Publications

Fatty acids have been used as plant and microbial biomarkers, and knowledge about their transformation pathways in soils and sediments is crucial for interpreting fatty acid signatures, especially because the formation, recycling and decomposition processes are concurrent. We analyzed the incorporation of free fatty acids into microbial fatty acids in soil by coupling position-specific 13C labeling with compound-specific 13C analysis. Position-specifically and uniformly 13C labeled palmitate were applied in an agricultural Luvisol. Pathways of fatty acids were traced by analyzing microbial utilization of 13C from individual molecule positions of palmitate and their incorporation into phospholipid fatty acids (PLFA). The fate of palmitate 13C in the soil was characterized by the main pathways of microbial fatty acid metabolism: Odd positions (C-1) were preferentially oxidized to CO2 in the citric acid cycle, whereas even positions (C-2) were preferentially incorporated into microbial biomass. This pattern is a result of palmitate cleavage to acetyl-CoA and its further use in the main pathways of C metabolism. We observed a direct, intact incorporation of more than 4% of the added palmitate into the PLFA of microbial cell membranes, indicating the important role of palmitate as direct precursor for microbial fatty acids. Palmitate 13C was incorporated into PLFA as intact alkyl chain, i.e. the C backbone of palmitate was not cleaved, but palmitate was incorporated either intact or modified (e.g. desaturated, elongated or branched) according to the fatty acid demand of the microbial community. These modifications of the incorporated palmitate increased with time. Future PLFA studies must therefore consider the recycling of existing plant and microbial-derived fatty acids. This study demonstrates the intact uptake and recycling of free fatty acids such as palmitate in soils, as well as the high turnover and transformation of cellular PLFA. Knowledge about the intact uptake and use of soil-derived free fatty acids is crucial for interpreting microbial fatty acid fingerprints and their isotopic composition.

A theoretical approach to the partitioning of carbon dioxide (CO2) efflux from soil with a C3 vegetation history planted with maize (Zea mays), a C4 plant, into three sources, root respiration (RR), rhizomicrobial respiration (RMR), and microbial soil organic matter (SOM) decomposition (SOMD), was examined. The δ 13C values of SOM, roots, microbial biomass, and total CO2 efflux were measured during a 40-day growing period. A three-source isotopic mass balance based on the measured δ 13C values and on assumptions made in other studies showed that RR, RMR, and SOMD amounted to 91%, 4%, and 5%, respectively. Two assumptions were thoroughly examined in a sensitivity analysis: the absence of 13C fractionation and the conformity of δ 13C of microbial CO2 and that of microbial biomass. This approach strongly overestimated RR and underestimated RMR and microbial SOMD. CO2 efflux from unplanted soil was enriched in 13C by 2.0‰ compared to microbial biomass. The consideration of this 13C fractionation in the mass balance equation changed the proportions of RR and RMR by only 4% and did not affect SOMD. A calculated δ 13C value of microbial CO2 by a mass balance equation including active and inactive parts of microbial biomass was used to adjust a hypothetical below-ground CO2 partitioning to the measured and literature data. The active microbial biomass in the rhizosphere amounted to 37% to achieve an appropriate ratio between RR and RMR compared to measured data. Therefore, the three-source partitioning approach failed due to a low active portion of microbial biomass, which is the main microbial CO2 source controlling the δ 13C value of total microbial biomass. Since fumigation–extraction reflects total microbial biomass, its δ 13C value was unsuitable to predict δ 13C of released microbial CO2 after a C3–C4 vegetation change. The second adjustment to the CO2 partitioning results in the literature showed that at least 71% of the active microbial biomass utilizing maize rhizodeposits would be necessary to achieve that proportion between RR and RMR observed by other approaches based on 14C labelling. The method for partitioning total below-ground CO2 efflux into three sources using a natural 13C labelling technique failed due to the small proportion of active microbial biomass in the rhizosphere. This small active fraction led to a discrepancy between δ 13C values of microbial biomass and of microbially respired CO2.

Rice is one of the world's most important staple crops and a major source of agricultural methane emissions. Breeding strategies such as photosynthate allocation modification and biomass enhancement show potential, but their effectiveness is highly context dependent, shaped by water regimes and soil organic carbon levels. Cultivars effective under continuous flooding may fail, or even increase emissions, under optimized water regimes. This perspective argues for integrated strategies that combine cultivar improvement with water and organic matter management, microbiome regulation, and climate-resilient breeding to build climate-smart rice systems that ensure both yield stability and methane mitigation.

. Agricultural land covers 5100 million ha (ca. 50 % of potentially suitable land area) and agriculture has immense effects on soil formation and degradation. Although, the concepts or theories of agropedogenesis have already been advanced; but still need further consideration to better understand the dynamics of soil development under agricultural practices. We introduce a theory of anthropedogenesis – soil development under the main factor "humankind" – the 6th factor of soil formation, and deepen it to encompass agropedogenesis as the most important direction of anthropedogenesis. The developed theory of agropedogenesis consists of (1) broadening the classical concept of Factors – Processes – Properties with the addition of Functions along with their feedbacks to the Processes, (2) a new concept of attractors of soil degradation, (3) selection and analysis of master soil properties, (4) analysis of phase diagrams of master soil properties to identify thresholds and stages of soil degradation, and finally (5) a definition of multi-dimensional attractor space of agropedogenesis. We show that the factor "humankind" dominates over the effects of the five natural soil-forming factors and that agropedogenesis is therefore much faster than natural soil formation. The direction of agropedogenesis is mainly opposite to that of natural soil development and is thus mainly associated with soil degradation. In contrast to natural pedogenesis leading to divergence of soil properties, agropedogenesis leads to their convergence because of the efforts to optimize conditions for crop production. Agricultural practices lead soil development toward a quasi-steady state with a predefined range of measured properties – attractors (an attractor is a minimal or maximal value of a soil property, toward which the property will develop via long-term intensive agricultural use from any natural state). Based on phase diagrams and expert knowledge, we define a set of "master properties" (bulk density and macroaggregates, soil organic matter content and pH, microbial biomass and basal respiration). These master properties are especially sensitive to land use and determine the other properties during agropedogenesis. Phase diagrams of master soil properties help identify thresholds and stages of soil degradation. Combining individual attractors to a multi-dimensional attractor space enables predicting the trajectory and the final state of agrogenic soil development and to develop measures to combat soil degradation.

The transformation of “energy to (soil organic) matter’’ has long been the focus of scientific attention, but a definitive conceptual framework does not yet exist. Following the classical definition of energy given by Odum and Odum (1977) and the principles and laws of energy, we have developed an experiment-based review of the complex process of microbial conversion of energy and carbon (C) from litter to soil organic matter (SOM). Based on the transformation rate of plant residues, the amount of plant-derived energy persisting in soil (after one year) ranges from 7 to 20 % of total energy input depending on the plant community (for example, spruce and broadleaf forests and grasslands were taken). This represents 0.8-10 % of the energy already stored in SOM but only adds 0.4-5 % C to the existing SOM pool. We have introduced two new parameters - energy quality representing primarily substance, and energy availability representing the ability of microorganisms to utilize that substance (or pool of substances) under actual soil conditions. According to these parameters, we have assigned the main classes of organic substances to one of the three groups that show the availability of energy stored in microorganisms. When the energy availability is >1, microorganisms gain more energy than invest by the decomposition of organic substances; when energy availability is <1, then energy investment is required for the co-mining of nutrients, and some compounds are unsuitable for energy mining due to low efficiency, and in this case, they will be partially decomposed by co-metabolism (no energy gain). We have estimated the energy investment of soil microorganisms for exoenzyme production and concluded that the disadvantage of enzymatic degradation could explain the ‘stability’ of the SOM because the energy input (investment) required for degradation exceeds the energy gain. Following the linear decrease in energy density (by 106 kJ mol-1 C) of a broad range of organic substances per nominal oxidation state of C (NOSC) unit upon oxidation and experimental data on litter decomposition, we have developed the concept showing changes in the NOSC and the energy content of plant residues during decomposition and formation of SOM. Mineralization, recycling, and accumulation processes control energy and NOSC changes in organic pools. Mineralization processes lead to energy losses and an increase in NOSC, while SOM accumulation increases energy content and decreases NOSC. Recycling can shift both the energy content and NOSC values depending on the environmental conditions of the soil and the quality/quantity of litter input. As a result, the SOM pool is different from the initial litter in the energy content and NOSC. The SOM has a more diverse molecular composition but a narrower range of NOSC values than plant residues, consists of microbial necromass and substances recycled by microorganisms, and contains, on average, substances with a higher energy content than the initial plant residues. Based on the developed concept, we have concluded that plant-derived C and energy that persist in the form of SOM ensure energy fluxes in the soil system.

. 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.

A recent meta-analysis (Zhang et al., 2020) stated that acidification induced by nitrogen (N) (over)fertilization increases soil organic carbon (SOC) accumulation. This Letter disagrees with that statement regarding acidification effects on SOC accumulation. We especially wish to show how processing of large datasets might mislead conclusions, and may have fatal consequences for land management. Another crucial point we wish to raise is that the role of carbonates for carbon stocks and induced CO2 losses to the atmosphere has been completely disregarded in the soil acidification discussion.