A. V. Golovchenko

The role of microorganisms in the ecological functions of soils

The results of long-term investigations performed by researchers from the Department of Soil Biology at the Faculty of Soil Science of Moscow State University into one of the major functions of soil microorganisms—sustenance of the turnover of matter and energy in the biosphere—are discussed. Data on the population densities of soil microbes and on the microbial biomass in different types of soils are presented. The systemic approach has been applied to study the structural-functional organization of the soil microbial communities. The role of eukaryotic and prokaryotic microorganisms in the carbon and nitrogen cycles is elucidated. It is argued that the high population density and diversity of microorganisms are necessary to maintain the turnover of chemical elements in terrestrial ecosystems. The viability of microbes stored in the soils is important. New data on the preservation and survival of bacteria in nanoforms are presented. It is shown that peatlands and paleosols are natural banks, where microbes can be preserved in a viable state for tens of thousands years.

Abundance, Diversity, Viability, and Factorial Ecology of Fungi in Peatbogs

This review presents an analysis of the results of mycological investigations of peat obtained by the authors and other Russian and foreign scientists. High-moor peat, unlike low-moor peat, is shown to contain great reserves of fungal biomass mainly represented by mycelium. The viability of the mycelium and spores is high in the upper peat horizons and does not exceed 50% in the lower ones. In high-moor peat, fungi that are capable of destroying the complex structural polymers composing up to 50% of the peat rarely occur. The analysis of the factors limiting the activity of fungi in the high-moor peatbogs showed that, in the upper layers, the main factor was the strength of the sphagnum cellular walls. In the lower layers, the significant oxygen deficit and the accumulation of sphagnans, sphagnols, phenol-containing compounds, and antioxidants that block the activity of hydrolytic and oxidizing enzymes are of great importance.

The structure of the microbial communities in low-moor and high-moor peat bogs of Tomsk oblast

The number, structure, and physical state of the microbial communities in high-moor and low-moor peat bogs were compared. Distinct differences in these characteristics were revealed. The microbial biomass in the high-moor peat exceeded that in the low-moor peat by 2–9 times. Fungi predominated in the high-moor peat, whereas bacteria were the dominant microorganisms in the low-moor peat. The micromycetal complexes of the high-moor peat were characterized by a high portion of dark-colored representatives; the complexes of the low-moor peat were dominated by fast-growing fungi. The species of the Penicillum genus were dominant in the high-moor peat; the species of Trichoderma were abundant in the low-moor peat. In the former, the bacteria were distinguished as minor components; in the latter, they predominated in the saprotrophic bacterial complex. In the high-moor peat, the microorganisms were represented by bacilli, while, in the low-moor peat, by cytophages, myxobacteria, and actinobacteria. The different physiological states of the bacteria in the studied objects reflecting the duration of the lag phase and the readiness of the metabolic system to consume different substrates were demonstrated for the first time. The relationships between the trophic characteristics of bacterial habitats and the capacity of the bacteria to consume substrates were established.

Assessment of the bacterial diversity in soils: Evolution of approaches and methods

This review analyzes the publications of Russian and foreign microbiologists presenting new approaches and methods for assessing the bacterial diversity of soils in the last twenty years. Using the example of peat soils, it is shown how the concepts of the diversity of the bacterial communities changed in conformity with the evolution of the analytical methods—from the traditional cultural to the molecular-biological ones. The data on the new phylotypes, genera, and species of bacteria adapted to growth in the acid medium and low temperatures characteristic of bog ecosystems are presented. Presently, one of the principal problems of soil microbiology is the necessity of the transfer from the databases on the microbial diversity constructed on the basis of molecular-biological methods to the analysis of the ecological functions of soil microorganisms. The prospects of the ecological evaluation of the bacterial diversity in soils based on the integration of different methods are discussed.

The influence of aeration and temperature on the structure of bacterial complexes in high-moor peat soil

The number and taxonomic structure of the heterotrophic block of aerobic and facultative anaerobic bacteria were studied in monoliths from a high-moor peat (stored at room temperature and in a refrigerator) and in the peat horizons mixed in laboratory vessels. The monitoring lasted for a year. In the T0 horizon, spirilla predominated at room and low temperatures; in the T1 and T2 horizons, bacilli were the dominants. The continuous mixing of the peat layers increased the oxygen concentration and the peat decomposition; hence, the shares of actinomycetes and bacilli (bacteria of the hydrolytic complex) increased. In the peat studied, the bacilli were in the active state; i.e., vegetative cells predominated, whose amount ranged from 65 to 90%. The representatives of the main species of bacilli (the facultative anaerobic forms prevailed) hydrolyzed starch, pectin, and carboxymethylcellulose. Thus, precisely sporiferous bacteria can actively participate in the decomposition of plant polysaccharides in high-moor peat soils that are characterized by low temperatures and an oxygen deficit. The development of actinomycetes is inhibited by low temperatures; they can develop only under elevated temperature and better aeration.

Functioning of microbial complexes in aerated layers of a highmoor peat bog.

Monitoring was carried out using the luminescent-microscopic method of the abundance parameters of different groups of microorganisms in a monolith and in the mixed layers of a highmoor peat bog (oligotrophic residual-eutrophic peat soil) in a year-long model experiment. The increase of the aeration as a result of mixing of the layers enhanced the activity of the soil fungi. This was attested to by the following changes: the increase of the fungal mycelium length by 6 times and of the fungal biomass by 4 times and the double decrease of the fraction of spores in the fungal complex. The response of the fungal complex to mixing was different in the different layers of the peat bog. The maximal effect was observed in the T1 layer and the minimal one in the T2 layer. The emission of CO2 in the mixed samples was 1.5–2 times higher than that from the undisturbed peat samples. In contrast with the fungi, the bacteria and actinomycetes were not affected by the aeration of the highmoor layers.

The structure of the bacterial heterotrophic block in tundra soils of Yamal Peninsula.

The tundra cryogenic soils of Yamal Peninsula have a high pool of prokaryote microorganisms characteristic of ecosystems where the environmental conditions are unfavorable for microbiological processes. The lowering of the cultivation temperature from 20 to 5°C did not affect the number of bacteria and their taxonomic structure. Psychrotolerant gram-negative bacteria represented by oligotrophs and copiotrophs predominated in the bacterial communities. Among the bacteria of the hydrolytic block, only bacilli were isolated upon cultivation on the media. The species spectrum of the Bacillus genus was determined by the capability of its representatives for growth at low temperatures. The bacteria isolated from the cryogenic soils had a high nitrogenase activity, which increased under the lower cultivation temperature. This fact shows that the majority of the bacteria in tundra soils has adapted to functioning at low temperatures.

Structure of epiphytic bacterial communities of weeds

Dynamics of the taxonomic structure of epiphytic bacterial communities of the rhizosphere and phyllosphere of seven weed species was studied. The major types of isolated organisms were identified using phenotypic and molecular biological approaches. Dispersion analysis revealed that the ontogenesis stage and plant organ were the factors with the greatest effect on the taxonomic structure of the communities. The dominant microorganisms of weeds were similar to those of cultivated plants. The minor components revealed in the spectra of bacterial communities of weeds belonged to poorly studied genera of chemolithotrophic proteobacteria.

Analysis of ecological factors limiting the destruction of high-moor peat

This review presents an analysis of literature data and original studies by the authors aimed at revealing the factors inhibiting the destruction of high-moor (oligotrophic) peat. Each of the ecological factors that prevent the decomposition of the high-moor peat by different groups of microorganisms is considered. The acid reaction, low temperatures, and lack of nutrients were found not to be the primary factors inhibiting the destruction of the peat. The limited content of oxygen in the peatbogs leads to a drastic decrease in the number of mycelial microorganisms and a reduction of the activity of hydrolytic and oxidizing enzymes. The main factor inhibiting the decomposition of sphagnum is its mechanical and chemical stability, since animals crushing sphagnum are absent in the soil, and this moss has polysaccharides of special composition. The toxicity of phenol compounds, which is manifested under the aerobic conditions, prevents the activity of all the hydrolytic enzymes. This is the main reason for the slow decomposition of sphagnum peat and the long-term preservation of the residues of bodies and food in high-moor peatlands.

Bacterial complexes of a high moor related to different elements of microrelief

The analysis of bacterial complexes, including the number, taxonomic composition, physiological state, and proportion of ecological trophic groups was performed in a high moorland related to different elements of the microrelief. The abundance of bacteria, their ability for hydrolysis of polymers and the share of r-strategists were found to be higher in the sphagnum hillocks than on the flat surfaces. The total prokaryote biomass was 4 times greater in the sphagnum samples from microhighs (hillocks). On these elements of the microrelief, the density of actinomycetal mycelium was higher. Bacteria of the hydrolytic complex (Cytophaga and Chitinophaga genera) were found only in microhigh samples.