Extracellular dissolved organic carbon released from phytoplankton as a source of carbon for heterotrophic bacteria in lakes of different humic content

The quantitative importance of photosynthetically produced dissolved organic carbon (PDOC) released from phytoplankton as a source of carbon for pelagic, heterotrophic bacteria was investigated in four temperate Swedish lakes, of which two had low (≈20 mg Pt 1⁻¹), and two moderately high (60–80 mg Pt 1⁻¹) humic content. The bacterial assimilation of PDOC was estimated with the ¹⁴C method, and the total production of the heterotrophic bacteria was estimated with the [3H]thymidine incorporation method. The release of PDOC from natural communities of phytoplankton was not restricted to periods of photosynthesis, but often continued during periods of darkness. Heterotrophic bacteria often assimilated the labile components of the PDOC at high rates (up to 73% of the released PDOC was assimilated during the incubation in our experiments). The contribution of PDOC to bacterial production exhibited large within-lake seasonal variations, but PDOC was at certain times, both in humic and non-humic lakes, a quantitatively very important carbon source for the heterotrophic bacteria. Under periods of comparatively low primary production, heterotrophic bacteria in humic lakes appear to utilize allochthonous, humic substances as a substrate.     

The role of dissolved organic matter bioavailability in promoting phytoplankton blooms in Florida Bay

The clear, shallow, oligotrophic waters of Florida Bay are characterized by low phytoplankton biomass, yet periodic cyanobacteria and diatom blooms do occur. We hypothesized that allochthonous dissolved organic matter (DOM) was providing a subsidy to the system in the form of bound nutrients. Water from four bay sites was incubated under natural light and dark conditions with enrichments of either DOM ( > 1 kD, 2×DOM) or inorganic nutrients (N+P). Samples were analyzed for bacterial numbers, bacterial production, phytoplankton biomass, phytoplankton community structure, and production, nutrients, and alkaline phosphatase (AP) activity. The influence of 2×DOM enrichment on phytoplankton biomass developed slowly during the incubations and was relatively small compared to nutrient additions. Inorganic nutrient additions resulted in an ephemeral bloom characterized initially as cyanobacterial and brown algae but which changed to dinoflagellate and/or brown algae by day six. The DIN:TP ratio decreased 10-fold in the N+P treatments as the system progressed towards N limitation. This ratio did not change significantly for 2×DOM treatments. In addition, these experiments indicated that both autotrophic and heterotrophic microbial populations in Florida Bay may fluctuate in their limitation by organic and inorganic nutrient availability. Both N+P and 2×DOM enrichments revealed significant and positive response in bioavailability of dissolved organic carbon (BDOC). Potential BDOC ranged from 1.1 to 35.5%, with the most labile forms occurring in Whipray Basin. BDOC at all sites was stimulated by the 2×DOM addition. Except for Duck Key, BDOC at all sites was also stimulated by the addition of N+P. BDOC was lower in the dry season than in the wet season (5.56% vs. 16.86%). This may be explained by the distinct chemical characteristics of the DOM produced at different times of year. Thus, both the heterotrophic and autotrophic microbial communities in Florida Bay are modulated by bioavailability of DOM. This has ramifications for the fate of DOM from the Everglades inputs, implicating DOM bioavailability as a contributing factor in regulating the onset, persistence, and composition of phytoplankton blooms.     

Productivity of clear and humic lakes: nutrients,phytoplankton, bacteria

The relationships between long-term surface average concentrations of humic acids measured as water colour, dissolved organic carbon (DOC) or Secchi disk transparency and trophic state variables were studied with literature data from more than 600 freshwater lakes. The geometric means of summer surface average nutrient (phosphorus and nitrogen) concentration, phytoplankton biomass (chlorophyll concentration), and hypolimnetic anoxia (anoxic factor) were significantly higher in coloured than in clear lakes. The regressions of colour or DOC on these trophic state variables were positive and significant throughout a range of three orders of magnitude. Phytoplankton or primary productivity was higher in coloured lakes, when expressed per volume of epilimnion. Annual integral primary productivity expressed on an areal basis was smaller in coloured lakes, probably a reflection of shallower phototrophic depths in these lakes. There is evidence that annual integral bacteria productivity is much higher in coloured lakes for two reasons: first, epilimnetic bacteria production was ca. four times higher in coloured lakes, second, other studies have shown that hypolimnetic bacteria production is commonly higher than epilimnetic production, especially in anoxic hypolimnia that are frequent in coloured lakes. All volumetrically expressed variables indicated higher productivity in coloured lakes. In addition, high bacteria productivity reflects a different food chain involving mixotrophs, possibly compensating for low light conditions. Our analyses indicate that primary and secondary productivity is as high as or higher than in clear lakes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Supercritical fluid CO2 extraction accelerates isolation of humic acid from livePilayella littoralis (Phaeophyta)

Supercritical fluid CO₂ extraction of the live, dried algaPilayella littoralis efficiently removes non-humic substances in hours instead of the days required for sequential extraction with ether, acetone, ethanol and dioxane. Completion of extraction (including aqueous removal of alginic acids) with either preliminary in a standard procedure gives humic acid samples with closely comparable properties.Authors for correspondence     

Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils

AIM: To establish a rapid, improved soil environmental DNA extraction and purification protocol. METHODS AND RESULTS: Three different soil DNA isolation and four purification strategies were compared on different soil samples with variable rates of success. Bead beating extraction gave significantly higher DNA yields than microwave-based and liquid nitrogen grinding DNA extraction methods. The inclusion of soil washing prior to cell lysis decreased the amount of purification steps required. Although these soil types differed, polyvinylpolypyrrolidone (PVPP)-sepharose 2B column elution was sufficient for all three samples, yielding DNA pure enough for successful application in molecular studies. One soil sample retained 80% of the initial DNA after successful purification. CONCLUSIONS: Optimization of a purification protocol confirmed that only a combination of previously described methods proved sufficient in yielding pure environmental DNA from humic-rich soils. Total processing time for DNA extraction and subsequent purification from multiple samples was considerably more rapid than the previously described methods. SIGNIFICANCE AND IMPACT OF THE STUDY: This study developed a new optimized soil DNA extraction and purification protocol that is suitable for different environmental sources that are rich in humic acid content.     

Isolation of humic acid from the brown algaPilayella littoralis

A standard humic acid extraction procedure has been used to isolate dark brown organic residues from samples of the macroscopic marine brown algaPilayella littoralis. The residues are insoluble in water, but soluble at high pH, and are similar in elemental composition, ash content, UV-visible, IR, PMR and X-Ray fluorescence spectra, X-Ray diffractograms and scanning electron micrographs to residues of a humic acid isolated from municipal compost. These results indicate thatPilayella produces humic acids.Author for correspondence     

Relations between production and biomass of phytoplankton in four Swedish lakes of different trophic status and humic content

Production and biomass values from phytoplankton populations in four different Swedish lakes were analysed. The production in all lakes was directly proportional to biomass during homothermal periods. When the lakes were stratified there was a strong negative relation between specific growth rate and biomass. The data fitted to a logistic density dependent growth equation of the form: dB/ dt = µ_mB(1-B · K^–1) where B is the biomass, µ_m the maximum specific growth rate and K the carrying capacity. The equation was used to derive the parameters µ · µ_m ^–1 and carrying capacity (the maximum possible biomass). These parameters were then discussed in relation to light climate, phosphorus concentration and humic content.     

高砷含水层参与腐殖酸-铁矿物转化的关键微生物群落及其对砷迁移转化的影响

【目的】探究不同腐殖酸浓度下参与含砷水铁矿转化的微生物类群组成和丰度变化及对砷释放的影响,预测原位高砷含水层中功能微生物群参与有机质—含砷铁矿物转化过程对砷转化释放的作用。【方法】对河套平原高砷地下水和同深度高砷沉积物中的铁还原功能群落进行富集培养,构建室内厌氧微宇宙体系,将富集菌群分别加入到实验室条件下合成的不同浓度腐殖酸(0、1.5、7、14 mg C/L)-含砷水铁矿体系中,通过体系中砷、铁形态及浓度的变化分析,结合高通量测序技术、X-射线衍射(X-ray diffractometer, XRD),探究不同条件下砷的释放固定和群落的演替。【结果】高砷地下水组(G组)和沉积物组(S组)富集得到的铁还原功能群落具有明显差异,G组中以Aeromonadaceae为特殊优势菌群,而S组中以Shewanellaceae为特殊优势菌群。微宇宙实验结果显示,S组的铁还原量相对较高且速率较快;G组与S组中液相砷形态存在明显差异,整个培养期内G组均以As(Ⅴ)为主,而S组中前期以As(Ⅴ)为主,当反应到达20 d时液相As(Ⅲ)高达3.4μmol/L,推测此时具有砷还原功能的群落占优势地位。当反应...     

A method of extraction of DNA from birch

A method of DNA extraction is given which is suitable for use with birch (Betula spp.) material collected from natural populations. Such material is frequently old and insect-damaged, and contains high levels of polyphenols. The method relies on repeated extraction of the material with a high molarity urea phosphate buffer, and yields DNA suitable for RFLP analysis.     

Isolation of high molecular weight DNA from wholeEuglena cells

Summary A method for isolating high quality DNA from wholeEuglena cells is described. The procedure consists in: the weakening of the cell pellicle in glycerol avoiding the mechanical disruption of cells and shearing damage in DNA molecules; the decondensation ofEuglena compact chromatin directly inside the cells; the complete dissociation of cells and nucleoproteins in sarkosyl detergent; the optional digestion of proteins and RNA with DNase-free enzymes and the final purification of DNA by isopycnic banding in CsCl gradients. Degradation of DNA is prevented all along the extraction procedure by glycerol, antioxydants, EDTA and sarkosyl detergent. Using the enzymatic digestion step, DNA containing few single-stranded nicks is obtained with a yield approaching 100%. DNA with no single-stranded nick could be obtained with a 35% yield when the enzymatic digestion step was omitted. In both cases, the double-stranded DNA has an average molecular weight equal or greater than 6×10⁷. It is free of contaminants and could be easily digested with restriction enzymes. After digestion with Eco RI and size-fractionation in agarose gel this DNA has permitted specific hybridization of the rDNA sequences with a radioactive rRNA probe.Abbreviations Kbp kilobasepairs - Kb kilobases     

Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of juncaceae

Seven DNA extraction protocols were used to obtain DNA from herbarium specimens ofJuncus andLuzula (Juncaceae) of various ages. DNA of historical samples is difficult to extract, and the extracts are seldom of good quality. The quality of DNA obtained was estimated by using a spectrophotometer to measure the A260/280 absorbance ratio. The total DNA yield was measured by a fluorometer. The results indicate the success of using both mixer mill grinding and a DNeasy Plant Kit. Another extraction protocol (grinding with mortar and pestle, using liquid nitrogen) yielded DNA from many samples. Modified CTAB extraction, with a lengthy precipitation, usually provided good amounts of DNA. Other protocols did not give satisfactory results.     

Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components

A relatively quick, inexpensive and consistent protocol for extraction of DNA from expanded leaf material containing large quantities of polyphenols, tannins and polysaccharides is described. Mature strawberry leaves, which contain high levels of these secondary components, were used as a study group. The method involves a modified CTAB extraction, employing high salt concentrations to remove polysaccharides, the use of polyvinyl pyrrolidone (PVP) to remove polyphenols, an extended RNase treatment and a phenol-chloroform extraction. Average yields range from 20 to 84 μg/g mature leaf tissue for both wild and cultivated octoploid and diploidFragaria species. Results from 60 plants were examined, and were consistently amplifiable in the RAPD reaction with as little as 0.5 ng DNA per 25-μL reaction. Presently, this is the first procedure for the isolation of DNA from mature strawberry leaf tissue that produces consistent results for a variety of different species, both octoploid and diploid, and is both stable and PCR amplifiable before and after extended storage. This procedure may prove useful for other difficult species in the family Rosaceae.     

DNA extraction from a previously recalcitrant plant genus

Numerous DNA extraction methods failed to remove contaminants that interfere with restriction digests ofCuphea DNA. The method described here removes those contaminants and maintains relatively high DNA yields. The primary purification process consists of washing the DNA with phenol while it is complexed with CTAB and dissolved in 1 M NaCl.     

Protocol for DNA extraction from potato tubers

A method to extract high-quality DNA from potato tubers was developed and tested on 3 wild potato species (Solanum raphanifolium, S. megistracrolobum, S. bukasovii) and on the tetraploid B3 bred population, (population number 393228, derived fromS. tuberosum subsp.tuberosum). The average yield of extracted DNA varied from 10–30 μg of DNA per gram of processed tissue. The DNA was pure and suitable for ligation-mediated polymerase chain reaction (LM-PCR) amplification, producing clear, distinctive, and reproducible banding patterns in polyacrylamide gels.     

Enhanced DNA extraction and PCR amplification of SSU ribosomal genes from crustose coralline algae

As crustose Corallinales on the coasts of Chile are usually flat, thin,strongly adherent to the rocks and with a high concentration ofpolysaccharides,there is a need to improve DNA extraction for molecular studies. The paperdescribes a protocol to achieve this, which includes steps for disruption ofcell walls and precipitation of polysaccharides and proteins; this leads to aPCR-quality product. The DNA obtained permitted amplification of SSU and rbcLgenes from small amounts of material (< 1 g) of several generaand species of Corallinales. Comparison of the sequences of small SSU fragments(approximately 500 bp), combined with morphological characters,together provide sufficient resolution to distinguish organisms at the genusandspecies levels.     

吉安地区典型景观湖泊浮游植物群落特征及其与水环境因子的关系

2012年8月至2013年7月,对吉安地区将军湖、龙湖、庐陵湖和挹翠湖4个景观湖泊水体浮游植物群落及其主要水环境因子进行了调查,并利用生物多样性指数法(Shannon指数H、Margalef指数D和Pielou指数J)和主成分分析(PCA)法分别对湖泊水质和水环境因子进行了评价。结果表明:4个湖泊共鉴定浮游植物7门82属163种,主要优势种为硅藻或绿藻;浮游植物细胞丰度呈季节性变化,秋夏居高,冬春季偏低,平均丰度变化范围为25.45×10~6~54.04×10~6cells·L~(-1);将军湖、龙湖、庐陵湖和挹翠湖的H值分别为1.26~2.08、1.82~2.61、2.27~2.62和1.10~2.32;D值分别为2.03~3.51、2.36~3.71、2.48~3.93和3.12~3.96;J值分别为0.45~0.69、0.59~0.80、0.67~0.77和0.50~0.84。综合评价结果显示,4个湖泊处于富营养化状态、中等污染水平。而对污染较重的庐陵湖水环境因子PCA分析结果表明,水温(WT)、溶解氧(DO)和总氮(TN)是影响小型封闭景观水体浮游植物群落变化的主要因素。建议对小型封闭景观水体进行必要的治理和生态修复。     

Pyrolysis-field ionization mass spectrometry of agricultural soils and humic substances: Effect of cropping systems and influence of the mineral matrix

Whole soil samples, extracted humic substances, the corresponding fulvic (FA) and humic acids (HA) and the extraction residues (humins) from long-term, agricultural test plots were investigated by in-source pyrolysis-field ionization mass spectrometry (Py-FIMS). For the soils distinct differences in the chemical composition of the organic matter in differently managed fields were observed. The FI mass spectra of the extracted humic substances gave complementary chemical information, as they cover a larger mass range compared to the whole soil spectra. The chemical, structural information of the conventional alkaline extraction residues was demonstrated by Py-FIMS spectra to be similar to that of the related soil samples. Influences of mineral matrix to organic matter ratios were studied on mixtures of extracted humic substances with defined mineral components such as quartz, basalt, iron oxide (Fe₂O₃), Ca-montmorillonite, kaolinite and illite. It was shown that in these mixtures the number of mass signals detected and the covered mass range decreased, when organic carbon concentrations (C_org) in this synthetic mineral matrix dropped below 2% (w/w). Limitations in the direct application of Py-FIMS might arise in the case of natural soil samples with C_org concentrations below 0.5% (w/w), high contents of swelling clay minerals and iron oxides. ei]{gnR}{fnMerckx}     

Isolation and PCR amplification of genomic DNA from dried capsules of cardamon (Elettaria cardamomum M.)

Cardamom is an important spice, condiment and medicine, and international commodity. DNA-based molecular profiling will be aid in protecting the intellectual property rights of those who trade cardamom on the world market. Commercial cardamom has so far proven recalcitrant to traditional DNA extraction methods. In this paper we report a protocol for the isolation of amplifiable genomic DNA from traded cardamom. The method involves a modified CTAB (hexadecyltrimethylammonium bromide) extraction step, followed by a purification step to remove polysaccharides, proteins, and polyphenols, which are abundant in storage tissue such as cardamom capsules. The yield of DNA was 6–7 μg g⁻¹ tissue. Spectrophotometric and electrophoretic analysis indicated that the isolated DNA was highly pure and of high molecular weight. The isolated DNA could be amplified using different random decamer primers. The protocol has trade implications as it will help in the PCR-based characterisation of traded cardamom. This protocol can be further extended to develop Sequence Characterised Amplified Regions (SCAR) markers for profiling cardamoms.     

Effects of different molecular weight fractions of dissolved organic matter on the growth of bacteria,algae and protozoa from a highly humic lake

Effects of different molecular size fractions (< 1000 MW, < 10 000 MW, < 100 000 MW and <0.1 μm) of dissolved organic matter (DOM) on the growth of bacteria, algae and protozoa from a highly humic lake were investigated. DOM from catchment drainage water as well as from the lake consisted mostly (59–63%) of high molecular weight (HMW) compounds (> 10 000 MW). With excess inorganic nutrients, the growth rate and yield of bacteria were almost identical in all size fractions. However, in < 1000 MW fractions and with glucose added, a longer lag phase occurred. Without added nutrients both the growth rates and biomasses of bacteria decreased towards the smaller size fractions and the percentage of dissolved organic carbon (DOC) used during the experiment and the growth efficiency of bacteria were lower than with excess nutrients. The growth efficiency of bacteria was estimated to vary between 3–66% in different MW fractions, largely depending on the nutrient concentrations, but the highest growth efficiencies were observed in HMW fractions and with glucose. The growth of algae was clearly lowest in the < 1000 MW fraction. In dim light no net growth of algae could be found. In contrast, added nutrients substantially enhanced algal growth and in deionized water with glucose, algae achieved almost the same growth rate and biomass as in higher MW fractions of DOM. The results suggested that bacteria and some algae were favoured by DOM, but protozoans seemed to benefit only indirectly, through bacterial grazing. The utilization of DOM by bacteria and algae was strongly affected by the availability of phosphorus and nitrogen.