The effect of reindeer grazing on decomposition, mineralization and soil biota in a dry oligotrophic Scots pine forest

Reindeer grazing in the Fennoscandian area has a considerable influence on the ground vegetation, and this is likely in turn to have important consequences for the soil biota and decomposition processes. The effects of reindeer grazing on soil biota, decomposition and mineralization processes, and ecosystem properties in a lichen‐dominated forest in Finnish Lapland were studied inside and outside a large long term fenced reindeer exclosure area. Decomposition rates of Vaccinium myrtillus leaves in litter bags were retarded in the grazed area relative to the ungrazed area, as well as in subplots from which lichens had been artificially removed to simulate grazing. The effect of reindeer grazing on soil respiration and microbial C was positive in the lichen and litter layers of the soil profile, but retarded in the humus layer. There was no effect of grazing on gross N mineralization and microbial biomass N in the humus and upper mineral soil layer, but net N mineralization was increased by grazing. In these layers soil respiration was reduced by grazing, indicating that reindeer effects reduce the ratio of C to N mineralized by soil microorganisms. Grazing stimulated populations of all trophic groupings of nematodes in the lichen layer and microbe feeding nematodes in the litter layer, indicating that grazing by reindeer has multitrophic effects on the decomposer food‐web. Grazing decreased lichen and dwarf shrub biomasses and increased the mass of litter present in the litter layer on an areal basis, but did not significantly alter total C storage per unit area in the humus and mineral soil layers. The N concentration of lichens was increased by grazing, but the N concentrations of both living and dead Pinus sylvestris needles and Empetrum hermaphroditum leaves were not affected.
There was some evidence for each of three mechanisms which could account for the grazing effects that we observed in our study. Firstly, reindeer may have changed the composition and quality of litter input by affecting plant species composition and through addition of N from urine and faeces, resulting in a lack of available C relative to N for decomposer organisms. Secondly, the organic matter in the soil may be older in the grazed area, because of reduction of recent production of lichen litter relative to the ungrazed area. The organic matter in the grazed area may have been in a different phase of decomposition from that in the exclosure. Thirdly, the soil microclimate is likely to be affected by reindeer grazing through physical removal of lichen cover on the ground, and this can have a significant influence on soil microbial processes. This is supported by the strong observed effects of experimental removal of lichens on decomposer processes. The impact of reindeer grazing on soil processes may be a result of complex interactions between different mechanisms, and this could help to explain why the below‐ground effects of reindeer grazing have different consequences to those which have been observed in recent investigations on other grazing systems.     

Ecosystem properties and microbial community changes in primary succession on a glacier forefront

We studied microbial community composition in a primary successional chronosequence on the forefront of Lyman Glacier, Washington, United States. We sampled microbial communities in soil from nonvegetated areas and under the canopies of mycorrhizal and nonmycorrhizal plants from 20- to 80-year-old zones along the successional gradient. Three independent measures of microbial biomass were used: substrate-induced respiration (SIR), phospholipid fatty acid (PLFA) analysis, and direct microscopic counts. All methods indicated that biomass increased over successional time in the nonvegetated soil. PLFA analysis indicated that the microbial biomass was greater under the plant canopies than in the nonvegetated soils; the microbial community composition was clearly different between these two types of soils. Over the successional gradient, the microbial community shifted from bacterial-dominated to fungal-dominated. Microbial respiration increased while specific activity (respiration per unit biomass) decreased in nonvegetated soils over the successional gradient. We proposed and evaluated new parameters for estimating the C use efficiency of the soil microbial community: “Max” indicates the maximal respiration rate and “Acc” the total C released from the sample after a standard amount of substrate is added. These, as well as the corresponding specific activities (calculated as Max and Acc per unit biomass), decreased sharply over the successional gradient. Our study suggests that during the early stages of succession the microbial community cannot incorporate all the added substrate into its biomass, but rapidly increases its respiration. The later-stage microbial community cannot reach as high a rate of respiration per unit biomass but remains in an “energy-saving state,” accumulating C to its biomass. Received: 4 June 1998 / Accepted: 11 January 1999     

Reindeer grazing and soil microbial processes in two suboceanic and two subcontinental tundra heaths

In oceanic, nutrient-rich Fennoscandian arctic-alpine tundra heaths, grazing by reindeer has been found to increase herbs and graminoids in relation to dwarf shrubs. In continental lichen heaths in the inland with nutrient-poor conditions, however, slowly decomposable dwarf shrubs are favoured by grazing. According to a hypothesis, by favouring easily decomposing plants in nutrient-rich conditions and slowly decomposing plants in nutrient-poor conditions, herbivory enhances soil nutrient cycling in nutrient-rich and retards it in nutrient-poor areas. We tested this hypothesis by comparing the impact of reindeer grazing on soil C and N mineralization between two oceanic and two continental arctic-alpine tundra heaths.
Although soil respiration and microbial metabolic activity were enhanced by grazing in the suboceanic but not in the subcontinental tundra heaths, gross N mineralization rates were higher in the grazed areas in soils from all study sites, indicating that reindeer grazing leads to increased rates of nutrient cycling in both nutrient-poor and nutrient-rich tundra heaths. Thus, in the subcontinental tundra heaths, the increase in soil N concentrations due to mammalian waste products enhances N mineralization rates, even though the organic C quality is not improved by reindeer grazing. There was some site-specific variation in the strength of the reindeer effects on various microbial processes and soil properties, which can be related to spatial variation in grazing intensity and timing, as these factors in turn affect the nutrient sink strength of the vegetation.     

Transcriptional analysis of genes encoding Shiga toxin 2 and its variants in Escherichia coli

Six of 37 non-O157 Escherichia coli strains possessing Shiga toxin (Stx) 2 gene variant stx(2d) or stx(2e) secreted no detectable Stx. These isolates produced significantly less stx mRNA than Stx2d, Stx2e, Stx2c, or Stx2 secretors did. Standard screening procedures miss a significant subset of E. coli harboring stx(2) variants.     

Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak

Background

Waterborne Campylobacter jejuni outbreaks are common in the Nordic countries, and PFGE (pulsed field gel electrophoresis) remains the genotyping method of choice in outbreak investigations. However, PFGE cannot assess the clonal relationship between isolates, leading to difficulties in molecular epidemiological investigations. Here, we explored the applicability of whole genome sequencing to outbreak investigation by re-analysing three C. jejuni strains (one isolated from water and two from patients) from an earlier resolved Finnish waterborne outbreak from the year 2000.

Results

One of the patient strains had the same PFGE profile, as well as an identical overall gene synteny and three polymorphisms in comparison with the water strain. However, the other patient isolate, which showed only minor differences in the PFGE pattern relative to the water strain, harboured several polymorphisms as well as rearrangements in the integrated element CJIE2. We reconstructed the genealogy of these strains with ClonalFrame including in the analysis four C. jejuni isolated from chicken in 2012 having the same PFGE profile and sequence type as the outbreak strains. The three outbreak strains exhibited a paraphyletic relationship, implying that the drinking water from 2000 was probably contaminated with at least two different, but related, C. jejuni strains.

Conclusions

Our results emphasize the capability of whole genome sequencing to unambiguously resolve the clonal relationship between isolates of C. jejuni in an outbreak situation and evaluate the diversity of the C. jejuni population.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-768) contains supplementary material, which is available to authorized users.     

Characterization of Multiple Helicobacter bizzozeronii Isolates From a Finnish Patient With Severe Dyspeptic Symptoms and Chronic Active Gastritis

Background:  Helicobacter pylori is the primary cause of gastritis and peptic ulceration in humans. In a minority of patients with upper gastrointestinal symptoms, long tightly coiled spiral bacteria, provisionally named " Helicobacter heilmannii, " are observed in gastric biopsies. These bacteria are extremely fastidious and only one previous study has succeeded in obtaining an isolate in vitro.
Materials and Methods:  We used two different selective media to isolate " H. heilmannii " from the gastric mucosa of a Finnish patient presenting with severe dyspeptic symptoms. The isolates were characterized by testing for urease and catalase activity, by using light and electron microscopy, and by sequencing of the partial 16S rRNA and ureAB genes. Single-enzyme amplified fragment length polymorphism (sAFLP) was used to analyze the genetic diversity among the isolates.
Results:  We obtained 15 isolates from different gastric biopsies prior and three after unsuccessful treatment of the patient. The isolates were identified as Helicobacter bizzozeronii . Eradication therapy was unsuccessful most probably due to high level of resistance to metronidazole. Persistent colonization by the same H. bizzozeronii clone was confirmed by sAFLP, however, small differences between the profiles suggested long-term colonization of the patient.
Conclusions:  Helicobacter bizzozeronii remains the only " H. heilmannii " species isolated from human gastric mucosa although it has been an infrequent observation among " H. heilmannii "-infected patients in PCR-based screening studies. The relevance of H. bizzozeronii and other potentially zoonotic gastric Helicobacter spp. in human disease remains to be determined.     

The microbial threat: Can rare earths help?

Despite an ever increasing demand for reliable and cheap methods in the detection and quantification of microbes, surprisingly few investigations have explored or utilized the luminescence of rare earths in the microbial context, neither in conventional, that is, plating and microscopic imaging techniques, nor in advanced methods like fluorescence flow cytometry. We have thus investigated the potential of some rare earth complexes and hybrid materials for microbiological analysis. We found fairly simple procedures for internal staining (dyes inside the bacterial cell) and external staining (dyes on the cell surface). The present paper is predominantly relying on microscopic imaging and luminescence spectroscopies (excitation, emission, decay times), but also evaluates model rare earth microspheres to estimate an eventual rare earth based stain for a fast and sensitive bacteria enumeration with luminescence flow cytometry.     

Biological activity and amount of FDA mycelium in mor humus of Scots pine stands (Pinus sylvestris L.) in relation to soil properties and degree of pollution

The biological activity and the amount of living fungal mycelium in the mor humus of pine forests around an industrialized city were studied. The activities were lower in the more polluted zone than in a cleaner one but varied between sites within the zones. The relationship of these activities to the microbial environment was determined in both the total data and in the various zones separately. Soil respiration rate was positively related to ammonium nitrogen concentration of the humus in the less polluted zone but negatively in the more polluted zone, while it related negatively to total nitrogen concentration of the humus in the entire data set. DHA was partly accounted for by the variation in acidity parameters, and best by pH(CaCl₂), with a positive relation. The length of FDA active fungal mycelium showed no significant variation between the zones or sites, and was thus poorly explained by the environmental variables. The weather conditions prevailing at two seasons did not explain any variation of the activities or the length of FDA mycelium, though the biological variables were in general positively related to the moisture of the humus.