Distinct interaction between management history and nitrogen source drive microbial nitrogen processes in soil

Understanding changes in soil functions in response to land‐use change is important for guiding agricultural practices towards sustainable soil management. We evaluated the differences in soil properties (soil organic matter, water extractable carbon (C) and nitrogen (N), microbial biomass, pHKCLand exchangeable cations) and microbial processes (respiration potential, net N mineralization, net nitrification and metabolic potential of soil bacteria), as well as the relative importance of soil properties in explaining changes in processes under three land uses (potato crops, fallow fields and eucalyptus plantations) in the agricultural highlands of the Central Andes. Soils under potato crops were characterized by the highest net N mineralization and net nitrification rates, and extractable phophorus (P), and the lowest microbial biomass P. Conversion to eucalyptus plantations led to an increase in soil organic matter, water extractable C and microbial biomass, and a decrease in extractable P and metabolic diversity of soil bacteria. Higher exchangeable aluminium (Al) indicated soil acidification under eucalyptus. Fallow practices did not lead to major changes in soil properties and microbial processes, indicating that fallow practices for up to 6 years were too short to substantially contribute to soil fertility restoration. Hot water extractable carbon (HWC) showed the best relationship with soil processes (respiration potential, net N mineralization and net nitrification). Our results highlight the necessity of alternative management practices for maintaining soil fertility under potato crops, the drastic modification of soil properties and processes under eucalyptus plantations, and the potential of HWC as a proxy for monitoring land‐use‐induced changes in soil functions related to C and N cycling.HighlightsEffects of conversion from potato crops to eucalyptus and fallow on soil properties and processes were assessed.Under eucalyptus, soil respiration increased; metabolic diversity and N transformations decreased.Short fallow periods did not result in soil fertility restoration.Hot water extractable C was the best indicator of changes in soil processes.

Microbial transformations of fertilizers and pesticides in the surface soil have a direct impact on the mass of the agrochemical that is susceptible to leaching losses. Thus, our greatest potential for controlling leaching losses of agrochemicals is through the management of these compounds in the surface soil. A variety of strategies have been employed to maximize the residence time of applied chemical in the surface soil, including: timing of application, formulation (e.g., slow‐release fertilizers and encapsulated pesticides), and the use of compounds that modify microbial activity in soil (e.g., nitrification inhibitors). Although these strategies have met with some success, more precise quantification of the microbial transformations of agrochemicals is required to aid the development of improved management strategies. The high spatial variability exhibited by many microbial processes, in many cases, precludes precise quantification. A greater understanding of the factors contributing to the variability of microbial processes allows for improved estimation, as well as for the assessment of key driving variables controlling microbial processes in soil. This article reviews several aspects of spatial variability associated with microbial populations and processes. The discussion focuses on the scale at which variability is expressed, and the soil and environmental variables that serve to control variability at each scale. Implications for the development of new management strategies are also discussed, and finally, some statistical considerations for characterizing variability are presented.

This paper reviews methods for modeling coupled microbial and transport processes in variably saturated porous media. Of special interest in this work are interactions between active microbial growth and other transport processes such as gas diffusion and interphase exchange of O2 and other constituents that partition between the aqueous and gas phases. The role of gas–liquid interfaces on microbial transport is also discussed, and various possible kinetic and equilibrium formulations for bacterial cell attachment and detachment are reviewed. The primary objective of this paper is to highlight areas in which additional research may be needed—both experimental and numerical—to elucidate mechanisms associated with the complex interactions that take place between microbial processes and flow and transport processes in soils. In addition to their general ecological significance, these interactions have global-scale implications for C cycling in the environment and the related issue of climate change.

This paper reviews methods for modeling coupled microbial and transport processes in variably saturated porous media. Of special interest in this work are interactions between active microbial growth and other transport processes such as gas diffusion and interphase exchange of O2 and other constituents that partition between the aqueous and gas phases. The role of gas–liquid interfaces on microbial transport is also discussed, and various possible kinetic and equilibrium formulations for bacterial cell attachment and detachment are reviewed. The primary objective of this paper is to highlight areas in which additional research may be needed—both experimental and numerical—to elucidate mechanisms associated with the complex interactions that take place between microbial processes and flow and transport processes in soils. In addition to their general ecological significance, these interactions have global‐scale implications for C cycling in the environment and the related issue of climate change.

Influence of organic and mineral amendments on microbial soil properties and processes

Pseudomonas putida PPO301 (pRO103), genetically engineered to degrade 2,4-dichlorophenoxyacetate, affected microbial populations and processes in a nonsterile xeric soil. In soil amended with 2,4-dichlorophenoxyacetate (500 micrograms/g soil) and inoculated with PPO301 (pRO103), the rate of evolution of carbon dioxide was retarded for approximately 35 days; there was a transient increase in dehydrogenase activity; and the number of fungal propagules decreased below detection after 18 days. In unamended soil inoculated with PPO301(pRO103), the rate of evolution of carbon dioxide and the dehydrogenase activity were unaffected, and the numbers of fungal propagules were reduced by about two orders of magnitude. The numbers of total, spore-forming, and chitin-utilizing bacteria were reduced transiently in soil either amended or unamended with 2,4-dichlorophenoxyacetate and inoculated with PPO301(pRO103). The activities of arylsulfatases and phosphatases in soil were not affected by the presence of PPO301(pRO103), either in the presence or absence of 2,4-dichlorophenoxyacetate. In soil amended with 2,4-dichlorophenoxyacetate and inoculated with the parental strain (PPO301) or not inoculated, the evolution of carbon dioxide, the numbers of fungal propagules and of total, spore-forming, and chitin-utilizing bacteria, and the dehydrogenase activity were not affected as in soil inoculated with PPO301(pRO103). These results demonstrated that a genetically engineered microorganism, in the presence of the substrate on which its novel genes can function, is capable of inducing measurable ecological effects in soil.

With a contribution of about one third, methane is the second most important greenhouse gas in the climate system. In addition to a biogenic formation, e.g. in wetlands, methane also is emitted during anthropogenic industrial activities. BGR is investigating abandoned onshore oil and gas wells in Germany, which are generally plugged and buried, for their relevance as sources of methane. Initial results from studied wells examined so far (about 75 wells) indicated no or very low methane emissions at very few sites. A controlling process for low methane emissions for the wells could be microbial methane oxidation, which is an important process in organic-rich soils overlying wells in Northern Germany (Jordan et al., accepted).We present here data from soil above a plugged oil well, drilled in the early 1920s and located at Nienhagen near Hannover (Germany). At the well ~40 mg CH4 h-1 were emitted (average range for plugged US oil wells ~50 to 170 mg h-1 per well; Williams et al. 2021). Gas geochemical analyses of the soil gas confirm the presence of natural gas (up to 8 % methane and 600 ppm ethane) and the δ13C of the methane supports that the majority is thermogenic (-47.1 ‰). In addition to natural gas, we also found petroleum in the soil, which reached up to 80 % soil total organic carbon. Our data suggest a complex mosaic of hydrocarbon-altering effects dominated by products from the microbial degradation of well-derived oil and natural gas (e.g., propane oxidation). It is likely that O2 availability controls the degradation of petroleum in the soil under investigation, because the strongest degree of degradation was found in the upper soil horizons. The properties of the formerly produced oil exclude biodegradation in the reservoir, so the degraded oil must have been formed during the ascent or in the topsoil. The gas geochemical composition of the soil gases indicates also deeper, anaerobic processes, such as methanogenesis, probably with petroleum as the carbon source. Soil microcosms from different depths showed, indeed, a rapid onset of microbial degradation of added oil both under aerobic and anaerobic conditions in the lab. Although processes in a deeper biosphere appear to play a role here, it is likely that mostly the microbial processes in the soil surrounding the well regulate the composition and quantity of oil and gas. In conclusion, the (i) high degree of degradation in the natural gas components in the soil and petroleum, as well as the overall (ii) only low methane emissions, indicate that the Nienhagen well is only leaking relatively little and that a “microbial hydrocarbon filter” is established and active.ReferencesJordan, S.F.A., Schloemer, S., Krüger, M., Heffner, T., Horn, M.A., Blumenberg, M., (accepted) Preprint. Interferences caused by the microbial methane cycle during the assessment of abandoned oil and gas wells. EGUsphere. doi:10.5194/egusphere-2024-1461Williams J. P., Regehr A. and Kang M. (2021) Methane Emissions from Abandoned Oil and Gas Wells in Canada and the United States. Environmental Science & Technology 55, 563–570.

<p>Mechanistic simulation models are an essential tool for predicting soil functions such as nutrient cycling, water filtering and storage, productivity and carbon storage as well as the complex interactions between these functions. Most soil functions are driven or affected by soil organisms. Yet, biological processes are often neglected in soil function models or implicitly described by rate parameters. This can be explained by the high complexity of the soil ecosystem with its dynamic and heterogeneous environment, and by the range of temporal and spatial scales these processes are taking place at. On the other hand, the technical capabilities to explore microbial activity and communities in soil has greatly improved, resulting in new possibilities to understand soil microbial processes on various scales.</p><p>However, to integrate such biological processes in soil modelling, we need to find the right level of detail. Here, we present a systemic soil model approach to simulate the impact of different management options and changing climate on soil functions integrating biological activity on the profile scale. We use stoichiometric considerations to simulate microbial processes involved in different soil functions without explicitly describing community dynamics or functional groups. With this approach we are able to mechanistically describe microbial activity and its impact on the turnover of organic matter and nutrient cycling as driven by agricultural soil management.</p><p>Further, we discuss general challenges and ongoing developments to additionally consider, e.g., microbe-fauna-interactions or microbial feedback with soil structure dynamics.</p>

Fire frequency impacts soil properties and processes in sagebrush steppe ecosystems of the Columbia Basin

Phase transformation of schwertmannite changes microbial iron and sulfate-reducing processes in flooded paddy soil and decreases arsenic accumulation in rice (Oryza sativa L.)

Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.

Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.

Seasonal variation in functional properties of microbial communities in beech forest soil

Direct effects of increased above‐ground CO2 concentration on soil microbial processes are unlikely, due to the high pCO2 of the soil atmosphere in most terrestrial ecosystems. However, below‐ ground microbial processes are likely to be affected through altered plant inputs at elevated CO2. A major component of plant input is derived from litter fall and root turnover. Inputs also derive from rhizodeposition (loss of C‐compounds from active root systems) which may account for up to 40% of photoassimilate. This input fuels the activity of complex microbial communities around roots. These communities are centrally important not only to plant–microbe interactions and consequent effects on plant growth, but also, through their high relative activity and abundance, to microbially mediated processes in soil generally. This review focuses on approaches to measure C‐flow from roots, in particular, as affected by increased atmospheric CO2 concentration. The available evidence for impacts on microbial communities inhabiting this niche, which constitutes an interface for possible perturbations on terrestrial ecosystems through the influence of environmental change, will also be discussed. While methodologies for measuring effects of increased CO2 concentration on plant growth, physiology and C‐partitioning are abundant and widely reported, there is relatively little information on plant‐mediated effects on soil microbial communities and processes. Importantly, many studies have also neglected to recognize that any secondary effects on microbial communities may have profound effects on plant parameters measured in relation to environmental change. We critically review approaches which have been used to measure rhizodeposition under conditions of increased atmospheric CO2 concentration, and then consider evidence for changes in microbial communities and processes, and the methodologies which have been recently developed, and are appropriate to study such changes.

Sewage sludge disposal on arable land is viewed as a method to reduce waste accumulation and to enrich soil fertility. However, such disposal can degrade soil ecosystems due to the presence of potentially harmful substances, such as heavy metals. Pb has assumed greater significance because currently its dispersal through anthropogenic activities has exceeded the inputs from natural sources by about 17 fold. Several soil variables such as texture, organic matter content, clay, cation exchange capacity, soil pH, and CaCO{sub 3} content influence the toxic effects of heavy metals on sol microbes and their activities. Microbes have an essential function in cycling of nutrients through mineralization activities. However, the addition of 375 and 1500 {mu}g Pb g{sup -1} soil in sandy loam and clay loam has been reported to cause a 15% decrease in soil microbial respiration. Contrarily, in an organic soil microbial respiration and enzyme activities were observed to remain unaltered by the addition of 1000 {mu}g Pb g{sup -1} soil. While the nitrification process in a sandy loam soil has been reported to be significantly inhibited at 100 {mu}g Pb g{sup -1} soil, the addition of similar amount of Pb to alluvial and clay loam had no effect onmore » nitrification and ammonifying and nitrifying bacteria. This study assesses the effects of lead and sewages sludge on microbial biomass and mineralization processes in soils of varied texture and organic matter content. 17 refs., 4 tabs.« less