An optimized method for the extraction of ancient eukaryote DNA from marine sediments

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo‐communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead‐beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica‐solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size‐selection of low molecular‐weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead‐beating, DNA binding in silica‐solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post‐library LMW size‐selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data‐processing protocol should improve quantitative paleo‐monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.     

The transformation of the cytoplasmic oestradiol–receptor complex into the nuclear complex in a uterine cell-free system

Experiments performed with a cell-free system in tris-EDTA buffer, pH 7.4, indicate that the high-speed supernatant fraction of the rat uterus contains all the factors necessary to transform the 8S cytoplasmic oestradiol-receptor complex to the nuclear complex. The transformation is temperature-dependent. This nuclear complex was extracted in the form of a 5S particle with 0.4m-KCl from sediments of either uterine or heart nuclei that had been incubated together with the cytoplasmic soluble fraction of the uterus at 2 degrees C for 30min. This complex can also be obtained similarly from the soluble fraction of the uterus, incubated in the absence of nuclei. Previous warming of the soluble fraction to 37 degrees C for 7min was necessary for the successful extraction of the nuclear particle under these conditions of incubation. After an incubation of the transformed complex with the nuclear sediment at 37 degrees C for 7min, the 5S complex was extractable from the uterine nuclear sediment but not from the heart nuclear sediment, which may indicate the tissue specificity of the nuclear acceptor sites for the transformed complex. The extracted uterine nuclear complex sediments in the 5S region, but whether it is the native complex or a subunit or other part of the native complex resulting from the extraction with salt is unknown.     

Hot-Alkaline DNA Extraction Method for Deep-Subseafloor Archaeal Communities

A prerequisite for DNA-based microbial community analysis is even and effective cell disruption for DNA extraction. With a commonly used DNA extraction kit, roughly two-thirds of subseafloor sediment microbial cells remain intact on average (i.e., the cells are not disrupted), indicating that microbial community analyses may be biased at the DNA extraction step, prior to subsequent molecular analyses. To address this issue, we standardized a new DNA extraction method using alkaline treatment and heating. Upon treatment with 1 M NaOH at 98°C for 20 min, over 98% of microbial cells in subseafloor sediment samples collected at different depths were disrupted. However, DNA integrity tests showed that such strong alkaline and heat treatment also cleaved DNA molecules into short fragments that could not be amplified by PCR. Subsequently, we optimized the alkaline and temperature conditions to minimize DNA fragmentation and retain high cell disruption efficiency. The best conditions produced a cell disruption rate of 50 to 80% in subseafloor sediment samples from various depths and retained sufficient DNA integrity for amplification of the complete 16S rRNA gene (i.e., ∼1,500 bp). The optimized method also yielded higher DNA concentrations in all samples tested compared with extractions using a conventional kit-based approach. Comparative molecular analysis using real-time PCR and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the new method produced an increase in archaeal DNA and its diversity, suggesting that it provides better analytical coverage of subseafloor microbial communities than conventional methods.     

Effects of sediment pretreatment on the performance of sediment microbial fuel cells

In the present study, the effects of different pretreatment methods for sediments on the performance of sediment microbial fuel cells (SMFCs) were evaluated. Autoclaved (30 and 60 min), and heated (150 °C, 3 h) sediments demonstrated high power density, compared with control and heated (60 °C, 3 h) sediments. An SMFC with heated (60 °C, 3 h) sediment was found to easily form a biocathode. The power density of an SMFC with heated (150 °C, 3 h) sediment was 214 mW m(-2) on day 24. Furthermore, autoclaved (30 and 60 min) and heated (3 h, 60 and 150 °C) sediments accelerated the production of dissolved organic matter (DOM). The DOM in heated (60 °C, 3 h) sediments had larger molecular sizes. The present study demonstrates that SMFCs can have high power density and high loss on ignition removal efficiencies when produced from sediments by suitable pretreatment methods.     

Detection of Naegleria fowleri cysts in environmental samples by using a DNA probe

Abstract In this study we tried to detect DNA Naegleria fowleri in artificially contaminated environmental samples, with or without sediments, containing 10⁴ cysts of this pathogenic amoeba. We used two assays to extract DNA from samples: first, direct DNA extraction, which gave positive results only for water samples without sediment; second, DNA extraction after sample incubation on agar plates, which allowed us to remove amoeba growing out of the sediments, and which gave positive results for all samples, even those initially with sediments (5, 500 or 500 mg). Thus, this molecular identification appears as a powerful tool to investigate N. fowleri growth in environmental samples.     

A Simple Silica-based Method for Metagenomic DNA Extraction from Soil and Sediments

A new method is described for extraction of metagenomic DNA from soil and sediments which is based on DNA adsorption to silica without the use of phenol, ethanol precipitation or a cesium chloride gradient. High-quality DNA was obtained, and PCR inhibition was overcome by adding bovine serum albumin and adjusting magnesium concentration. By using PCR-DGGE with Firmicutes and lactic acid bacteria-specific primers the extracted metagenomic DNA was shown to contain a mixture of bacterial genomes. This method can be used for screening bacterial diversity in soil and sediment samples.     

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes

Methane (CH(4)) flux to the atmosphere is mitigated via microbial CH(4) oxidation in sediments and water. As arctic temperatures increase, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is important to predicting future CH(4) emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), and pyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C, and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH(4) oxidation activity was measured in microcosm incubations containing sediments at all temperatures, with the highest CH(4) oxidation potential of 37.5 μmol g(-1) day(-1) in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and of the 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in (13)C-labeled DNA obtained by SIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisition from CH(4) in the sediments. The identity and relative abundance of active methanotrophs differed with the incubation temperature. Methylotrophs were also abundant in the microbial community that derived carbon from CH(4), especially in the deeper sediments (depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R = 0.82) with the relative abundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophic communities in arctic lake sediments respond to temperature variations.     

DNA extraction from archival formalin-fixed,paraffin-embedded tissues: heat-induced retrieval in alkaline solution

Based on the antigen retrieval principle, our previous study has demonstrated that heating archival formalin-fixed, paraffin-embedded (FFPE) tissues at a higher temperature and at higher pH value of the retrieval solution may achieve higher efficiency of extracted DNA, when compared to the traditional enzyme digestion method. Along this line of heat-induced retrieval, this further study is focused on development of a simpler and more effective heat-induced DNA retrieval technique by testing various retrieval solutions. Three major experiments using a high temperature heating method to extract DNA from FFPE human lymphoid and other tissue sections were performed to compare: (1) different concentrations of alkaline solution (NaOH or KOH, pH 11.5–12) versus Britton and Robinson type of buffer solution (BR buffer) of pH 12 that was the only retrieval solution tested in our previous study; (2) several chemical solutions (SDS, Tween 20, and GITC of various concentrations) versus BR buffer or alkaline solution; and (3) alkaline solution mixed with chemicals versus BR buffer or single alkaline solution. Efficiency of DNA extraction was evaluated by measuring yields using spectrophotometry, electrophoretic pattern, semiquantitation of tissue dissolution, PCR amplification, and kinetic thermocycling-PCR methods. Results showed that boiling tissue sections in 0.1 M NaOH or KOH or its complex retrieval solutions produced higher yields and better quality of DNA compared to BR buffer or chemical solutions alone. The conclusion was that boiling FFPE tissue sections in 0.1 M alkaline solution is a simpler and more effective heat-induced retrieval protocol for DNA extraction. Combination with some chemicals (detergents) may further significantly improve efficiency of the heat-induced retrieval technique.     

Effect of hot-water extraction on alkaline pulping of bagasse

The effect of hot-water extraction on alkaline pulping was investigated. The properties of black liquor and pulp strength of bagasse were analyzed. The extraction was conducted at 160 °C for 30 min where 13.2% of the mass was dissolved in the extraction liquor. Untreated bagasse and extracted bagasse were digested by soda and soda-AQ processes at 17% and 15.5% (with 0.1% AQ) alkali charge (NaOH). Cooking temperatures were 160 °C and 155 °C respectively. The pulp from extracted bagasse had a lower Kappa number and a higher viscosity compared to the pulp from the untreated bagasse. The black liquor from pulping extracted bagasse had a lower solid content, a lower viscosity and a lower silica content, but a higher heating value than that from pulping of untreated bagasse. Hot-water extraction resulted in a significant decrease in bleaching chemical consumption and the formation of chlorinated organics. Pulp strength properties such as the tensile index and the burst index were found to be lower, but the tear index, bulk, opacity and pulp freeness were found to be higher when hot-water extraction was applied.     

Assessment of Preparation Methods for Organic Phosphorus Analysis in Phosphorus-Polluted Fe/Al-Rich Haihe River Sediments Using Solution 31P-NMR

Fe/Al-rich river sediments that were highly polluted with phosphorus (P) were used in tests to determine the optimum preparation techniques for measuring organic P (Po) using solution ³¹P nuclear magnetic resonance spectroscopy (³¹P-NMR). The optimum pre-treatment, extraction time, sediment to solution ratio and sodium hydroxide-ethylenediaminetetraacetic acid (NaOH-EDTA) extractant solution composition were determined. The total P and Po recovery rates were higher from freeze- and air-dried samples than from fresh samples. An extraction time of 16 h was adequate for extracting Po, and a shorter or longer extraction time led to lower recoveries of total P and Po, or led to the degradation of Po. An ideal P recovery rate and good-quality NMR spectra were obtained at a sediment:solution ratio of 1∶10, showing that this ratio is ideal for extracting Po. An extractant solution of 0.25 M NaOH and 50 mM EDTA was found to be more appropriate than either NaOH on its own, or a more concentrated NaOH-EDTA mixture for ³¹P-NMR analysis, as this combination minimized interference from paramagnetic ions and was appropriate for the detected range of Po concentrations. The most appropriate preparation method for Po analysis, therefore, was to extract the freeze-dried and ground sediment sample with a 0.25 M NaOH and 50 mM EDTA solution at a sediment:solution ratio of 1∶10, for 16 h, by shaking. As lyophilization of the NaOH-EDTA extracts proved to be an optimal pre-concentration method for Po analysis in the river sediment, the extract was lyophilized as soon as possible, and analyzed by ³¹P-NMR.     

Oil extraction from Scenedesmus obliquus using a continuous microwave system--design, optimization, and quality characterization

A 1.2 kW, 2450 MHz resonant continuous microwave processing system was designed and optimized for oil extraction from green algae (Scenedesmus obliquus). Algae-water suspension (1:1 w/w) was heated to 80 and 95°C, and subjected to extraction for up to 30 min. Maximum oil yield was achieved at 95°C and 30 min. The microwave system extracted 76-77% of total recoverable oil at 20-30 min and 95°C, compared to only 43-47% for water bath control. Extraction time and temperature had significant influence (p<0.0001) on extraction yield. Oil analysis indicated that microwaves extracted oil containing higher percentages of unsaturated and essential fatty acids (indicating higher quality). This study validates for the first time the efficiency of a continuous microwave system for extraction of lipids from algae. Higher oil yields, faster extraction rates and superior oil quality demonstrate this system's feasibility for oil extraction from a variety of feedstock.     

Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment

Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO(2)) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction.     

水丝蚓对太湖沉积物有机磷组成及垂向分布的影响

以太湖常见底栖动物——水丝蚓为研究对象,借助室内流动培养装置和31P核磁共振技术(phosphorus-31 nuclearmagnetic resonance spectroscopy)(31P-NMR),研究生物扰动对太湖沉积物有机磷组成及垂向分布的影响。结果表明:短时间内水丝蚓扰动对沉积物有机磷化合物种类组成影响并不显著,但会引起上层沉积物中稳定性较差的有机磷化合物磷脂和DNA含量出现显著降低,同时沉积物中总磷和有机磷的垂向分布亦发生明显改变。此外,水丝蚓扰动下沉积物含水率、孔隙率和碱性磷酸酶活性显著增加,使活性较高的有机磷化合物分解加速,最终导致表层沉积物中的磷脂与DNA含量降低。     

Comparison of Metagenomic DNA Extraction Methods for Soil Sediments of High Elevation Puga Hot Spring in Ladakh,India to Explore Bacterial Diversity

Extraction of good-quality metagenomic DNA from extreme environments is quite challenging, particularly from high elevation hot spring sediments. Low microbial load, high humic acid content and other contaminants complicate the process of extraction of metagenomic DNA from hot spring sediments. In the present study, efficacy of five manual DNA extraction protocols with modifications has been evaluated for metagenomic DNA extraction from boron–sulfur rich high elevation Puga hot spring sediments. Best suited protocol was identified based on the cell lysis efficiency, DNA yield, humic acid content, PCR reproducibility and representation of bacterial diversity. Quantity as well as quality of crude metagenomic DNA differed remarkably between various protocols used and were not pure enough to give PCR amplification using 16S rRNA bacterial and archaeal primers. Crude metagenomic DNA extracted using five different DNA extraction protocols was purified using spin column based purification method. Even after purification, only three protocols C, D and E yielded metagenomic DNA that could be amplified using both archaeal and bacterial primers. To evaluate the degree of microbial diversity represented by protocols C, D and E, phylogenetic genes amplified were subjected to amplified ribosomal DNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis analysis (DGGE) analysis. ARDRA banding pattern of amplicons generated for all the three extraction protocols, i.e., C, D and E were found to be similar. DGGE of protocol E derived amplicons resulted in the similar number of dominant bands but a greater number of non-dominant bands, i.e., the highest microbial diversity in comparison to protocols C and D, respectively. In the present study, protocol E developed from Yeates et al. protocol has been found to be best in terms of DNA yield, DNA purity and bacterial diversity depiction associated with boron–sulfur rich sediment of high elevation hot springs.     

Available phosphorus in lake sediments in The Netherlands

The amount of phosphorus available to algae in the sediments of four lakes in the western part of the Netherlands has been assessed by means of chemical extraction and bioassay techniques. In addition to direct chemical sediment analyses, extractions were carried out with an NTA column method and a stepwise NH₄ Cl-NaOH-HCI shaking method, the latter supposedly separating the weakly bound, the Fe- and Al-bound and the Ca-bound phosphates in the sediments. Bioassays, with sediment as the sole source of P, were made withScenedesmus quadricauda in modified Skulberg's 28 medium to determine the amount of phosphates available to algae.The average total P concentration of the sediments varied from 0.8 to 3.6 mg P g^–1 dry wt and correlated well with the net external P loading of the lakes. Uptake of P by algae in the bioassays varied from 0.4 to 36% — while NTA extracted 36–69% of the total P. The ratio NH₄Cl extracted/ NaOH extracted/ HCI extracted phosphates is different from lake to lake, although in all lakes the highest extractions (27–62% of total P) are found in the NaOH fraction. However, in the peaty sediments of these lakes, the NaOH step extracted not only the Fe- and Al-bound phosphates but, also, large amounts of humus compounds. Hence, this fraction also contains non-available organic P.The results are related to soil type and chemical characteristics of the sediments, and compared with data from other authors. A positive correlation was found between phosphate available to algae and NTA- and NaOH-extractable P, but the correlation with total phosphorus was higher. Moreover, algal-extractable P proved to be positively correlated with total iron and clay content and negatively with the amount of organic matter.It is concluded that the sediments in the investigated lakes show great variability and that the chemical extraction techniques cannot replace the bioassays to assess the amount of phosphorus available to algae.     

Comparison of three wet-alkaline methods of digestion of biogenic silica in water

SUMMARY. Methods for determination of low levels of biogenic silica (0.2–0.4 mg SiO₂) in aqueous samples after digestion with three wetalkaline extraction procedures compared favourably in both precision of replicates and recovery of silica utilized by diatoms in budgeted cultures. Leaching samples with 0.2 M NaOH for 10–15 min at 100°C was the least time consuming procedure. Also interference from silicate minerals was lower for this method than leaching with either 0.5 or 5% Na₂CO₃ for 2 h at 85°C. The use of filters to concentrate samples enables detection of low levels of biogenic silica with colorimetric procedures. Polycarbonate filters are recommended in preference to cellulose acetate or polyvinyl chloride filters for sample collection. Time-course experiments are recommended for establishing digestion times and determining the presence of mineral silicate interference. Wet-alkaline digestion methods are recommended for routine analysis of biogenic silica in suspended matter in preference to infra-red analysis, alkaline fusion and hydrofluoric acid/nitric acid methods.     

Differential extraction of sediment phosphates with NTA solutions

An extraction technique is described for the separation of iron- and calcium-bound phosphate. The iron-bound phosphate is extracted with a 0.05 M solution of Ca-NTA under reducing conditions. Iron, also, is brought into solution, which is an advantage over the NaOH extraction. The calcium-bound phosphate is extracted with a 0.05 M solution of Na-NTA. The NTA also extracts humic compounds. Organic phosphate compounds can be measured in the NTA extracts, unlike the NaOH or H₂SO₄ extracts such as are used in the (modified) Jackson procedure.Examples of some test compound extractions and of a calcareous sediment are given.     

Microbial Populations Stimulated for Hexavalent Uranium Reduction in Uranium Mine Sediment

Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO₂) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction.     

Evaluation of quantitative recovery of bacterial cells and DNA from different lake sediments by Nycodenz density gradient centrifugation

While purified bacterial cells and DNA – the signature of life – from soil and sediment matrices have been extensively studied in a wide range of environments and in different microbial ecosystems, the paucity of data on DNA extraction from contaminated sediments emphasizes the need for further research on the isolation and quantification of bacterial cells and DNA in sediments. Consequently, the Nycondez gradient centrifugation method was applied to extract bacterial cells from contaminated and uncontaminated sediments. Quantitative estimates of recovered bacterial cells were obtained from direct counts performed using DAPI (4′,6′-diamino-2-phenylindole hypochloride) staining couples with fluorescence microscopy and indirect counts (colony-forming units). The estimation was improved by using an efficient method of comparing sediment types composed of quantifying bacterial densities in three steps: S₁ the initial freshwater sediments; S₂ the first supernatant recovered after mixing the sediments with sodium hexametaphosphate solution followed by centrifugation; and S₃ the extracted cells. Total and extracellular DNA were extracted and quantified in each of the three steps. Additional analysis of faecal indicator bacteria (FIB) including E. coli and Enterococcus (ENT) was also performed in each step. The results display considerable variability in the quantity of bacteria cells depending on sediment type, ranging from 1.2 × 10⁵ to 6.2 × 10⁹ cell g^?1 dry sediments. The treatment with sodium hexametaphosphate solution (2%) leads to the desorption of bacterial populations which were firmly adsorbed on contaminated sediment surfaces resulting in more than 90% of the FIB being recovered. The Nycondez density gradient centrifugation method makes it possible to extract bacterial cells from freshwater sediments without extracellular DNA so it is ideal for metagenomic analysis of bacteria.     

Use of the [(14)C]leucine incorporation technique to measure bacterial production in river sediments and the epiphyton.

Bacterial production is a key parameter for the understanding of carbon cycling in aquatic ecosystems, yet it remains difficult to measure in many aquatic habitats. We therefore tested the applicability of the [(14)C]leucine incorporation technique for the measurement of bulk bacterial production in various habitats of a lowland river ecosystem. To evaluate the method, we determined (i) extraction efficiencies of bacterial protein from the sediments, (ii) substrate saturation of leucine in sediments, the biofilms on aquatic plants (epiphyton), and the pelagic zone, (iii) bacterial activities at different leucine concentrations, (iv) specificity of leucine uptake by bacteria, and (v) the effect of the incubation technique (perfused-core incubation versus slurry incubation) on leucine incorporation into protein. Bacterial protein was best extracted from sediments and precipitated by hot trichloroacetic acid treatment following ultrasonication. For epiphyton, an alkaline-extraction procedure was most efficient. Leucine incorporation saturation occurred at 1 microM in epiphyton and 100 nM in the pelagic zone. Saturation curves in sediments were difficult to model but showed the first level of leucine saturation at 50 microM. Increased uptake at higher leucine concentrations could be partly attributed to eukaryotes. Addition of micromolar concentrations of leucine did not enhance bacterial electron transport activity or DNA replication activity. Similar rates of leucine incorporation into protein calculated for whole sediment cores were observed after slurry and perfused-core incubations, but the rates exhibited strong vertical gradients after the core incubation. We conclude that the leucine incorporation method can measure bacterial production in a wide range of aquatic habitats, including fluvial sediments, if substrate saturation and isotope dilution are determined.