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Humic Fractions (humic + fraction)

Distribution by Scientific Domains

Earth and Environmental Science	75%

Selected Abstracts

Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments

ENVIRONMENTAL MICROBIOLOGY, Issue 7 2005
Juan M. Gonzalez
Summary Microbial assessment of natural biodiversity is usually achieved through polymerase chain reaction (PCR) amplification. Deoxyribonucleic acid (DNA) sequences from natural samples are often difficult to amplify because of the presence of PCR inhibitors or to the low number of copies of specific sequences. In this study, we propose a non-specific preamplification procedure to overcome the presence of inhibitors and to increase the number of copies prior to carrying out standard amplification by PCR. The pre-PCR step is carried out through a multiple displacement amplification (MDA) technique using random hexamers as priming oligonucleotides and ,29 DNA polymerase in an isothermal, whole-genome amplification reaction. Polymerase chain reaction amplification using specific priming oligonucleotides allows the selection of the sequences of interest after a preamplification reaction from complex environmental samples. The procedure (MDA-PCR) has been tested on a natural microbial community from a hypogean environment and laboratory assemblages of known bacterial species, in both cases targeting the small subunit ribosomal RNA gene sequences. Results from the natural community showed successful amplifications using the two steps protocol proposed in this study while standard, direct PCR amplification resulted in no amplification product. Amplifications from a laboratory assemblage by the two-step proposed protocol were successful at bacterial concentrations ,,10-fold lower than standard PCR. Amplifications carried out in the presence of different concentrations of fulvic acids (a soil humic fraction) by the MDA-PCR protocol generated PCR products at concentrations of fulvic acids over 10-fold higher than standard PCR amplifications. The proposed procedure (MDA-PCR) opens the possibility of detecting sequences represented at very low copy numbers, to work with minute samples, as well as to reduce the negative effects on PCR amplifications of some inhibitory substances commonly found in environmental samples. [source]

Quantitative solid-state 13C NMR spectroscopy of organic matter fractions in lowland rice soils

EUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2004
R. J. Smernik
Summary Spin counting on solid-state 13C cross-polarization (CP) nuclear magnetic resonance (NMR) spectra of two humic fractions isolated from tropical lowland soils showed that only 32,81% of potential 13C NMR signal was detected. The observability of 13C NMR signal (Cobs) was higher in the mobile humic acid (MHA) than in the calcium humate (CaHA) fraction, and increased with increasing intensity of irrigated rice cropping. NMR observability appeared to be related to the nature of the organic carbon, with phenol- and methoxyl-rich samples having the higher values of Cobs. The Bloch decay (BD) technique provided more quantitatively reliable 13C NMR spectra, as evidenced by values of Cobs in the range 91,100% for seven of the eight humic fractions studied. The BD spectra contained considerably more aryl and carbonyl signal, and less O,alkyl and alkyl signal, with the greatest differences between CP and BD spectra observed for the samples with low Cobs(CP). The causes of low CP observability were investigated using the spectral editing technique RESTORE ( REstoration of Spectra via TCH and T One Rho (T1,H) Editing). Rapid T1,H relaxation was found to be primarily responsible for the under-representation of carbonyl carbon, whereas inefficient cross-polarization was primarily responsible for the under-representation of aryl carbon in CP spectra. Proton NMR relaxation rates T1H and T1,H were found to correlate with other NMR properties and also with cropping management. Non-uniform rates of T1H relaxation in two of the CaHA fractions enabled the generation of proton spin relaxation editing subspectra. [source]

FTIR-spectroscopic characterization of humic acids and humin fractions obtained by advanced NaOH, Na4P2O7, and Na2CO3 extraction procedures

JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 4 2007
Michael Tatzber
Abstract Aim of our study was the development of the methodological basis for the characterization of humic fractions of a long-term field experiment. Humic acids (HAs) were extracted from three layers of a nontilled soil using three different extractants (1 M NaOH, 0.1 M Na4P2O7, 1 M Na2CO3), and the humin fraction was enriched. NaOH as extractant for FTIR analysis of humic substances yields higher resolved IR spectra, especially in the important regions of stretching vibrations including aromatic and aliphatic groups and in the fingerprint area including amides, aliphats, and aromats than the other extractants. The NaOH extraction has lower extraction yields as compared to Na4P2O7 and Na2CO3 and represents a different part of the soil organic matter (SOM). This is reflected by lower C : N ratios and higher E4 : E6 and fulvic acid,to,humic acid ratios as compared to the other extractants. The FTIR band areas of HA fraction obtained by NaOH showed an increase of the aromatic and carbonyl groups and a decrease of amide groups with increasing soil depth. Aliphatic groups showed contradicting results: The bands of the stretching vibrations increased, and the band of the bending vibrations decreased. We assume that band interactions in the bending vibrations were responsible for that phenomenon under the assumption of an increase of aliphatic groups with increasing soil depth. The IR bands of the enriched humin fraction showed a decreasing trend in case of both aliphatic bands deriving from stretching vibrations and an increase of aromatic characteristics with depth. Our study led to the conclusion that HA fractions obtained by 1 M NaOH represent a small and dynamic fraction indicated by the measured yields in combination with values of Nt, C : N, E4 : E6 ratios, and ratios of fulvic acids (FA) to HA. The humin fraction has a high contribution to the total organic C and represents a more stabilized fraction of SOM which still shows changes in its aromatic and aliphatic characteristics with soil depth. [source]

Recalcitrant soil organic materials mineralize more efficiently at higher temperatures

JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 3 2003
Roland Bol
Abstract As concentrations of atmospheric CO2 increase, it is important to know whether this may result in feedbacks that could modify the rate of increase of CO2 in the atmosphere. Soil organic matter (SOM) represents one of the largest pools of C and mineralization rates are known to be temperature dependent. In this study, we investigated whether different OM fractions present in a forest soil (F/A1 horizon) would respond in a similar manner to elevated temperatures. We examined the trends in isotopic content (12C, 13C, and 14C) of soil respired CO2 at various temperatures (10, 20, and 35 0C) over a two year period in the laboratory. We also examined the total C, total N, and C,:,N ratio in the remaining soil and isolated humic fractions, and the distribution of the individual amino acids in the soil after 5 years of laboratory incubation at the various temperatures. We found that the rate at which C mineralization increases with temperature was occasionally greater than predicted by most models, more C from recalcitrant OM pools being mineralized at the higher temperature. This confirmed that the relationship between soil organic matter decomposition and temperature was complex and that the different pools of organic matter did respond in differing ways to elevated temperatures. Rekalizitrante organische Bodensubstanz mineralisiert bei höheren Temperaturen effizienter Vor dem Hintergrund ansteigender atmosphärischer CO2 -Konzentrationen gewinnt die Erforschung möglicher Rückkopplungs-Mechanismen zunehmend an Bedeutung. Die organische Bodensubstanz stellt eines der größten terrestrischen C-Reservoirs dar. Die Rate der C-Mineralisation aus der organischen Bodensubstanz gilt allgemein als temperaturabhängig. In der hier vorgestellten Untersuchung sollte geprüft werden, ob verschiedene Fraktionen der organischen Bodensubstanz eines Waldstandortes (F/A1-Horizont) ähnlich stark auf erhöhte Temperaturen reagieren. Über einen Zeitraum von zwei Jahren wurde unter Laborbedingungen die Veränderung der Isotopen-Gehalte (12C, 13C und 14C) des bei verschiedenen Temperaturen (10, 20 und 35 °C) inkubierten Bodens untersucht. Ebenfalls erfasst wurden Gesamt-C, Gesamt-N und C,:,N-Verhältnis im Gesamt-Boden und in isolierten Humus-Fraktionen sowie das Verteilungsmuster der Aminosäuren im Boden nach fünfjähriger Inkubationsdauer. Die Ergebnisse zeigen, dass die temperaturbedingte Erhöhung der Mineralisationsrate in einigen Fällen deutlich stärker ausgeprägt ist, als anhand von Modellberechnungen erwartet wurde. Ursache hierfür ist unter erhöhten Temperaturen intensivere C-Mineralisation aus rekalzitranter organischer Bodensubstanz. Dies bestätigt unsere Vermutung, dass es keinen einfachen Zusammenhang zwischen Mineralisationsrate und Temperatur gibt, da verschiedene Humusbestandteile unterschiedlich auf erhöhte Temperaturen reagieren. [source]