Distribution and molecular weight of dissolved DNA in subtropical estuarine and oceanic environments

DeFlaun, Mary F.; Paul, John H.; Jeffrey, Wade H.

doi:10.3354/meps038065

Cited by 140 publications

(94 citation statements)

References 24 publications

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“…Ethanolic precipitation has been used by DeFlaun et al (1986DeFlaun et al ( , 1987 and Paul et al ( 1986Paul et al ( , 1987 to isolate D-DNA from freshwater and marine habitats. This procedure is widely used in molecular biology and seems to perform well.…”

Section: Discussionmentioning

confidence: 99%

“…DeFlaun et al (1986) investigated the possibility of microbial cell lysis during vacuum filtration and concluded that lysis was not contributing to D-DNA levels at vacuum pressures I 150 mm Hg. It is conceivable that small, viable cells, spores, virus particles, or detrital aggregates may have contained the nucleic acids that we classify as dissolved.…”

Section: Discussionmentioning

confidence: 99%

“…As early as 1972, however, deoxyribonucleic acid (DNA), the fundamental molecule of heredity for all self-replicating organisms, was reported as a constituent of the DOM pool of both marine (Pillai and Ganguly 1972) and freshwater (Minear 1972) environments. More recently, the presence of dissolved DNA (D-DNA) has been confirmed by the comprehensive investigations of DeFlaun et al (1986DeFlaun et al ( , 1987 and . Regional studies performed by the above-mentioned workers in the NE Gulf of Mexico and in coastal Florida environments indicate that D-DNA concentrations are highest in ncarshore surface waters and that the steady state levels decrease with increasing distance from land and with increasing water depth.…”

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confidence: 89%

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The measurement and distribution of dissolved nucleic acids in aquatic environments

Karl

Bailiff

1989

Limnology & Oceanography

180

157

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Nucleic acids (DNA and RNA) are ubiquitous components of the dissolved organic matter (DOM) pool of all oceanic, neritic, estuarine, and freshwater habitats studied to date. A new method for the quantitative determination ofdissolved nucleic acids (DNA and RNA) in water and scdimcnt samples was developed, evaluated, and utilized in a study of various marine and freshwater ecosystems. Under appropriate reaction conditions, dissolved DNA (D-DNA) and dissolved RNA (D-RNA) are efficiently removed from solution with the addition of cctyltrimethylammonium bromide (CTAB) and subsequent formation of insoluble CTA-nucleic acid salts. The insoluble salts are collected, by filtration, onto glass-fiber filters and analyzed for DNA and RNA with fluorometric and calorimetric procedures, respectively. The pcrformancc of this CTAB method is simple, reliable, and reproducible for measuring dissolved nucleic acids in natural aquatic environments. For the ecosystems investigated hcrcin, D-DNA and D-RNA concentrations ranged from 0.56 to 88 pg liter-' and 4.03 to 871 pg liter I; the ratio of D-RNA to D-DNA ranged from 4.1 to 11.5.In most aquatic environments, the organic carbon inventory is dominated by nonliving materials, present both in dissolved and particulate states. This nonliving, or detrital carbon is derived from nonpredatory losses of organic matter at all trophic levels (e.g. egestion, excretion, secretion, etc.) and from allochthonous sources (Wetzel et al. 1972). Detrital carbon food webs, initiated by the activities of heterotrophic bacteria (Pomeroy 1974), provide a mechanism for the utilization of the chemical energy contained in the nonliving carbon pool. The potential importance of this putative "microbial loop" carbon flux pathway has focused attention on studies of the concentration, molecular composition, and cycling rates of dissolved organic matter (DOM; Azam et al. 1983).

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 89%

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The measurement and distribution of dissolved nucleic acids in aquatic environments

Karl

Bailiff

1989

Limnology & Oceanography

180

157

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“…Water samples were then filtered as described above and frozen at À80 1C. Substrate additions were designed to approach what is typically measured in estuarine environments: 2-7 mM AAs (Evens and Braven, 1988), 25 mg l À1 FAs (Stauffer and Macintyre, 1970) and 10 mg l À1 DNA (DeFlaun et al, 1987).…”

Section: Methodsmentioning

confidence: 99%

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

et al. 2011

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Most microorganisms remain uncultivated, and typically their ecological roles must be inferred from diversity and genomic studies. To directly measure functional roles of uncultivated microbes, we developed Chip-stable isotope probing (SIP), a high-sensitivity, high-throughput SIP method performed on a phylogenetic microarray (chip). This approach consists of microbial community incubations with isotopically labeled substrates, hybridization of the extracted community rRNA to a microarray and measurement of isotope incorporation-and therefore substrate use-by secondary ion mass spectrometer imaging (NanoSIMS). Laboratory experiments demonstrated that Chip-SIP can detect isotopic enrichment of 0.5 atom % 13 C and 0.1 atom % 15 N, thus permitting experiments with short incubation times and low substrate concentrations. We applied Chip-SIP analysis to a natural estuarine community and quantified amino acid, nucleic acid or fatty acid incorporation by 81 distinct microbial taxa, thus demonstrating that resource partitioning occurs with relatively simple organic substrates. The Chip-SIP approach expands the repertoire of stable isotope-enabled methods available to microbial ecologists and provides a means to test genomics-generated hypotheses about biogeochemical function in any natural environment.

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“…The typical proportion of lipids in the EPS dry mass of different non-soil biofilms amounts up to 10 % (More et al, 2014). Sparse molar mass data from different environments comprise 0.5 × 10 6 to 2 × 10 6 Da for polysaccharides (Flemming and Wingender, 2010), 7.75 × 10 4 to 2.32 × 10 7 Da for eDNA (DeFlaun et al, 1987) and 750 to 1500 Da for lipids . The extracellular matrix is exuded not only by soil bacteria and archaea but also by fungi and algae.…”

Section: Introductionmentioning

confidence: 99%

Enzymatic biofilm digestion in soil aggregates facilitates the release of particulate organic matter by sonication

Büks

Kaupenjohann

2016

SOIL

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Abstract. The stability of soil aggregates against shearing and compressive forces as well as water-caused dispersion is an integral marker of soil quality. High stability results in less compaction and erosion and has been linked to enhanced water retention, dynamic water transport and aeration regimes, increased rooting depth, and protection of soil organic matter (SOM) against microbial degradation. In turn, particulate organic matter is supposed to support soil aggregate stabilization. For decades the importance of biofilm extracellular polymeric substances (EPSs) regarding particulate organic matter (POM) occlusion and aggregate stability has been canonical because of its distribution, geometric structure and ability to link primary particles. However, experimental proof is still missing. This lack is mainly due to methodological reasons. Thus, the objective of this work is to develop a method of enzymatic biofilm detachment for studying the effects of EPSs on POM occlusion. The method combines an enzymatic pre-treatment with different activities of α-glucosidase, β-galactosidase, DNAse and lipase with a subsequent sequential ultrasonic treatment for disaggregation and density fractionation of soils. POM releases of treated samples were compared to an enzyme-free control. To test the efficacy of biofilm detachment the ratio of bacterial DNA from suspended cells and the remaining biofilm after enzymatic treatment were measured by quantitative real-time PCR. Although the enzyme treatment was not sufficient for total biofilm removal, our results indicate that EPSs may attach POM within soil aggregates. The tendency to additional POM release with increased application of enzymes was attributed to a slight loss in aggregate stability. This suggests that an effect of agricultural practices on soil microbial populations could influence POM occlusion/aggregate stability and thereby carbon cycle/soil quality.

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Distribution and molecular weight of dissolved DNA in subtropical estuarine and oceanic environments

Cited by 140 publications

References 24 publications

The measurement and distribution of dissolved nucleic acids in aquatic environments

The measurement and distribution of dissolved nucleic acids in aquatic environments

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Enzymatic biofilm digestion in soil aggregates facilitates the release of particulate organic matter by sonication

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