Matthias Koschorreck

Oxidation of atmospheric methane in soil: measurements in the field, in soil cores and in soil samples

Methane fluxes and vertical profiles of CH4 mixing ratios were measured in different German soils both in situ and in soil cores. Atmospheric CH4 was oxidized in the soil by microorganisms resulting in an average CH4 flux of −1.39±1.5 μmol-CH4 m−2 h−1. Methane deposition showed only a weak positive correlation (r2 = 0.38) with soil temperature but a relatively strong negative correlation (r2 = 0.61) with soil moisture indicating limitation of the CH4 flux by gas transport. Diffusion experiments in soil cores showed that gas transport between atmosphere and soil was faster than microbial CH4 oxidation. However, the diffusion from the gas-filled soil pores to the CH4 oxidizing microorganisms may have been limiting. The main CH4− oxidizing activity was located in a few centimeter thick subsurface soil layer at the top of the Ah horizon, whereas no activity was found in the overlying O horizons and in deep soil below about 20-cm depth. In contrast, the highest CO2 production was found in the topmost O horizon. The effective diffusion coefficient of CH4 in soil was determined using a method based on relaxation experiments with argon. The diffusion coefficient was used to model the CH4 oxidation in soil cores from the vertical profiles of CH4 mixing ratios. The thus calculated CH4 oxidation rates and their localization in the soil profile compared fairly well with those determined directly from incubated soil samples. Fluxes were similar within a factor of 2–4 whether derived from the model, calculated from the measured CH4 oxidation rates of soil samples, or measured directly.

Microbial sulphate reduction at a low pH

It is now well established that microbial sulphate-reduction can proceed in environments with a pH<5. This review summarizes existing reports on sulphate reduction at low pH and discusses possible pH effects on sulphate-reducing bacteria. Microbial sulphate reduction has been observed in acidic lakes, wetlands, mesocosms, acidic sulphate soils and bioreactors. Possible inhibitory factors include the metabolites H(2)S and organic acids, which can be toxic depending on pH. Metal sulphide precipitation and competition with other bacteria, namely iron-reducing bacteria, can inhibit sulphate reduction. Theoretical considerations show that normal sulphate reduction rates are too low to maintain a neutral micro niche in an acidic environment. The first acidotolerant sulphate-reducing bacteria have been isolated recently.

Occurrence and role of algae and fungi in acid mine drainage environment with special reference to metals and sulfate immobilization

Passive remediation of Acid Mine Drainage (AMD) is a popular technology under development in current research. Roles of algae and fungi, the natural residents of AMD and its attenuator are not emphasized adequately in the mine water research. Living symbiotically various species of algae and fungi effectively enrich the carbon sources that help to maintain the sulfate reducing bacterial (SRB) population in predominantly anaerobic environment. Algae produce anoxic zone for SRB action and help in biogenic alkalinity generation. While studies on algal population and actions are relatively available those on fungal population are limited. Fungi show capacity to absorb significant amount of metals in their cell wall, or by extracellular polysaccharide slime. This review tries to throw light on the roles of these two types of microorganisms and to document their activities in holistic form in the mine water environment. This work, inter alia, points out the potential and gap areas of likely future research before potential applications based on fungi and algae initiated AMD remediation can be made on sound understanding.

Functional Groups and Activities of Bacteria in a Highly Acidic Volcanic Mountain Stream and Lake in Patagonia, Argentina

Acidic volcanic waters are naturally occurring extreme habitats that are subject of worldwide geochemical research but have been little investigated with respect to their biology. To fill this gap, the microbial ecology of a volcanic acidic river (pH approximately equal to 0-1.6), Rio Agrio, and the recipient lake Caviahue in Patagonia, Argentina, was studied. Water and sediment samples were investigated for Fe(II), Fe(III), methane, bacterial abundances, biomass, and activities (oxygen consumption, iron oxidation and reduction). The extremely acidic river showed a strong gradient of microbial life with increasing values downstream and few signs of life near the source. Only sulfide-oxidizing and fermentative bacteria could be cultured from the upper part of Rio Agrio. However, in the lower part of the system, microbial biomass and oxygen penetration and consumption in the sediment were comparable to non-extreme aquatic habitats. To characterize similarities and differences of chemically similar natural and man-made acidic waters, our findings were compared to those from acidic mining lakes in Germany. In the lower part of the river and the lake, numbers of iron and sulfur bacteria and total biomass in sediments were comparable to those known from acidic mining lakes. Bacterial abundance in water samples was also very similar for both types of acidic water (around 10(5) mL(-1)). In contrast, Fe(II) oxidation and Fe(III) reduction potentials appeared to be lower despite higher biogenic oxygen consumption and higher photosynthetic activity at the sediment-water interface. Surprisingly, methanogenesis was detected in the presence of high sulfate concentrations in the profundal sediment of Lake Caviahue. In addition to supplementing microbiological knowledge on acidic volcanic waters, our study provides a new view of these extreme sites in the general context of aquatic habitats.

Microbial Fe(III) Reduction in Acidic Mining Lake Sediments after Addition of an Organic Substrate and Lime

To elucidate the role of Fe(III) reduction in mining lake sediments amended with organic substrates, we performed a large (10 m diameter) enclosure experiment in which sediments were amended with Carbokalk, a waste product from sugar industry containing organic carbon and lime. Fe(III) reduction rates were determined monthly by measuring the accumulation of Fe(II) in the sediments in the field. Fe(III) reduction rates were also determined by incubating sediment samples with synthetic Fe(III) oxyhydroxide under in situ temperature in the laboratory. Sulfate reduction was selectively inhibited in the Fe(III) reduction experiments by addition of sodium molybdate. Sulfate reduction was measured by accumulation of reduced inorganic sulfides in the field and by 35S radiotracer using a core injection technique. Sediment incubation and determination of sulfate reduction rates with radiotracer showed that sulfate reduction and direct microbial Fe(III) reduction occured simultaneously in the upper centimeters of the sediments and that both processes contributed to alkalinity generation. However, Fe(III) reduction was the initial process and rates were at least 3.5 fold higher than sulfate reduction rates. The results indicate that the presence of suitable anions for Fe(II) precipitation as carbonate or sulfide is needed in order to prevent loss of potential alkalinity by Fe(II) diffusion and reoxidation in the water column.

Carbon dioxide emissions from dry watercourses

Abstract Temporary watercourses that naturally cease to flow and run dry comprise a notable fraction of the world’s river networks, yet estimates of global carbon dioxide (CO2) emissions from watercourses do not consider emissions from these systems when they are dry. Using data from a sampling campaign in a Mediterranean river during the summer drought period, we demonstrate that the CO2 efflux from dry watercourses can be substantial, comparable to that from adjacent terrestrial soils and higher than from running or stagnant waters. With an up-scaling approach, we show that including emissions from dry watercourses could increase the estimate of CO2 emissions from watercourses in our study region by 0.6–15%. Moreover, our results tentatively illustrate that emissions from dry watercourses could be especially important in arid regions, increasing the estimate of global CO2 emissions from watercourses by 0.4–9%. Albeit relatively small, the contribution of dry watercourses could help to constrain the highly uncertain magnitude of the land carbon sink. We foresee that in many areas of the world, the expected increase in the extent of temporary watercourses associated with future global change will increase the relevance of CO2 emissions from dry watercourses.

Functions of Straw for In Situ Remediation of Acidic Mining Lakes

The addition of straw in combination with ‘Carbokalk’, a by-product from the sugar-industry, was successfully used to stimulate microbial alkalinity generation in an acidic mining lake. To get detailed information about functions of straw, anenclosure experiment was carried out. Straw bundles were placedat the sediment surface of an acidic mining lake (ML 111) and thephysiochemical conditions and the microbiology of the sediment-water contact zone were studied. Straw was degraded by anaerobic microorganisms and dissolved organic carbon (DOC) leached from straw bundles. Pigmented flagellates responded to the DOC supply in the water column anda considerable amount of algal carbon was transported to the sediment. Straw addition led to microbial reduction of iron andsulfate in the sediment. Sulfate reduction was observed at a pHof 5.5. The pH, however, was not high enough to precipitate H2S completely. Thus, some H2S diffused into the watercolumn, where it was reoxidized. Straw did not create orstabilize an anoxic water body above the sediment. Microbial sulfate reduction and pyrite formation only took place in the sediment,whereas iron reduction also took place in the straw. Straw, however, altered the flow conditions above the sediment surfaceand prevented complete mixing of the profundal water. Straw didnot serve as a substratum for a reactive biofilm. We conclude that the most important function of straw for mining lake remediation is to be a long-term nutrient source for microbialalkalinity generation in the sediment.

Oxidative and reductive microbial consumption of nitric oxide in a heathland soil

Abstract An acidic heathland podzol exhibited almost zero rates of NO production but high rates of NO consumption. The NO uptake rate constants decreased with soil depth. They were about two times higher and exhibited different kinetic characteristics under oxic than under anoxic incubation conditions. Under anoxic conditions, NO uptake followed Michaelis-Menten kinetics with Km values around 1 ppmv NO (1 μl NO 1−1 gas phase). Similar kinetics are known from the literature for NO reduction by denitrifying bacteria. Anoxic NO uptake was stimulated by addition of nitrate and glucose. When the podzol was gassed with nitrogen containing 9.5 ppmv NO, most (94%) of the anoxically-consumed NO was recovered as N2O demonstrating that NO was consumed by denitrification to N2O. Under oxic conditions, on the other hand, NO uptake followed apparent first-order kinetics up to NO mixing ratios of >4ppmv, suggesting a NO consumption pathway different from denitrification. Uptake of NO was abolished by autoclaving and exhibited a temperature optimum at 40°C demonstrating that it was due to biological activity. The activity exhibited a sharp optimum at the in-situ pH of 3.3, and a broad optimum at soil moistures between 10 and 60% of the maximum water holding capacity. Oxic NO uptake was not stimulated by addition of nitrate plus glucose. When the podzol was gassed with air containing 9.5 ppmv NO, only a small proportion (5%) of the consumed NO was recovered as N2O. Instead, labelling experiments with 15NO showed that most (90±17%) of the oxically consumed NO was converted to 15NO3−. Our results show that NO is consumed in soil both by oxidation to nitrate and by reduction through the denitrification pathway depending on oxic or anoxic conditions, respectively.

Nitrogen dynamics in seasonally flooded soils in the Amazon floodplain

Large areas of the Amazon are subject to seasonal flooding due to water level changes of the river. This ‘flood pulse’ causes rapidly changing conditions for microorganisms living in the soils which affects the cycling of nitrogen in the ecosystem. An understanding of the nitrogen dynamics in the seasonally flooded soils is essential for the development of productive and sustainable management concepts. We measured nitrogen concentrations, denitrifier enzyme activity (DEA), cell numbers of nitrifying and denitrifying bacteria, respiration, pH and total carbon in the seasonally flooded soils over one entire annual hydrological cycle. By comparing three sites with different vegetation (forest, aquatic macrophyte stand and bare sediment with annual herbs) we assessed the effect of vegetation on soil nitrogen dynamics. Inorganic nitrogen was always dominated by ammonium indicating reduced conditions in the soil even during the terrestrial phase. Although conditions were generally poor for nitrification we observed high numbers of nitrifying bacteria between 104 and 107cells g−1. Pulses of ammonium as well as high DEA were observed during the transition periods between aquatic and terrestrial phase. Thus the alternation between aquatic and terrestrial phase promotes nitrogen mineralization and denitrification in the soils. There were no plausible correlations between microbial activities and numbers with soil physical or chemical parameters except a relation between the numbers of nitrate reducing bacteria and soil moisture (R2 = 0.81) and ammonium (R2 = 0.92) at one site. This shows the complex regulation patterns in this habitat. Different vegetation did not alter the general patterns of nitrogen dynamics but the absolute extend of fluctuations. We conclude that both the soil physical and chemical changes directly caused by the flood pulse and the vegetation have a great impact on microbial nitrogen turnover in the soils. The effects of the flood pulse can be buffered by a fine soil texture or a litter layer which prevents desiccation of the soil during the terrestrial phase.

Structure and function of the microbial community in an in situ reactor to treat an acidic mine pit lake

Sulfate-reducing bioreactors are a promising option for the treatment of acid mine drainage. We studied the structure and function of a biofilm in a methanol-fed fixed-bed in-lake reactor for the treatment of an acidic pit lake by a combination of laboratory incubations, chemical and molecular analyses and confocal laser scanning microscopy to determine whether competition by different groups of microorganisms as well as the precipitation of minerals affect reactor performance negatively. The biofilm growing on the surface of a synthetic carrier material consisted of dense microbial colonies covered by iron-sulfide precipitates. The microorganisms continuously had to overgrow this mineral coating, resulting in a high biomass turnover. About one third of the added methanol was used by sulfate reduction, and the rest by competing reactions. Sulfate-reducing bacteria as well as methanogens and acetogens were involved in methanol consumption. Six different groups of Deltaproteobacteria, dominated by the genera Desulfomonile, Desulfobacterium and a phylotype related to Geobacter, Gram-positive sulfate reducers of the genus Desulfosporosinus, acetogenic Acetobacteria, different fermenting bacteria as well as methylotrophic methanogens were identified. The versatility of the microbial food web is probably an important factor stabilizing the biofilm function under fluctuating and partly oxidizing conditions in the reactor.