Carbon flow into microbial and fungal biomass as a basis for the belowground food web of agroecosystems

Krämer, Susanne; Marhan, Sven; Rueß, Liliane; Armbruster, Wolfgang; Butenschoen, Olaf; Haslwimmer, Heike; Kuzyakov, Yakov; Pausch, Johanna; Scheunemann, Nicole; J, Schoene; Schmalwasser, Andreas; Totsche, Kai Uwe; Walker, Frank; Scheu, Stefan; Kandeler, Ellen

doi:10.1016/j.pedobi.2011.12.001

Cited by 103 publications

(53 citation statements)

References 67 publications

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“…Based on the analysis of phospholipid fatty acids (see Table S13 in the supplemental material), the ratio of Gram-positive to Gram-negative bacterial biomass approximated 3 for all three soils. Due to the different numbers of signature molecules for Gram-positive and Gramnegative organisms, this ratio is a rough estimate and is mainly used for comparison between different soil samples (55). Based on the analysis of 16S rRNA genes, the ratios of most abundant Gram-positive taxa (i.e., Actinobacteria and Firmicutes) to most abundant Gram-negative taxa (i.e., Acidobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Proteobacteria) were highly variable and depended on the extraction method (see Tables S7 to S12).…”

Section: Resultsmentioning

confidence: 99%

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

Wüst

Nacke

Kaiser

et al. 2016

Appl Environ Microbiol

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dModern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actinobacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms. Soil is one of the most complex and diverse microbial habitats, with 1 g containing up to 10 10 cells and 10 4 bacterial species (1, 2). While DNA sequences provide information about the total microbial community, RNA can be used to analyze the fraction of microorganisms that has the capacity to actively synthesize proteins (3-5). The ratio of bacterial 16S rRNA transcripts to 16S rRNA gene copies has been used as an indicator of the potential specific activity since it reflects the cellular ribosome content (6, 7). However, nucleic acid extraction from soils is affected by insufficient cell lysis or losses during extraction, variable reproducibility, and various effects of soil pH, clay content, and organic carbon content (8-13), and coextracted organic compounds can inhibit DNA polymerase and reverse transcriptase employed in downstream molecular analyses (14).Direct nucleic acid extraction methods are based on the lysis of cells inside the soil matrix, whereas indirect methods commence with the isolation of bacterial cells from soil prior to nucleic acid extraction (8). Indirect methods typically yield longer nucleic acid fragments which are useful for metagenomic studies (10, 15) but often result in a significantly lower yield and diversity of nucleic acid molecules (10, 16). Existing protocols for the direct extraction of DNA and RNA from soils (13, 17-25) have partly been evaluated (19,21,24,(26)(27)(28)(29)(30)), but only a few studies have compared extraction efficiencies of methods recovering both DNA and RNA (21, 24). In particular, these methods have so far not been compared with extraction protocols optimized for either DNA or RNA alone. Information about the effects of different extraction methods on the phylogenetic analysis is scant (31, 32). As a result, ...

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Section: Resultsmentioning

confidence: 99%

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

Wüst

Nacke

Kaiser

et al. 2016

Appl Environ Microbiol

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“…The literature has emphasized our lack of understanding of organic matter cycling in the subsurface, especially in non-contaminated settings, and suggests that it may be more dynamic than previously thought (Trumbore et al, 1995;Richter et al, 1999;Kracht and Gleixner, 2000;Baisden et al, 2002a,b;Prokushkin et al, 2007;Steinbeiss et al, 2008;Kindler et al, 2011). By using both 13 C and 14 C carbon isotopes in the karst setting of the Hainch CZE we will be able to trace C atoms through the foodweb (Kramer et al, 2012) and the various organic matter pools transiting the CZ-for example using radiocarbon signatures to distinguish C recently fixed from the atmosphere from more ancient C sources, and 13 C to distinguish plant-derived from inorganic C sources (Gillon et al, 2009(Gillon et al, , 2012.…”

Section: How Do Surface Conditions Like Land Use and Events And Locmentioning

confidence: 99%

“…In this context, a number of field scale experiments have been established over the past decades. For example, one study demonstrated the importance of fungal and microbial turnover of plant-derived carbon for fueling the food web in agricultural soils (Kramer et al, 2012). This experiment also showed that bacteria originating in the rhizosphere can be translocated from topsoil to subsoil and beyond with snowmelt, demonstrating the role of weather events for the translocation of biota to the deeper subsurface (Dibbern et al, 2014).…”

Section: Introductionmentioning

confidence: 96%

How Deep Can Surface Signals Be Traced in the Critical Zone? Merging Biodiversity with Biogeochemistry Research in a Central German Muschelkalk Landscape

et al. 2016

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The Earth's Critical Zone (CZ) is a thin living layer connecting atmosphere and geosphere, including aquifers. Humans live in the CZ and benefit from the vital supporting services it provides. However, the CZ is increasingly impacted by human activities including land and resource use, pollution, and climate change. Recent interest in uniting the many disciplines studying this complex domain has initiated an international network of research infrastructure platforms that allow access to the CZ in a range of geologic settings. In this paper a new such infrastructure platform associated with the Collaborative Research Center AquaDiva is described, that uniquely seeks to combine CZ research with detailed investigation of the functional biodiversity of the subsurface. Overall, AquaDiva aims to test hypotheses about how water connects surface conditions set by land cover and land management to the biota and biogeochemical functions in the subsurface. With long-term and continuous observations, hypotheses about how seasonal variations and extreme events at the surface impact subsurface processes, community structure and function are tested. AquaDiva has established the Hainich Critical Zone Exploratory (CZE) in central Germany in an alkaline geological setting of German Triassic Muschelkalk formations. The Hainich CZE includes specialized monitoring wells to access the vadose zone and two main groundwater complexes in limestone and marlstone parent materials along a ∼6 km transect spanning forest, pasture, and agricultural land uses. Initial results demonstrate fundamental differences in the biota and biogeochemistry of the two aquifer complexes that trace back to the land uses in their respective recharge areas. They also show the importance of antecedent conditions on the impact of precipitation events on responses in terms of groundwater dynamics, chemistry and ecology. Thus, we find signals of surface land use and events can be detected in the subsurface CZ. Future research will expand to a second CZE in contrasting siliciclastic parent rock, to evaluate the relative importance of parent material lithology vs. surface conditions for the emergent characteristics of the subsurface CZ Küsel et al.Tracing Surface Signals into Subsurface and biodiversity. The Hainich CZE is open to researchers who bring new questions that the research platform can help answer.

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“…The soil type was classified as a haplic Luvisol. Detailed information about soil properties and the experimental site are given by Kramer et al (2012). Maize (Zea mays L. cv.…”

Section: Rhizodeposition-to-root Ratiomentioning

confidence: 99%

Estimation of rhizodeposition at field scale: upscaling of a 14C labeling study

et al. 2012

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Background and aims Rhizodeposition of plants is the most uncertain component of the carbon (C) cycle. By existing approaches the amount of rhizodeposition can only roughly be estimated since its persistence in soil is very short compared to other organic C pools. We suggest an approach to quantify rhizodeposition at the field scale by assuming a constant ratio between rhizodeposited-C to root-C. Methods Maize plants were pulse-labeled with 14 CO 2 under controlled conditions and the soil 14 CO 2 efflux was separated into root and rhizomicrobial respiration. The latter and the 14 C activity remaining in the soil corresponded to total rhizodeposition. By relating rhizodeposited-14 C to root-14 C a rhizodeposition-toroot ratio of 0.56 was calculated. This ratio was applied to the root biomass C measured in the field to estimate rhizodeposition under field conditions. Results Maize allocated 298 kg C ha −1 as root-C and 166 kg C ha −1 as rhizodeposited-C belowground, 50 % of which were recovered in the upper 10 cm. The fate of rhizodeposits was estimated based on the 14 C data, which showed that 62 % of total rhizodeposition was mineralized within 16 days, 7 % and 0.3 % was incorporated into microbial biomass and DOC, respectively, and 31 % was recovered in the soil.Conclusions We conclude that the present approach allows for an improved estimation of total rhizodeposition, since it accounts not only for the fraction of rhizodeposits remaining in soil, but also for that decomposed by microorganisms and released from the soil as CO 2 .

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Carbon flow into microbial and fungal biomass as a basis for the belowground food web of agroecosystems

Cited by 103 publications

References 67 publications

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

How Deep Can Surface Signals Be Traced in the Critical Zone? Merging Biodiversity with Biogeochemistry Research in a Central German Muschelkalk Landscape

Estimation of rhizodeposition at field scale: upscaling of a 14C labeling study

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