The terrestrial carbon (C) cycle has received increasing interest over the past few decades, however, there is still a lack of understanding of the fate of newly assimilated C allocated within plants and to the soil, stored within ecosystems and lost to the atmosphere. Stable carbon isotope studies can give novel insights into these issues. In this review we provide an overview of an emerging picture of plant-soil-atmosphere C fluxes, as based on C isotope studies, and identify processes determining related C isotope signatures. The first part of the review focuses on isotopic fractionation processes within plants during and after photosynthesis. The second major part elaborates on plant-internal and plant-rhizosphere C allocation patterns at different time scales (diel, seasonal, interannual), including the speed of C transfer and time lags in the coupling of assimilation and respiration, as well as the magnitude and controls of plant-soil C allocation and respiratory fluxes. Plant responses to changing environmental conditions, the functional relationship between the physiological and phenological status of plants and C transfer, and interactions between C, water and nutrient dynamics are discussed. The role of the C counterflow from the rhizosphere to the aboveground parts of the plants, e.g. via CO₂ dissolved in the xylem water or as xylem-transported sugars, is highlighted. The third part is centered around belowground C turnover, focusing especially on above- and belowground litter inputs, soil organic matter formation and turnover, production and loss of dissolved organic C, soil respiration and CO₂ fixation by soil microbes. Furthermore, plant controls on microbial communities and activity via exudates and litter production as well as microbial community effects on C mineralization are reviewed. The last part of the paper is dedicated to physical interactions between soil CO₂ and the soil matrix, such as CO₂ diffusion and dissolution processes within the soil profile. From the presented evidence we conclude that there exists a tight coupling of physical, chemical and biological processes involved in C cycling and C isotope fluxes in the plant-soil-atmosphere system. Generally, research using information from C isotopes allows an integrated view of the different processes involved. However, complex interactions among the range of processes complicate or impede the interpretation of isotopic signals in CO₂ or organic compounds at the plant and ecosystem level. This is where new research approaches should be aimed at

Abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NHOH) for NO production have been indicated recently. The latter process would require the availability of substantial amounts of free NHOH for chemical reactions during ammonia (NH) oxidation, but little is known about extracellular NHOH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NHOH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NHOH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NHOH was also formed by the comammox enrichment during NH oxidation. This enrichment exhibited the largest NHOH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH converted to NO via extracellular NHOH during incubation, estimated on the basis of NHOH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH:NO conversion ratios for AOB and AOA.

Nitrous oxide is a powerful greenhouse gas whose atmospheric growth rate has accelerated over the past decade. Most anthropogenic N2O emissions result from soil N fertilization, which is converted to N2O via oxic nitrification and anoxic denitrification pathways. Drought-affected soils are expected to be well oxygenated; however, using high-resolution isotopic measurements, we found that denitrifying pathways dominated N2O emissions during a severe drought applied to managed grassland. This was due to a reversible, drought-induced enrichment in nitrogen-bearing organic matter on soil microaggregates and suggested a strong role for chemo- or codenitrification. Throughout rewetting, denitrification dominated emissions, despite high variability in fluxes. Total N2O flux and denitrification contribution were significantly higher during rewetting than for control plots at the same soil moisture range. The observed feedbacks between precipitation changes induced by climate change and N2O emission pathways are sufficient to account for the accelerating N2O growth rate observed over the past decade.

Abstract. Fluxes of greenhouse gases (GHG) carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) were measured during a two month campaign at a drained peatland forest in Finland by the eddy covariance (EC) technique (CO2 and N2O), and automatic and manual chambers (CO2, CH4 and N2O). In addition, GHG concentrations and soil parameters (mineral nitrogen, temperature, moisture content) in the peat profile were measured. The aim of the measurement campaign was to quantify the GHG fluxes before, during and after thawing of the peat soil, a time period with potentially high GHG fluxes, and to compare different flux measurement methods. The forest was a net CO2 sink during the two months and the fluxes of CO2 dominated the GHG exchange. The peat soil was a small sink of atmospheric CH4 but a small source of N2O. Both CH4 oxidation and N2O production took place in the top-soil whereas CH4 was produced in the deeper layers of the peat. During the thawing of the peat distinct peaks in CO2 and N2O emissions were observed. The CO2 peak followed tightly the increase in soil temperature, whereas the N2O peak occurred with an approx. one week delay after soil thawing. CH4 fluxes did not respond to the thawing of the peat soil. The CO2 and N2O emission peaks were not captured by the manual chambers and hence we conclude that automatic chamber measurements or EC are necessary to quantify fluxes during peak emission periods. Sub-canopy EC measurements and chamber-based fluxes of CO2 and N2O were comparable, although the fluxes of N2O measured by EC were close to the detection limit of the EC system. We conclude that if fluxes are high enough, i.e. greater than 5–10 μg N m−2 h−1, the EC method is a good alternative to measure N2O and CO2 fluxes at ecosystem scale, thereby minimizing problems with chamber enclosures and spatial representativeness of the measurements.

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36–48%, end: 27–30%) and Firmicutes (start: 13–33%, end: 12–16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.