Microbial communities and activities in alpine and subalpine soils

Soil samples were collected along two slopes (south and north) at subalpine (1500–1900 m, under closed vegetation, up to the forest line) and alpine altitudes (2300–2530, under scattered vegetation, above the forest line) in the Grossglockner mountain area (Austrian central Alps). Soils were analyzed for a number of properties, including physical and chemical soil properties, microbial activity and microbial communities that were investigated using culture-dependent (viable heterotrophic bacteria) and culture-independent methods (phospholipid fatty acid analysis, FISH). Alpine soils were characterized by significantly ( P <0.01) colder climate conditions, i.e. lower mean annual air and soil temperatures, more frost and ice days and higher precipitation, compared with subalpine soils. Microbial activity (soil dehydrogenase activity) decreased with altitude; however, dehydrogenase activity was better adapted to cold in alpine soils compared with subalpine soils, as shown by the lower apparent optimum temperature for activity (30 vs. 37 °C) and the significantly ( P <0.01–0.001) higher relative activity in the low-temperature range. With increasing altitude, i.e. in alpine soils, a significant ( P <0.05–0.01) increase in the relative amount of culturable psychrophilic heterotrophic bacteria, in the relative amount of the fungal population and in the relative amount of Gram-negative bacteria was found, which indicates shifts in microbial community composition with altitude.     

Adaptation of microbial activities to the environmental conditions in alpine soils

Summary The adaptation of soil microorganisms to different environmental conditions was investigated in the Austrian Central Alps (Hohe. Tauern). The floristic composition of the soil fungi at different sites was determined and the CO₂-release from soils taken from different altitudes was measured at different temperatures. The results showed a decreasing diversity of soil fungi with increasing altitude and a change in the dominating species at different altitudes and/or with vegetation patterns. The relative rates of CO₂-release from soils from different altitudes did not differ at different incubation temperatures. It was concluded that, among soil fungi the selection of species is a more effective mechanism for the adaption to changed environmental conditions than metabolic adaptations.This study was supported in part by the Österreichische MaB-Hochgebirgsprogramm Hohe TauernDedicated to Dr. K.F. Springer     

Mineralization responses at near-zero temperatures in three alpine soils

Cold-season processes are known to contribute substantially to annual carbon (C) and nitrogen (N) budgets in continental high elevation and high-latitude soils, but their role in more temperate alpine ecosystems has seldom been characterized. We used a 4-month lab incubation to describe temperature (−2, 0, 5°C) and moisture [50, 90% water-holding capacity (WHC)] effects on soil C and N dynamics in two wet and one dry meadow soil from the Sierra Nevada, California. The soils varied in their capacity to process N at and below 0°C. Only the dry meadow soil mineralized N at −2°C, but the wet meadow soils switched from net N consumption at −2°C to net N mineralization at temperatures ≥0°C. When the latter soils were incubated at −2°C at either moisture level (50 or 90% WHC), net NO₃ ⁻ production decreased even as NH₄ ⁺ continued to accumulate. The same pattern occurred in saturated (90% WHC) soils at warmer temperatures (≥0°C), suggesting that dissimilatory processes could control N cycling in these soils when they are frozen.     

Bioremediation of diesel-oil-contaminated alpine soils at low temperatures

Bioremediation of two diesel-oil-contaminated alpine subsoils, differing in soil type and bedrock, was investigated in laboratory experiments at 10 °C after supplementation with an inorganic fertilizer. Initial diesel oil contamination of 4000 mg kg⁻¹ soil dry matter (dm) was reduced to 380–400 mg kg⁻¹ dm after 155 days of incubation. In both soils, about 30 % of the diesel oil contamination (1200 mg kg⁻¹ dm) was eliminated by abiotic processes. The residual decontamination (60 %–65 %) could be attributed to microbial degradation activities. In both soils, the addition of a cold-adapted diesel-oil-degrading inoculum enhanced biodegradation rates only slightly and temporarily. From C/N and N/P ratios (determined by measuring the contents of total hydrocarbons, NH₄ ⁺ N, NO₃ ⁻ N and PO₄ ³⁻ P) of soils␣it could be deduced that there was no nutrient deficiency during the whole incubation period. Soil biological activities (basal respiration and dehydrogenase activity) corresponded to the course of biodegradation activities in the soils. Received: 9 September 1996 / Accepted: 7 December 1996     

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

The prototypical representatives of the Euryarchaeota—the methanogens—are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ¹³C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.     

Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils

Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding the response of the soil nitrogen cycle to shifts in temperature and other global change factors is crucial for predicting the fate of cold biome carbon stores. Measurements of soil enzyme activities at different positions of the nitrogen cycling network are an important tool for this purpose. We review a selection of studies that provide data on potential enzyme activities across natural, seasonal and experimental gradients in cold biomes. Responses of enzyme activities to increased nitrogen availability and temperature are diverse and seasonal dynamics are often larger than differences due to experimental treatments, suggesting that enzyme expression is regulated by a combination of interacting factors reflecting both nutrient supply and demand. The extrapolation from potential enzyme activities to prediction of elemental nitrogen fluxes under field conditions remains challenging. Progress in molecular '-omics' approaches may eventually facilitate deeper understanding of the links between soil microbial community structure and biogeochemical fluxes. In the meantime, accounting for effects of the soil spatial structure and in situ variations in pH and temperature, better mapping of the network of enzymatic processes and the identification of rate-limiting steps under different conditions should advance our ability to predict nitrogen fluxes.     

Field studies of nitrogen fixation of Australian alpine plants and soils

Alpine grassland areas in Victoria and New South Wales have been subjected to summer grazing by cattle and sheep for well over a hundred years. Legumes other than a few species of shrubs, which provide a very small percentage of the vegetation cover in the grasslands, are absent. Other alpine communities include Sphagnum ‘mossbeds’ in the valleys and areas of snowgum woodland and shrubland. Virtually nothing is known of the mineral status of these communities and nothing of their nitrogen economy. On the Bogong High Plains, enclosure of grassland and of Sphagnum mossbeds from grazing and trampling has resulted, in the last few decades, in considerable changes in both cover and composition of the vegetation. A portable gas chromatogram was used to carry out determinations of the capacity of samples of the grassland and Sphagnum to support acetylene reduction to ethylene, by convention equated to a capacity to fix nitrogen. There appears to be a substantial capacity for acetylene reduction associated with the rhizosphere of the grasses (Poa australis agg.). The capacity of the Sphagnum for acetylene reduction is even greater and appears to be due to facultative anaerobes, abundant only in the upper, living part of the Sphagnum. These organisms may depend in part on leakage of photosynthate from the living Sphagnum. Associations of Sphagnum with blue-green algae appear to be unusual in contrast with work on Swedish subarctic mosses, which is discussed. The only non-leguminous Australian alpine plant so far examined for nitrogen fixation is Podocarpus lawrencei. A capacity for acetylene reduction was found for neither the nodules of the roots of this plant nor the associated soils.     

Pools and composition of soils in the alpine zone of the Tatra Mountains

The basic physical, chemical, and biochemical properties of mountain soils were determined in alpine-zone meadow and moraine areas of the Tatra Mountains (Slovakia, Poland) in 2000–2001. The amount of soil (dry weight soil < 2 mm) varied from 38 to 255 kg m^?2 (average of 121 kg m^?2) in alpine meadows and averaged 13 kg m^?2 in moraine areas. Concentration of organic C was the parameter that most strongly and positively correlated with N, P, S, effective cation exchange capacity (CEC), exchangeable base cations, exchangeable acidity, and all biochemical parameters (C, N, and P in microbial biomass and C mineralisation rates). The relationship between C and P was less straightforward due to inorganic P forms associated with Fe and Al oxides. The average pools of C, N, P, and S, were respectively 696, 41, 2.9, and 1.9 mol m^?2 (i.e., 84, 5.7, 0.91 and 0.61 t ha^?1) in meadow soils, and 38, 2.1, 0.45 and 0.12 mol m^?2 (i.e., 4.5, 0.30, 0.14 and 0.04 t ha^?1) in moraine areas. Soil pH was generally low, with the lowest pH_{H 2 O} values (3.8–4.9) in the A-horizons. Average pools of CEC were 12 and 0.7 eq m^?2 in meadows and moraine areas, respectively. The base saturation (BS) was 4–45% (12% on average) of CEC, and was primarily based on Ca²⁺ and K⁺ (～40% and ～22% of BS, respectively). C:N molar ratios (14–20) were only slightly lower than those observed in the alpine Tatra Mountain zone ～40 years ago. Concentrations of C, N, and P in soil microbial biomass were high (on average 1.6, 3.4, and 25% of total C, N, and P concentrations), suggesting high microbial activity in alpine soils.     

Effect of plant waste on the biomass and abundance of micromycetes in alpine soils

Examination of the total biomass of soil micromycetes and their abundance in four soil types in the Furkota Valley (High Tatra Mountains) modified by adding plant waste at 1 and 5% revealed the following. The effect of the addition of organic matter was manifested by increased values of both the total biomass of soil micromycetes and their abundance. The highest values were always detected in soils to which the waste was added at 5%. The effect of organic matter was most pronounced during the first phase of the experiment (from the beginning of the experiment up to 2–3 months). A gradual exhaustion of nutrients and energy resulted in decreased values.     

Fluxes of nitrous oxide and methane from nitrogen-amended soils in a Colorado alpine ecosystem

In order to determine the effect of increased nitrogen inputs on fluxed of N₂O and CH₄ from alpine soils, we measured fluxes of these gases from fertilized and unfertilized soils in wet and dry alpine meadows. In the dry meadow, the addition of nitrogen resulted in a 22-fold increase in N₂O emissions, while in the wet meadow, we observed a 45-fold increase in N₂O emission rates. CH₄ uptake in the dry meadow was reduced 52% by fertilization; however, net CH₄ production occurred in all the wet meadow plots and emission rates were not significantly affected by fertilization. Net nitrification rates in the dry meadow were higher in fertilized plots than in non-fertilized plots throughout the growing season; net mineralization rates in fertilized dry meadow pots were higher than those in non-fertilized plots during the latter half of the growing season.     

Methanogenic bacteria in mangrove sediments

The occurrence of methanogenic bacteria in the Kodiakkarai (10° 18 N; 79° 52 E) mangrove sediments, whereAvicennia spp are predominant, was studied. Trimethylamine under N₂:CO₂ (80:20% v/v) was used as the substrate. Most Probable Number (MPN) of methanogenic bacteria was determined for a period of one year from July 1987 to June 1988 with monthly sampling. The methanogenic bacterial populations were found to be at the maximum of 1.1 × 10⁵ MPN gm^–1 of wet sediment during August 1987 and from February to June 1988. The bacterial numbers were found to decrease during October to December 1987 with a minimal value of 3.6 × 10² MPN gm^–1 during December 1987. Environmental factors were correlated with the methanogenic bacterial population.     

Methanogenic pathways in Methanosphaera stadtmanae

Methanosphaera stadtmanae reduces methanol to CH4 in a similar way as Methanosarcina barkeri. Low activities of 5,10-methylenetetrahydromethanopterin dehydrogenase (MTDH) and reductase (MTR) were found. From studies on formaldehyde oxidation and reduction it was concluded that most likely the inability to reduce CO2 to CH4 was due to the lack of an active or the presence of an inactive CO2 reductase system and methyltetrahydromethanopterin (methyl-H4MPT): coenzyme M methyltransferase. Methanofuran was not detected, while the presence of a pterin, analogous to H4MPT, could be substantiated from its degradation products in boiled extracts.     

Elevated CO2 alters community-level physiological profiles and enzyme activities in alpine grassland.

Plots of an alpine grassland in the Swiss Alps were treated with elevated (680 microl l(-1)) and ambient CO2 (355 microl l(-1)) in open top chambers (OTC). Several plots were also treated with NPK-fertilizer. Community level physiological profiles (CLPPs) of the soil bacteria were examined by Biolog GN microplates and enzyme activities were determined through the release of methylumbelliferyl (MUF) and methylcoumarin (MC) from MUF- or MC-labelled substrates. A canonical discriminant analysis (CDA) followed by multivariate analysis of variance showed a significant effect of elevated CO2 on the CLPPs both under fertilized and unfertilized conditions. Further, the installation of the OTCs caused significant shifts in the CLPPs (chamber effect). Of the four enzyme activities tested, the beta-D-cellobiohydrolase (CELase) and N-acetyl-beta-D-glucosaminidase (NAGase) activity were enhanced under elevated CO2. L-Leucin-7-aminopeptidase (APEase) activity decreased, when the plots received fertilizer. Beta-D-glucosidase (GLUase) remained unaffected. The results suggest effects of elevated CO2 on specific microbial activities even under low mineral nutrient conditions and when bulk parameters like microbial biomass or respiration, which have been investigated on the same site, remain unaffected. The observed medium-term changes point at possible long-term consequences for the ecosystem that may not be specified yet.     

Methanogenic Activity in Human Periodontal Pocket

Samples of subgingival dental tissues were examined for the presence of methanogenic activities. Using enrichment cultures, methanogenic activities were detected in 9 of 17 individuals. A mesophilic, Gram-positive, irregular coccoid methanogen, which showed close resemblance to a Methanosarcina sp., was isolated from one sample collected from a patient with type IV periodontal pocket (the periodontal pocket is a space bounded by the tooth on one side and by ulcerated epithelium lining the soft tissue wall on the other). The isolate used methanol, methylamine, acetate, and H₂-CO₂ as the sole source of carbon. However, the isolate was unable to use formate and trimethylamine as growth substrates. The organism had an optimum pH of 6.5 and an optimum temperature of 37°C. The isolate not only used ammonia, but also used nitrate as a nitrogen source. The niche of this methanogen in periodontal pockets may be to carry out terminal oxidation of simple organic compounds such as methanol and acetate produced by other obligate anaerobes present in periodontal pockets. This methanogen may also play a vital role in interspecies hydrogen transfer, as demonstrated by its use of H₂-CO₂ as a substrate. The isolate produced significant amount of methane in vitro. Received: 27 February 2002 / Accepted: 29 March 2002     

Methanogenic Fermentation of Benzoate

A methanogenic enrichment culture decomposed small concentrations of (14)C-benzoate to (14)C(4) and (14)CO(2) under stringently anaerobic conditions with or without preceding exposure to benzoate.     

Propionate Exchange Reactions in Methanogenic Ecosystems

Propionate degradation was measured with [1-¹⁴C]- and [2-¹⁴C]propionate in an anaerobic digestor. When [1-¹⁴C]propionate was used, label disappeared more rapidly from the propionate pool than when [2-¹⁴C]propionate was used. This indicated that an exchange reaction involving the carboxyl group of propionate occurred. Labeled propionate added to digestor samples which were equilibrated with H₂ lost label from the carboxyl group but not from the methylene group.     

Seasonal variation in enzyme activities and temperature sensitivities in Arctic tundra soils

Arctic soils contain large amounts of organic matter due to very slow rates of detritus decomposition. The first step in decomposition results from the activity of extracellular enzymes produced by soil microbes. We hypothesized that potential enzyme activities are low relative to the large stocks of organic matter in Arctic tundra soils, and that enzyme activity is low at in situ temperatures. We measured the potential activity of six hydrolytic enzymes at 4 and 20 °C on four sampling dates in tussock, intertussock, shrub organic, and shrub mineral soils at Toolik Lake, Alaska. Potential activities of N‐acetyl glucosaminidase, β‐glucosidase, and peptidase tended to be greatest at the end of winter, suggesting that microbes produced enzymes while soils were frozen. In general, enzyme activities did not increase during the Arctic summer, suggesting that enzyme production is N‐limited during the period when temperatures would otherwise drive higher enzyme activity in situ. We also detected seasonal variations in the temperature sensitivity (Q₁₀) of soil enzymes. In general, soil enzyme pools were more sensitive to temperature at the end of the winter than during the summer. We modeled potential in situβ‐glucosidase activities for tussock and shrub organic soils based on measured enzyme activities, temperature sensitivities, and daily soil temperature data. Modeled in situ enzyme activity in tussock soils increased briefly during the spring, then declined through the summer. In shrub soils, modeled enzyme activities increased through the spring thaw into early August, and then declined through the late summer and into winter. Overall, temperature is the strongest factor driving low in situ enzyme activities in the Arctic. However, enzyme activity was low during the summer, possibly due to N‐limitation of enzyme production, which would constrain enzyme activity during the brief period when temperatures would otherwise drive higher rates of decomposition.     

Tannin impacts on microbial diversity and the functioning of alpine soils: a multidisciplinary approach

In alpine ecosystems, tannin-rich-litter decomposition occurs mainly under snow. With global change, variations in snowfall might affect soil temperature and microbial diversity with biogeochemical consequences on ecosystem processes. However, the relationships linking soil temperature and tannin degradation with soil microorganisms and nutrients fluxes remain poorly understood. Here, we combined biogeochemical and molecular profiling approaches to monitor tannin degradation, nutrient cycling and microbial communities (Bacteria, Crenarcheotes, Fungi) in undisturbed wintertime soil cores exposed to low temperature (0°C/−6°C), amended or not with tannins, extracted from Dryas octopetala . No toxic effect of tannins on microbial populations was found, indicating that they withstand phenolics from alpine vegetation litter. Additionally at −6°C, higher carbon mineralization, higher protocatechuic acid concentration (intermediary metabolite of tannin catabolism), and changes in fungal phylogenetic composition showed that freezing temperatures may select fungi able to degrade D. octopetala 's tannins. In contrast, negative net nitrogen mineralization rates were observed at −6°C possibly due to a more efficient N immobilization by tannins than N production by microbial activities, and suggesting a decoupling between C and N mineralization. Our results confirmed tannins and soil temperatures as relevant controls of microbial catabolism which are crucial for alpine ecosystems functioning and carbon storage.     

Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints

Permafrost environments in the Arctic are characterized by extreme environmental conditions that demand a specific resistance from microorganisms to enable them to survive. In order to understand the carbon dynamics in the climate-sensitive Arctic permafrost environments, the activity and diversity of methanogenic communities were studied in three different permafrost soils of the Siberian Laptev Sea coast. The effect of temperature and the availability of methanogenic substrates on CH4 production was analysed. In addition, the diversity of methanogens was analysed by PCR with specific methanogenic primers and by denaturing gradient gel electrophoresis (DGGE) followed by sequencing of DGGE bands reamplified from the gel. Our results demonstrated methanogenesis with a distinct vertical profile in each investigated permafrost soil. The soils on Samoylov Island showed at least two optima of CH4 production activity, which indicated a shift in the methanogenic community from mesophilic to psychrotolerant methanogens with increasing soil depth. Furthermore, it was shown that CH4 production in permafrost soils is substrate-limited, although these soils are characterized by the accumulation of organic matter. Sequence analyses revealed a distinct diversity of methanogenic archaea affiliated to Methanomicrobiaceae, Methanosarcinaceae and Methanosaetaceae. However, a relationship between the activity and diversity of methanogens in permafrost soils could not be shown.     

Methanogenic inhibition by arsenic compounds

The acute acetoclastic methanogenic inhibition of several inorganic and organic arsenicals was assayed. Trivalent species, i.e., methylarsonous acid and arsenite, were highly inhibitory, with 50% inhibitory concentrations of 9.1 and 15.0 microM, respectively, whereas pentavalent species were generally nontoxic. The nitrophenylarsonate derivate, roxarsone, displayed moderate toxicity.