T. G. Dobrovol’skaya

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.

The Saprotrophic Bacterial Complex in the Raised Peat Bogs of Western Siberia

The population density of bacteria in peat deposits along the landscape profile of the Vasyugan Marsh has been found to be as high as tens of millions of CFU/g peat. The abundance and diversity of bacteria increased with depth within the peat deposit, correlating with an increasing level of peat degradation. Variations in these parameters with depth and season were greater in peat deposits located in transaccumulative and transitional positions than in the sedge-sphagnum bogs located at the eluvial region of the profile. In the upper 1-m-thick layer of the peat deposits studied, bacilli, represented by five species, dominated, whereas, in the deeper layers, spirilla and myxobacteria prevailed. These bacteria are major degraders of plant polymers. Unlike the bacterial communities found in the peat deposits of European Russia, the dominant taxa in the studied peat deposits of western Siberia are represented by bacteria resistant to extreme conditions.

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.

Methodological aspects of assessing chitin utilization by soil microorganisms

A computational method for estimating specific activity of chitin decomposition by microorganisms is proposed. Spectrophotometric and gas chromatographic methods have been used to determine the rates of chitinase production, biomass accumulation, and carbon dioxide emission by pure cultures of microorganisms grown on a chitin-containing medium. Among dominants of the chitinolytic community of chernozem (Trichoderma viride, Stretomyces albolongus, Alcaligenes, and Arthrobacter), the highest chitinolytic activity is characteristic of prokaryotes. In brown desert-steppe soil, the main destructor prokaryotes are actinomycetes (S. roseolilacinus). The biomass of the fungus T. viride growth on the chitin-containing medium markedly exceeds that of prokaryotes, but the specific activity of respiration and chitinase production in actinomycetes S. roseolilacinus and S. albolongus is an order of magnitude higher than in T. viride.

Microbiological activity in the anthills of fallow lands (Ryazan Region)

A bacterial complex associated with several species of ants, the inhabiting soil, and their anthills was studied. The biodiversity of bacteria in ants was higher than that in the anthills and control soil. The latter was dominated by Bacillus (more than 80%); the anthill of Formica was dominated by the Flavobacterium-Bacteroides-Cytophaga group. In addition, actinomycetes were widespread in the anthills of Formica and Lisius. Numerous staphylococci (20%) were found in the L. flavus ants, but the main dominants of the bacterial community were Streptomyces bacteria (68.5%). Tetramorium had no pronounced dominants and many Bacteroides bacteria (28%). Actinomycetes of Streptomyces were detected in the bacterial complexes of all studied ants, except for F. cunicularia.

Biological Activities of "Beaver Landscape" Soils

This study considers microbiological activities in soils occupied by beaver populations. The intensities of nitrogen fixation, denitrification, and carbon and methane emissions were evaluated, the specific and functional diversities of microbial communities were identified, and the contents of nitrogen and carbon in the altered landscapes were measured. It was shown that nitrogen and carbon are transformed more intensively in the given soils than in the background soils, and accumulation of carbon and nitrogen in the former soils occurs.

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.

Microbial communities of lichens

The current state of scientific researches in lichen microbiology was reviewed. Analysis of the literature revealed the main areas and fundamental issues which refer to investigation of microbial consortia in lichen bodies. Special attention was focused on analysis of the prokaryotic community which plays a structural and functional role and is involved in metabolism and regulation of activity of the lichen symbiosis as a whole. In the review, for the first time the information on the yeast community, of which some members do not occur presently in other environmental substrates, was summarized. The data on the protozoa inhabiting lichen thalli were also provided. The reviewed literature enabled us to consider the growing and decaying thallus as a complex ecosystem with specific levels of regulation of abundance, taxonomic diversity, and activity of the members of five kingdoms: fungi, plants, protozoa, eubacteria, and archaea.

Functional features of microbial communities in the digestive tract of field voles (Microtus rossiaemeridionalis and Clethrionomys glareolus)

The nitrogen-fixating and cellobiohydrolase activity, the nitrogen (N) and carbon (C) contents, and the number of microorganisms in the prestomach, cecum, and colon of two vole species were studied: the southern vole (Microtus rossiaemeridionalis) and the bank vole (Clethrionomys glareolus), which is characterized by a mixed type of diet. The nitrogen-fixating activity in the cecum was found to be the highest in the voles compared with the mammals studied earlier. The seasonal dynamics of both nitrogenase and cellobiohydrolase activities was registered in the southern vole. The structure of the microbial complex in the southern vole is more varied and includes microorganisms associated with plant substrates.