Tenax提取法分析了重金属和有机物的生物有效性。生物有效性毒性单位分析更加准确地锁定了毒性主要贡献重金属为Zn、Ni和Pb,毒性主要贡献有机物为氯氰菊酯、氯氟氰菊酯和氟虫腈。沉积物的稀释降低了重金属的毒性并使其毒性贡献鉴定变得复杂,生物有效性测量可以有效地提高TIE结果的准确性。
精选自Xiaoyi Yi, Huizhen Li, Ping Ma and Jing You. Identifying the causes of sediment-associated toxicity in urban waterways in South China: Incorporating bioavailabillity-based measurements into whole-sediment toxicity identification evaluation. Environmental Toxicology and Chemistry: Volume 34, Issue 8, pages 1744–1750, August 2015. DOI: 10.1002/etc.2970
详情请见http://onlinelibrary.wiley.com/doi/10.1002/etc.2970/full     

“生物有效性测量”与“全沉积物毒性识别评估(TIE)”联用有效识别出沉积物中主要致毒污染物

沉积物中污染物种类繁多,准确判断其中产生生物毒性的主要来源是个难点,本文作者先采用TIE法初步判断出主要致毒污染物为有机物和重金属(毒性描述阶段(相I)),传统的毒性单位分析结果显示Cr、Cu、Ni、Pb和Zn主要致毒重金属,而为氯氰菊酯、氯氟氰菊酯、溴氰菊酯和氟虫腈为主要致毒有机物中(毒性鉴定阶段(相II))。采用4步分级提取法和Tenax提取法分析了重金属和有机物的生物有效性。生物有效性毒性单位分析更加准确地锁定了毒性主要贡献重金属为Zn、Ni和Pb,毒性主要贡献有机物为氯氰菊酯、氯氟氰菊酯和氟虫腈。沉积物的稀释降低了重金属的毒性并使其毒性贡献鉴定变得复杂,生物有效性测量可以有效地提高TIE结果的准确性。
精选自Xiaoyi Yi, Huizhen Li, Ping Ma and Jing You. Identifying the causes of sediment-associated toxicity in urban waterways in South China: Incorporating bioavailabillity-based measurements into whole-sediment toxicity identification evaluation. Environmental Toxicology and Chemistry: Volume 34, Issue 8, pages 1744–1750, August 2015. DOI: 10.1002/etc.2970
详情请见http://onlinelibrary.wiley.com/doi/10.1002/etc.2970/full     

Evaluation of dilute hydrochloric acid and acid ammonium oxalate as extractants for some heavy metals from Nile River sediments

The suitability of a 0.5 M HCl solution for extraction of Fe, Mn, Cd, Co, Cu, Pb, and Zn from Nile River sediments was evaluated by comparing its effectiveness with that of conventional acid ammonium oxalate (Tamm's solution) and aqua regia extraction solutions. The present study has shown that although the extraction data indicate that both 0.5 M HCl and acid ammonium oxalate solutions are able to extract heavy metals simultaneously from the adsorbed, organic, and precipitated phases of Nile sediments, the 0.5 M HCl solution is preferred. It provides a rapid, reliable, and inexpensive method of measuring environmentally mobile metal concentrations in the aquatic sediments. From an analytical chemistry point of view, the 0.5 M HCl extracts do not clog the atomizer of the spectrophotometer. Extraction with dilute HCl solution obviates the need to use chemicals, some of which are toxic or not available readily as a high-purity grade. A standard extraction method should be relatively simple, to conduct a routine analysis of large numbers of sediment samples, yet at the same time it should provide sufficient information for assessment of the environmental impact of particulate metals. Therefore, extraction with 0.5 M HCl solution is very suitable for heavy-metal pollution monitoring in the Nile River     

超临界流体萃取在研究土壤和沉积物结合态残留中的应用

许多有机污染物在土壤和沉积物中形成持久稳定的结合态残留；结合态残留对土壤和沉积物的解毒过程、污染物长期分配行为、生物可用性和生物毒性都具有重要影响。为了揭示结合态残留的形成机制及其对污染物环境行为和毒理学参数的影响，从土壤或沉积物中提取出不同结合状态的有机污染物就显得非常重要。超临界流体萃取(SFE)可以实现选择性萃取，从而得到有关污染物一基体间相互作用的信息。文章介绍了SFE应用类型、超临界流体种类以及影响SFE萃取率的因素，对SFE模拟有机污染物长期吸附／解吸行为和生物可用性研究进行了论述，并认为SFE势必发展成为土壤或沉积物中结合态残留形成机理研究、土壤修复和生态风险评价的一种强有力的技术。     

Adenosine triphosphate and adenylate energy charge in marine sediments

The determination of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) concentrations in sediments from both Puget Sound and the Washington State continental shelf (USA) has been investigated. Major losses during the extraction procedure included sediment sorption, coprecipitation, and unreactivity of the soluble adenylates presumably through irreversible binding to solubilized sediment organics. Addition of phosphoric acid and the non-ionic detergent Triton X-100 to cold sulfuric acid significantly increased the extraction efficiency and sensitivity over that of sulfuric acid alone, although both methods yielded similar results when corrected for losses. Vertical profiles of ATP, total adenylates (A_T), and adenylate energy charge (EC) in sediments from both areas are presented. Profiles of A_T are similar in both areas, but EC values in the shelf sediments are significantly lower, which suggests a depressed physiological condition in the shelf population relative to that in Puget Sound.Contribution No. 513 from the University of Washington's College of Fisheries, and Contribution No. 1135 from the University of Washington's Department of Oceanography     

基于分散固相萃取-超高效液相色谱串联质谱法测定沉积物中大环内酯类抗生素

采用分散固相萃取与超高效液相色谱串联质谱技术,建立了快速测定沉积物中9种大环内酯类抗生素(螺旋霉素、阿奇霉素、替米考星、竹桃霉素、红霉素、泰乐菌素、吉他霉素、罗红霉素和交沙霉素)的检测方法.沉积物经磷酸盐缓冲液和乙腈混合液浸提,再经过石墨化炭黑和C18硅胶分散固相萃取材料净化.采用超高效液相色谱串联质谱仪(UPLC-M...     

Mercury fractionation in the sediments of Vembanad wetland, west coast of India

Transformations among different mercury species associated with sediments can have a major effect on the metal's mobility and potential for methylation and hence bioaccumulation. In the present study, various fractions of mercury in the sediments of Vembanad wetland system analysed. Total mercury (THg) concentration in the surface sediment varied from 16.3 to 4,230?ng/g. The results of sequential extraction showed that the major portion of mercury in these sediments existed as elemental form followed by organo-chelated form. The least portion observed was the residual fraction (mercury of natural origin). Even though the percentage of mercury observed in the easily available fractions is relatively small, absolute values of these mobile Hg fractions are quite high due to the very high total mercury values. The fractionation of mercury in the sediment was controlled by the organic matter, sulphur complexes and concentration of THg. The results showed that the bioavailability of mercury is high as the amount of mercury found in the initial three fractions is high, which can also enhance the methylation potential of the Vembanad wetland sediments. The fractionation pattern of mercury also revealed the presence of anthropogenic mercury content in the Vembanad wetland sediments.     

Deoxyribonuclease activity in seawater and sediment

This paper describes a fluorometric method for assaying deoxyribonuclease (DNase) activity in natural seawater and sediment. DNase activity was detected in a sea-water sample taken from Tokyo Bay (Japan), and in various sediment samples taken from Suruga, Sagami and Tokyo Bays, and from Aburatsubo Inlet. Much more DNase occurred in seawater in a state bound to suspended particles or microbial cells than dissolved free in seawater. Although viable DNA-hydrolyzing bacteria were found to be widely distributed in seawater and sediment, poor correlation existed between the bacterial population and the intensity of DNase activity in the sediments examined. In addition, intensities of DNase activity in various surface sediments had no apparent correlation with the DNA contents and the sediment types. However, a close correspondence was found between the vertical variation of DNase activities and the gradient of DNA contents and of Eh in the core sediment at Aburatsubo Inlet.     

Improved methodology for ATP determination in marine environments

A simple technique is described for de-salting and concentrating adenosine triphosphate (ATP) extracted from seawater or marine sediment samples prior to assays with the standard luciferin-luciferase procedure. The technique involves chromatography of H₂SO₄ extracts on columns of activated carbon. The efficiency of ATP recovery from marine sediments using this pre-treatment was superior to that attained with either boiling Tris extraction or with H₂SO₄ extraction without subsequent purification. All ions which interfere with the luciferase reaction or precipitate ATP upon neutralization of acid extracts are removed with this procedure, thus eliminating the 50- to 100-fold dilutions required with other acid-extraction procedures. In addition, the purified ATP extracts may be concentrated up to 100-fold, thus greatly improving the sensitivity of ATP measurement in samples containing very low biomass. This procedure has been applied to ATP determination in marine sediments in the upwelling area off northwest Africa. The average ATP concentrations in the upper 6 cm of sediment from 1000 and 200 m were 195 and 545 ng per ml wet sediment, respectively.     

Distributions of heavy metals in the sediments of South Korean harbors

Mechanisms of natural attenuation of arsenic (As) by wetland plants may be classified by plant uptake and adsorption and/or co-precipitation by iron (oxy)hydroxide formed on the root surface of plants or in rhizosediment. A natural Cattail (Typha spp.) wetland impacted by tailings containing high levels of As from the Myungbong abandoned Au Mine, South Korea was selected, and the practical capability of this wetland to attenuate As was evaluated. The As concentrations in the plant tissues from the study wetland were several-fold higher than those from control wetland. SEM-EDX analyses demonstrated that iron plaques exist on the rhizome surface. Moreover, relatively high As contents bonded with hydrous iron oxides were found in the rhizosediments rather than in the bulk sediments. It was revealed through the leaching and sequential extraction analyses that As existed as more stable forms in the wetland sediment compared with adjacent paddy soil, which is also contaminated with As due to input of mine tailings. The As concentration ratios of extracted solution to sediment/soil represented that the wetland sediment showed significant lower values (10-fold) rather than the paddy soil with indicating high As stability. Also, As in the wetland sediment was predominantly bonded with residual phases on the basis of results from sequential extraction analysis. From these results, it is concluded that transformation of As contaminated agricultural field to wetland environment may be helpful for natural attenuation until active remediation action.     

Fractionation of Heavy Metals in Surface Sediments of Taihu Lake, East China

The BCR (European Communities Bureau of Reference) three-step sequential extraction procedure was applied to fractionate heavy metals in the sediment of Taihu Lake. For the determination of total metal concentration of the sediments, sample digestion was achieved by using HF/H₂O₂/HNO₃(2/1/1) acid mixture in a microwave-irradiated closed vessel system. The concentrations of Cd, Ni, Cr, Zn, Cu and Pb in various extracts solutions were analyzed by Inductively Coupled Plasma Atomic Emission Spectrometry (ICP-AES). The results obtained from the BCR three-step sequential extraction indicated relatively high mobility of Zn, Cu, Pb and Ni in the sediments while Cd and Cr were poorly mobile. Enrichment of heavy metals was found in the sediments collected in the northern parts of Taihu Lake. In the sediments collected in the southern and western sides of the Lake, heavy metal concentrations were relatively low. The relationship between total organic carbon (TOC) and heavy metals concentrations in the sediments is discussed.     

广东省不同水库底泥理化性质对内源氮磷释放影响

采用分级浸取分离方法,分析了广东省10个典型水库底泥的氮磷营养形态分布和污染状况;并通过模拟覆水试验,研究了不同水库底泥氮磷形态及理化性质对内源氮磷释放的影响。结果表明：广东省10个水库底泥氮磷污染较为严重,全氮含量为0.33~3.31 g.kg^-1,平均值为1.70 g.kg^-1;全磷含量为0.14~2.63 g.kg^-1,平均值为1.31 g.kg^-1。底泥氮磷主要以可转化态形式存在,可转化态氮磷含量占总氮磷含量百分比分别为41.2%~71.4%和53.6%~93.2%。底泥内源氮磷的释放主要受氮磷的赋存形态和含量的影响,水库底泥总氮的释放量与离子交换态氮（IEF-N）、碳酸盐结合态氮（WAEF-N）、铁锰氧化物结合态氮（SAEF-N）呈极显著正相关关系,相关系数分别为0.931、0.814、0.807;总磷的释放量与碳酸盐结合态磷（WAEF-P）、铁锰氧化物结合态磷（SAEF-P）呈极显著正相关,相关系数分别为0.960、0.957;这几种氮磷形态是上覆水体中氮磷的重要来源。同时底泥内源氮磷释放还与底泥机械组成有关,其中总氮和总磷释放量与底泥黏粒质量分数呈显著正相关,相关系数分别为0.738、0.638;而总氮的释放量与底泥砂粒质量分数呈显著负相关,相关系数为-0.685。这可能与可转化态氮磷更多的分布在细粒级底泥中有关,细颗粒底泥氮磷释放是上覆水体氮磷的主要来源。     

Mobilization of arsenic in groundwater of Bangladesh: evidence from an incubation study

The extensive extraction of arsenic (As)-contaminated groundwaters for drinking, household and agricultural purposes represents a serious health concern in many districts of Bangladesh. This laboratory-based incubation study investigated the sources and mechanisms of As mobilization in these groundwaters. Several incubation studies were carried out using sediments collected from the Bangladesh aquifer that were supplemented, or not, with different nutrients, followed by an analysis of the sediment suspensions for pH, ORP (oxidation-reduction potential), EC (electrical conductivity) and As and Fe(ΙΙ) concentrations. In the substrate-amended sediment suspensions incubated under anaerobic environment, there was a mobilization of As (maximum: 50–67 μg/l) and Fe(ΙΙ) (maximum: 182 μg/l), while the ORP value decreased immediately and drastically (as much as −468 mV to −560 mV) within 5–6 days. In the sediment suspensions incubated under control and aerobic conditions, no significant As mobilization occurred. The simultaneous mobilization of As and Fe(ΙΙ) from sediments is a strong indication that their mobilization resulted from the reduction of Fe oxyhydroxide by the enhanced activity of indigenous bacteria present in the sediments; this phenomenon also provides insights on the mobilization mechanism of As in groundwater. The concentrations of As in the sediments used in the incubation studies were strongly linked to the gradients of redox potential development that was stimulated by the quantity of organic nutrient (glucose) used. The penetration of surface-derived organic matter into the shallow aquifer may stimulate the activity of microbial communities, thereby leading to a reduction of iron oxyhydroxide and As release.     

广州流花湖底泥磷的垂直变化特征

广州流花湖是典型的城市景观浅水湖泊。应用经改进的Psenner连续提取法,分析了广州市流花湖底泥中各形态磷的垂直分布。结果表明,不同采样点底泥的理化性质和磷的形态垂直变化存在较大的差异;不同形态磷的质量分数由小到大的顺序是NaOH-P,Org-P,HCl-P,BD-P,NH4Cl-P,其中NaOH-P和Org-P是底泥磷的主要赋存形态,分别占底泥总磷质量的47.28%和24.23%,说明了流花湖底泥人为污染较严重;底泥生物可利用磷的质量分数在0.50～1.45 mg.g-1,平均质量分数为0.93 mg.g-1,约占总磷的58.57%,表明流花湖底泥的磷具有较好的生物可利用性,将为水体藻类大量繁殖提供潜在的有利条件。流花湖底泥中有机磷、金属结合态磷和生物可利用磷垂直方向上的分布变化规律较复杂。     

广州市流花湖表层底泥磷的形态与生物可利用性

应用经改进的Psenner连续提取法对广州市流花湖表层底泥中的磷进行了连续提取和测定。结果表明,流花湖底泥中总磷含量在1.28~2.15 mg/g,流花湖总磷含量最高在L2点,最低在L3点。湖泊表层底泥总磷主要由金属氧化物结合态磷、有机磷和钙结合态磷组成,可还原态磷和弱吸附态磷仅占很少部分。不同形态磷的含量顺序是金属氧化物结合态磷NaOH-P>有机磷Org-P>钙结合态磷HCl-P>可还原态磷BD-P>弱吸附态磷NH4Cl-P。底泥中生物可利用性磷的含量达0.76~1.00 mg/g,平均含量为0.91 mg/g,占总磷的45.47%~64.71%。说明流花湖底泥的磷有较好的生物可利用性,将为水体藻类大量繁殖提供潜在的有利条件,因此在湖泊治理恢复过程中,应该采样有效的措施来控制底泥磷的内源释放。     

Effects of previous drying of sediment on root functional traits and rhizoperformance of emerged macrophytes

• Sediment desiccation alters morphological characteristics of aquatic sediment. • Alternation in morphological properties of sediment limiting root characteristics. • Fibrous-rooted macrophytes root properties extra favor nutrients removal. • Thick-rooted macrophytes exhibit higher life-span in two sediment types. Purpose of the current study was to investigate the effects of constantly wet and dried-rewetted sediments on root functional traits of emerged macrophytes and their nutrients removal abilities. It is based on the hypothesis that root characteristics and nutrients removal abilities of plants will be altered in the course of sediment desiccation. Four emerged macrophytes including two fibrous-root plants (Canna indica and Acorus calamus) and two thick-root plants (Alocasia cucullata and Aglaonema commutatum) were investigated for their root functional traits and rhizoperformance in both wet and dried-rewetted sediments. Results showed that sediment desiccation followed by rewetting substantially altered the root functional traits (root surface area, radial oxygen loss, and root activity) of plants due to adverse changes in morphological characteristics (porosity, bulk density, particle density) of dried-rewetted sediments than by wet sediments. Consequently, limited plants growth and removal of nitrogen (N), phosphorus (P) and dissolved organic carbon (DOC) were recorded in dried-rewetted sediments and their pore water than in wet sediments. Radial oxygen loss from plant roots correlated positively with root functional traits, plants growth, and removal of N, P and DOC from pore water and sediment in both sediment types. Among the macrophyte species, the fibrous-root plants having advantages root functional traits, greatly influenced the rhizospheric conditions (pH, dissolved oxygen and redox potential), and demonstrated higher N, P and DOC reduction from both sediment types. While, the thick-rooted plants with thick diameter roots (D > 1 mm) and higher rhizome exhibited longer life-span in both sediment types.