Extractable dsDNA and product formation as measures of microbial growth in soil upon substrate addition

Marstorp, Håkan; Witter, Ernst

doi:10.1016/s0038-0717(99)00065-6

Cited by 85 publications

(41 citation statements)

References 31 publications

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“…The level of soil dsDNA correlates well with soil microbial biomass (6,46). In the upper layer, the total level of dsDNA was lower in the presence of protists than in the absence of protists (Fig.…”

Section: Discussionmentioning

confidence: 73%

Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

Murase

Noll

Frenzel

2006

Appl Environ Microbiol

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Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a ␥-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G؉C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH 4 ؉ was lower and the level of extractable SO 4 2؊ was higher without protists, indicating that nitrogen mineralization and SO 4 2؊ reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O 2 was a major control, and O 2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.

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Section: Discussionmentioning

confidence: 73%

Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

Murase

Noll

Frenzel

2006

Appl Environ Microbiol

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“…Yields of dsDNA, providing quantitative information about microbial growth in soil upon substrate addition (Marstorp and Witter 1999), increased with increasing cattle impact, ranging from 1.866 (±0.44) lg g -1 soil from non cattle impacted soil (NI) to 6.728 (±0.22) lg g -1 soil medium impacted (MI) and 7.272 (±0.49) lg g -1 soil from severely impacted soil (SI). The increase of dsDNA along the gradient from section NI over MI to SI clearly reflected the impact of cattle due to excretal returns.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of the denaturing gradient gel electrophoresis-apparatus as a parameter influencing soil microbial community fingerprinting

Ascher

Ceccherini

Chroňáková

et al. 2010

World J Microbiol Biotechnol

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We compared two denaturing gradient gel electrophoresis (DGGE) systems-DCode (Biorad, Hercules, CA, USA) and PhorU (Ingeny, Leiden, NL), performing community level 16S and 18S rRNA gene fragment-PCR-DGGE with total DNA extracted from upland pasture soil used for outdoor cattle husbandry. The methodological evaluation of the DGGE apparatus as parameter influencing DGGE fingerprinting, based on cluster analysis of soil bacterial and fungal community fingerprints, was made in terms of the resulting information about microbial community structures and their response to different degrees of cattle impact. Although the comparative DGGE analysis with different DGGE systems provided similar clustering of microbial community structures in correlation with the degree of cattle impact, our results suggest the DGGE system to be a factor influencing DGGE analysis. To our knowledge this is the first attempt to investigate the hypothetical impact of the DGGE system due to different technical characteristics, recommending the use of one and the same DGGE apparatus throughout an experiment, if the monitoring of microbial community structures requires multiple gel-to-gel analysis.

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“…They also found that the amount of the total extracted DNA corresponded to the microbial biomass C, as estimated by CFE (chloroform fumigation-extraction) (Toyota et al 1996;Marstorp and Witter 1999). In addition, some extracellular DNA (between 10% and 60% of the total DNA) might also be derived from non-microbial sources.…”

Section: Quantification Of Total Dna Amountmentioning

confidence: 95%

Changes in Microbial Functional Diversity and Activity in Paddy Soils Irrigated with Industrial Wastewaters in Bandung, West Java Province, Indonesia

Chaerun

Pangesti

Toyota

et al. 2010

Water Air Soil Pollut

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Characteristics, such as microbial biomass, basal respiration, and functional diversity of the microbial communities, were investigated in paddy soils located in Bandung, West Java Province, Indonesia, that have been heavily polluted by industrial effluents for 31 years. Paddy soil samples (10-20 cm) were taken from two sites: polluted soils and unpolluted soils (as control sites). The polluted soils contained higher salinity, higher sodicity, higher nutrient contents, and elevated levels of heavy metals (Cr, Mn, Ni, Cu, and Zn) than unpolluted soils. Soil physicochemical properties, such as maximum water holding capacity, exchangeable sodium percentage, sodium adsorption ratio, and swelling factor, in polluted soils were much greater than those in unpolluted soils (P<0.05). Changes in the physical and chemical soil properties were reflected by changes in the microbial communities and their activities. BIOLOG analysis indicated that the functional diversity of the microbial community of polluted soils increased and differed from that of unpolluted soils. Likewise, the average rate of color development (average well color development), microbial biomass (measured as DNA concentration), and the soil CO 2 respiration were higher in polluted soils. These results indicate that major changes in the chemical and physical properties of paddy soils following the application of industrial wastewater effluents have had lasting impacts on the microbial communities of these soils. Thus, the increased activity, biomass, and functional diversity of the microbial communities in polluted soils with elevated salinity, sodicity, and heavy metal contents may be a key factor in enhancing the bioremediation process of these heavily polluted paddy soils.

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Extractable dsDNA and product formation as measures of microbial growth in soil upon substrate addition

Cited by 85 publications

References 31 publications

Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

Evaluation of the denaturing gradient gel electrophoresis-apparatus as a parameter influencing soil microbial community fingerprinting

Changes in Microbial Functional Diversity and Activity in Paddy Soils Irrigated with Industrial Wastewaters in Bandung, West Java Province, Indonesia

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