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Drying and rewetting (D/W) of soil have significant impacts on soil organic matter (SOM) turnover. We hypothesised that frequent D/W cycles would release the labile organic matter locked away in soil aggregates, increasing the priming effect (PE) (acceleration or retardation of SOM turnover after fresh substrate addition) due to preferential utilisation by microbes. 13C-labelled lignocellulose was added to the soil, and the effects of 0, 1, or 4 cycles of D/W were evaluated at 5 °C and 25 °C after a 27-day incubation of undisturbed soil cores from a temperate forest (Araucaria araucana). Following the incubation, macroaggregates (> 250 μm), microaggregates (250–53 μm), and silt + clay materials (< 53 μm) were separated. For each aggregate size class, three organic matter (OM) fractions (light (fPOM < 1.6 g cm−3), occluded (oPOM 1.6–2.0 g cm−3), and heavy (Hf > 2.0 g cm−3) were determined. D/W cycles caused macroaggregates to increase and a decrease in microaggregates (> 15%) at warm temperatures, and preferential use of the novel particulate organic matter (13C labelled), formerly protected fPOM. CO2 efflux was three times higher at 25 °C than at 5 °C. The D/W cycles at 25 °C had a strong negative impact on cumulative CO2 efflux, which decreased by approximately − 30%, induced by a negative PE of −50 mg C kg−1 soil with 1 D/W cycle and − 100 mg C kg−1 soil with 4 D/W cycles, relative to soil under constant soil moisture receiving 13C-labelled lignocellulose, but no cycles. Increasing the temperature and the number of D/W cycles caused a decrease in substrate use efficiency of particulate lignocellulose. In conclusion, D/W cycles at warm temperatures accelerated OM turnover due to preferential use from fPOM, increasing macroaggregates at the expense of microaggregates. A novel pathway of OM release and PE due to the D/W cycles is discussed. [ABSTRACT FROM AUTHOR]

Microorganisms regulate the carbon (C) cycle in soil, controlling the utilization and recycling of organic substances. To reveal the contribution of particular microbial groups to C utilization and turnover within the microbial cells, the fate of 13C-labelled glucose was studied under field conditions. Glucose-derived 13C was traced in cytosol, amino sugars and phospholipid fatty acid (PLFA) pools at intervals of 3, 10 and 50 days after glucose addition into the soil. 13C enrichment in PLFAs ( ∼  1.5 % of PLFA C at day 3) was an order of magnitude greater than in cytosol, showing the importance of cell membranes for initial C utilization. The 13C enrichment in amino sugars of living microorganisms at day 3 accounted for 0.57 % of total C pool; as a result, we infer that the replacement of C in cell wall components is 3 times slower than that of cell membranes. The C turnover time in the cytosol (150 days) was 3 times longer than in PLFAs (47 days). Consequently, even though the cytosol pool has the fastest processing rates compared to other cellular compartments, intensive recycling of components here leads to a long C turnover time. Both PLFA and amino-sugar profiles indicated that bacteria dominated in glucose utilization. 13C enrichment decreased with time for bacterial cell membrane components, but it remained constant or even increased for filamentous microorganisms. 13C enrichment of muramic acid was the 3.5 times greater than for galactosamine, showing a more rapid turnover of bacterial cell wall components compared to fungal. Thus, bacteria utilize a greater proportion of low-molecular-weight organic substances, whereas filamentous microorganisms are responsible for further C transformations. Thus, tracing 13C in cellular compounds with contrasting turnover rates elucidated the role of microbial groups and their cellular compartments in C utilization and recycling in soil. The results also reflect that microbial C turnover is not restricted to the death or growth of new cells. Indeed, even within living cells, highly polymeric cell compounds are constantly replaced and renewed. This is especially important for assessing C fluxes in soil and the contribution of C from microbial residues to soil organic matter. [ABSTRACT FROM AUTHOR]

Microbial uptake and utilisation are the main transformation pathways of low molecular weight organic substances (LMWOS) in soil, but details on transformations are strongly limited. As various LMWOS classes enter biochemical cycles at different steps, we hypothesize that the percentage of their carbon (C) incorporation into microbial biomass and consequently stabilisation in soil are different. Representatives of the three main groups of LMWOS: amino acids (alanine, glutamate), sugars (glucose, ribose) and carboxylic acids (acetate, palmitate) - were applied at naturally-occurring concentrations into a loamy arable Luvisol in a field experiment. Incorporation of 13C from these LMWOS into extractable microbial biomass (EMB) and into phospholipid fatty acids (PLFAs) was investigated 3 d and 10 d after application. The microbial utilisation of LMWOS for cell membrane construction was estimated by replacement of PLFA-C with 13C. 35-80% of initially applied LMWOS-13C was still present in the composition of soil organic matter after 10 days of experiment, with 10-24% of 13C incorporation into EMB at day three and 1-15% at day 10. Maximal incorporation of 13C into EMB was observed from sugars and the least from amino acids. Strong differences in microbial utilisation between LMWOS were observed mainly at day 10. Thus, despite similar initial rapid uptake by microorganisms, further metabolism within microbial cells accounts for the specific fate of C from various LMWOS in soils. 13C from each LMWOS was incorporated into each PLFA. This reflects the ubiquitous utilisation of all LMWOS by all functional microbial groups. The preferential incorporation of palmitate into PLFAs reflects its role as a direct precursor for fatty acids. Higher 13C incorporation from alanine and glucose into specific PLFAs compared to glutamate, ribose and acetate reflects the preferential use of glycolysis-derived substances in the fatty acids synthesis. Gram-negative bacteria (16:1ω7c and 18:1ω7c) were the most abundant and active in LMWOS utilisation. Their high activity corresponds to a high demand for anabolic products, e.g. to dominance of pentose-phosphate pathway, i.e. incorporation of ribose-C into PLFAs. The 13C incorporation from sugars and amino acids into filamentous microorganisms was lower than into all prokaryotic groups. However, for carboxylic acids, the incorporation was in the same range (0.1-0.2% of the applied carboxylic acid 13C) as that of gram-positive bacteria. This may reflect the dominance of fungi and other filamentous microorganisms for utilisation of acidic and complex organics. Thus, we showed that despite similar initial uptake, C from individual LMWOS follows deviating metabolic pathways which accounts for the individual fate of LMWOS-C over 10 days. Consequently, stabilisation of C in soil is mainly connected with its incorporation into microbial compounds of various stability and not with its initial microbial uptake. [ABSTRACT FROM AUTHOR]

Abstract: Microbial utilization is a key transformation process of soil organic matter (SOM). For the first time, position-specific 13C labeling was combined with compound-specific 13C-PLFA analysis to trace metabolites of two amino acids in microbial groups and to reconstruct detailed biochemical pathways. Short-term transformation was assessed by applying position-specifically 13C labeled alanine and glutamic acid to soil in a field experiment. Microbial utilization of the amino acids' functional groups was quantified by 13C incorporation in total microbial biomass and in distinct microbial groups classified by 13C-PLFA. Loss from PLFAs was fastest for the highly oxidized carboxyl group of both amino acids, whereas the reduced C positions, e.g. C3–5, were preferentially incorporated into microorganisms and their PLFAs. The incorporation of C from alanines' C2 position into the cell membrane of gram negative bacteria was higher by more than one order of magnitude than into all other microbial groups. Whereas C2 of alanine was still bound to C3 at day 3, the C2 and C3 positions were partially split at day 10. In contrast, the C2 of glutamic acid was lost faster from PLFAs of all microbial groups. The divergence index, which reflects relative incorporation of one position to the incorporation of C from all positions in a molecule, revealed that discrimination between positions is highest in the initial reactions and decreases with time. Reconstruction of microbial transformation pathways showed that the C2 position of alanine is lost faster than its C3 position regardless of whether the molecule is used ana- or catabolically. Glutamic acid C2 is incorporated into PLFAs only by two out of eight microbial groups (fungi and part of gram positive prokaryotes). Its incorporation in PLFA can only be explained by either the utilization of the glyoxolate bypass or the transformation of glutamic acid into aspartate prior to being fed into the citric acid cycle. During these pathways, no C is lost as CO2 but neither is energy produced, making them typical C deficiency pathways. Glutamic acid is therefore a promising metabolic tracer in regard to ecophysiology of cells and therefore changing environmental conditions. Analyzing the fate of individual C atoms by position-specific labeling allows insight into the mechanisms and kinetics of microbial utilization by various microbial groups. This approach will strongly improve our understanding of soil C fluxes. [Copyright &y& Elsevier]

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4–50.4% and 63.7–74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic ( l -leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. [ABSTRACT FROM AUTHOR]

Abstract: We propose a novel pragmatic approach of in situ 15N and 13C isotope labelling of trees for subsequent litter decomposition and turnover studies under field conditions. Using this method the labelling of even large trees under natural conditions is possible and compared to tree labelling under artificial conditions in greenhouses the in situ approach is less expensive. 13C and 15N labelling were carried out simultaneously via photosynthesis by tree gassing with 13CO2 and by stem injection of 15NH4 15NO3. The aims of this study were: (i) to produce a sufficient quantity of labelled plant material for subsequent field incubation studies and (ii) to investigate the effectiveness and distribution of in situ 15N (15NH4 15NO3) and 13C (13CO2) labelling of Podocarpus falcatus, Croton macrostachys, Prunus africana and Cupressus lusitanica. The following targets need to be achieved: (i) Assuming almost natural litter fall conditions, enough labelled plant material must be produced in situ for the turnover experiment; (ii) intra-plant tracer enrichment shall be homogeneous; (iii) tracer enrichment should be comparable for different tree species; and (iv) tracer enrichment must be sufficient for subsequent litter turnover studies using the stable isotope approach. Our results clearly demonstrated that several kilograms of labelled plant material can be produced in situ. For many ecosystems, this amount is sufficient for a long term litter turnover experiment on a field scale under almost natural litter fall conditions. However, intra-plant label uptake of 13C and 15N was heterogeneous so that only leaves (litter) should be used for the turnover study. It could be shown that only a part of the labile C and N fraction in the leaves was labelled. Nevertheless, label uptake was sufficient for subsequent litter turnover studies. [Copyright &y& Elsevier]

The Tibetan Plateau hosts the highest and largest pasture ecosystem worldwide, and stores 2.5% of the global soil organic carbon (SOC) stock. Kobresia pygmaea grasslands form the basis for local pasture economy, prevent soils from erosion, and retain large amounts of water for SE Asia. Intensive grassland degradation in recent decades destroyed mainly the upper root-mat/soil horizon of the alpine Kobresia pastures with dramatic consequences for soil organic carbon (SOC) storage, nutrient cycling and water balance of the affected regions. To elucidate specific degradation processes, their interaction with SOC pools and on microbial communities and functions, we selected a degradation sequence in the core area of the Kobresia ecosystem that included six degradation stages (S0-S5). We showed that the intensified cracking of the topsoil caused a dying of the above- and belowground plant compartments and initiated soil erosion, as well as a subsequent loss of finer particle sizes with intensified degradation stages. Furthermore, root mat degradation and altered soil properties induced a shift in microbial community structure, with most pronounced changes in S4 and S5, and going along with altered microbial functions. SOC degrading enzymes shifted from easy to complex degradable substrates (e.g. fungal phenol oxidases) with degradation. Lower δ13C values of SOC with increasing degradation stage confirmed this intensified decomposition by the relative enrichment of more complex and 13C depleted organic substances (i.e. lignin and suberin). SOC stocks strongly decreased along the degradation sequence from undisturbed (S0) to the highly disturbed sites (S5). The total SOC loss for the strongest degraded stage (S5) was 70%. SOC loss in the upper root-mat horizons was mainly caused by erosion, while in the underlying root-mat horizons decreasing SOC concentration were basically attributed to SOM decomposition and decreasing C-input from plants. We conclude that pasture degradation decreases not only the mechanical protection of soil surface by Kobresia root mats, but also changes their biochemical and microbial functions. Consequently, a complex interaction of abiotic and biotic process underlies the largely irreversible degradation of Kobresia ecosystems on the Tibetan Plateau. [ABSTRACT FROM AUTHOR]

Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown. We characterized fossil and living microbial communities based on molecular markers in a Central European Late Pleistocene loess-paleosol sequence containing recent and ancient roots with ages of several millenia. The molecular approach, comprising free and phospholipid fatty acids (FAs), core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs), as well as 16S rRNA genes from bacterial DNA, revealed the presence of living microorganisms along the sequence, with bacterial community composition comparable to that of modern topsoils. Up to 88% redundancy between bacterial genetic fingerprint and molecular signature of fossil microorganisms suggested a time-integrated signal of the molecular markers accumulated over a time span potentially lasting from sedimentation over one or more rooting phases until today. Free FAs, core GDGTs and DNA, considered as remains of fossil microorganisms, corresponded with ancient and recent root quantities, whereas phospholipid FAs and intact polar GDGTs, presumably derived from living microorganisms, correlated only with living roots. The biogeochemical and ecological disequilibrium induced by postsedimentary rooting may entail long-term microbial processes like OM mineralization, which may continue even millenia after the lifetime of the root. Deep roots and their fossil remains have been observed in various terrestrial settings, and roots as well as associated microorganisms cause both, OM incorporation and mineralization. Therefore, these findings are crucial for improved understanding of OM dynamics and carbon sequestration potential in deep subsoils. [ABSTRACT FROM AUTHOR]

• Flooding in riparian areas counters the effects of land use change on C storage. • C preservation due to oxygen-limited mineralization under anaerobic conditions. • δ13C values represent changing environmental conditions. Progressive conversion of tropical rainforests to agricultural monocultures in South East Asia increasingly affects landscape types such as riparian areas. The impacts of conversions on soil organic matter (SOM) vary with changing landforms. However, this was often not accounted for in previous studies where SOM in soils in riparian areas was combined with SOM from well-drained adjacent slopes. Because riparian areas have a high carbon (C) storage potential, our objectives were i) to assess their C stocks after conversion to rubber and oil palm plantations in Sumatra (Indonesia) and ii) to compare the impacts of land use conversion on C stocks between riparian and well-drained areas. Average soil C stock losses from the top 30 cm were about 14% and 4% following conversion of riparian forest to rubber and oil palm plantations, respectively, indicating a high resistance of C to mineralization. C losses from well-drained areas were twice as high as from riparian areas after the respective conversion. δ13C values from riparian areas showed clear heterogeneity down soil profiles that was explained i) by alternating oxic and anoxic conditions, leading to reduced SOM and litter decomposition in riparian areas and ii) by mineral sediments and organic matter deposition and accumulation by erosion from adjacent slopes covered by plantations. We conclude that riparian areas are more resilient in terms of soil C storage towards land-use change than well-drained areas because of sediment deposition and reduced oxygen availability. On this basis, we developed a conceptual model of the effects of land-use change and various ecotone characteristics on SOM mineralization in the top- and subsoil of riparian areas. [ABSTRACT FROM AUTHOR]

To disentangle fluxes and biogeochemical cycling of OC and nutrients (N, P) in soil a detailed knowledge on the biogeochemical pathways and its controlling factors is required. Over the last decades, biomarker approaches and isotope analyses became the most applied and promising tools to study SOM cycling.We will firstly review current knowledge on combining biomarker with isotope analyses (13C, 15N, 18O, 33P) for identifying the mechanisms and rates of OC and nutrient transformation and cycling. As compound-specific isotope studies on uniformly labeled substances do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites, we will introduce position-specific labeling to trace molecule atoms separately - a prerequisite for metabolic flux tracing. This together with the quantification of isotope incorporation in CO2 and phospholipid fatty acids (PLFA), enables tracing specific metabolic pathways of individual microbial communities in situ.We then discuss changes in the transformation pathways caused by sorption. Sorption to mineral surfaces is one of the most important processes contributing to soil organic matter (SOM) stabilization. While this stabilization is commonly attributed to inaccessibility of the sorbed SOM to microorganisms, recent findings have revealed increased metabolic efficiency from sorbed substrates. The application of position-specifically 13C labeled sorbed tracer, combined with compound-specific 13C analysis of PLFA, enables determination of whether this higher efficiency is due to a metabolic shift in a) the whole microbial community or b) microbial specialists adapted to sorbed C sources. To assess metabolic changes induced by sorption in individual microbial groups, we added uniformly and position-specifically 13C labeled alanine to a loamy Luvisol and incubated the soil samples for 10 days. Two different amendments were compared: i) alanine sorbed to sterilized soil, and ii) free alanine in solution. Incorporation of C from individual alanine positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis. Most of the microbial groups took up sorbed and free alanine equally. The metabolic pattern was also similar in most microbial groups: incorporation of C from carboxylic C-1 into PLFA was negligible, whereas C from the amino-bound C-2 and the methyl C-3 were preferentially incorporated into PLFA. This pattern reflects the basic microbial metabolism of C3 molecules - fast mineralization of C-1 via pyruvate decarboxylation. Only fungi incorporated more C from sorbed than free alanine into their PLFA. Their metabolic pattern also revealed a more complex metabolization via gluconeogenesis, followed by pentose-phosphate pathway. While the incorporation into most microbial groups' PLFA remained stable or decreased over 10 days, the 13C in Actinobacteria's PLFA increased up to 7 times from day 1 to day 10. This strong 13C increase in Actinobacteria was explained by their uptake of secondary substrates derived from microbial necromass or secretion products. This experiment showed that the more efficient metabolization of sorbed substrates is the work of microbial specialists: While uniform labeling revealed the higher incorporation of sorbed than free substrate into fungis PLFAs, position-specific labeling allowed the reconstruction of metabolic changes triggered by sorption of the substrate. [ABSTRACT FROM AUTHOR]