Vol 87, No 6 (2018)

This review is focused on analysis of the biological diversity of phytase-producing microorganisms capable of degrading phytate to inorganic phosphate. General approaches to microbial phytase classification are discussed, with a particular emphasis on histidine acid phytases (HAPs), which catalyze specific cleaving of myo-inositol hexakisphosphate. The effect of glycosylation and various effectors on enzyme thermostability and activity of phytases are described. The data on the biosynthesis of histidine acid phytases, their substrate specificity, and on the mechanism of myo-inositol hexakisphosphate hydrolysis are considered. A conclusion is made concerning the biotechnological potential of this group of microbial enzymes.

Fermenting bacteria are usual components of oilfield microbial communities. Since pure cultures of fermenting bacteria utilize carbohydrates and do not grow on oil, their diversity and relationships in the community are of great interest. In the present work, enrichment and pure cultures of fermenting bacteria obtained from formation water of low-temperature oilfields (Russia) were studied. High-throughput sequencing of the V3–V4 region of the 16S rRNA gene was carried out for an enrichment culture. The library was found to contain the genes of anaerobic bacteria of the genus Halanaerobium, which are capable of growth on polysaccharides with thiosulfate reduction to sulfide, as well as the genes of Abyssivirga alkaniphila, which grows on C₅–C₂₅n-alkanes of oil with thiosulfate as an electron acceptor or in a syntrophic association with hydrogenotrophic methanogens. Members of the genus Sphaerochaeta were minor components of the community. Three strains (4-11, 5-8-5, and 17-50) were isolated from enrichment cultures. The isolates were anaerobic mesophilic slightly halophilic bacteria, which fermented a number of carbohydrates and grew as biofilms. The 16S rRNA gene sequences of the new strains exhibited 99.5–100% similarity between each other and 97.2–98.0% similarity to the sequences of the most closely related species Sphaerochaetaassociata and Sphaerochaetaglobosa, which indicated their affiliation to a new Sphaerochaeta species. The products of maltose fermentation were acetate, propionate, СО₂, Н₂, and sometimes iso-propanol. The strains did not grow on crude oil. In oilfields Sphaerochaeta species probably consume the products of oil biodegradation by other microorganisms, are involved in biofilms formation, and provide H₂ for methanogens and other components of the community.

A new design for a small growth container which was used for investigation of the microbiota of the White Sea littoral and sublittoral sediments is presented. These chambers made it possible to observe development of fungal mycelium under conditions of a natural ecotope (marine sediments) and to isolate this mycelium as pure cultures. The mycobiota isolated from the containers was compared to that obtained by standard plating method of the same sediments. The mycelium developed in 10% of the containers installed. Intensity of growth was found to be lower in the sublittoral than in the littoral. Most fungi isolated from the containers did not produce spores in pure cultures. Apart from non-sporulating cultures, colonies of marine species Paradendryphiellasalina and Acremoniumfuci were obtained. Standard plating of the sediments often resulted in isolation of Penicillium and Tolypocladium species, while the share of sterile isolates was considerably lower than in the case of isolation using growth containers.

Here, we present a phylogenetic analysis of a large group of the nearest homologues of a β-galactosidase, recently cloned from a soil metagenome and representing a new family of glycoside hydrolases. These proteins form an independent subfamily of hypothetical β-galactosidases and are almost exclusively represented in bacteria of the poorly studied phyla Planctomycetes and Verrucomicrobia, as well as Bacteroidetes. The phylogenetic tree of this subfamily consists of eleven highly stable clusters of branches, probably resulting from a series of gene duplications. An analysis of the tree topology suggested that the corresponding genes first evolved in Planctomycetes and most gene duplications occurred within this phylum. Later, these genes spread to several other bacterial phyla through horizontal transfers, the most numerous being transfers to Verrucomicrobia. The genomes of most Planctomycetes contain multiple paralogues of these genes of a different origin: in some cases, the horizontal transfers played a key role, while in other cases gene duplications played a key role. The importance of poorly studied groups of prokaryotes as a source of novel glycoside hydrolases is discussed.

Differences in the quantitative and qualitative compositions of various physiological and biochemical groups of cultured microorganisms were revealed in biofilms formed on stony substrates in the littoral zone of Southern Baikal (August 2012) in the areas with different anthropogenic load. Maximal abundance of microorganisms was registered in epilithic biofilms from the area of Baikalsk Pulp and Paper Plant: organotrophs (770.2 ± 290.3 × 10³ CFU/cm²); amylolytics (38.1 ± 7.7 × 10³ CFU/cm²); phosphate-solubilizing microorganisms (4.8 ± 1.4 × 10³ CFU/cm²); phosphate-mobilizing microorganisms (212.0 ± 27.6 × 10³ CFU/cm²); phenol-oxidizing microorganisms (15.7 ± 2.4 × 10³ CFU/cm²); molds (3.2 ± 0.4 × 10³ CFU/cm²); and total coliform bacteria (193.3 ± 28.2 CFU/cm²), with the total microbial abundance (TMA at 37°C) of 24.9 ± 1.7 × 10³ CFU/cm², which indicated high degrading activity of the biofilms in response to the anthropogenic load in the area. Epilithic biofilms of the Bol’shie Koty area exhibited the lowest abundance of organotrophic and phosphate-solubilizing microorganisms, while molds were absent.

The microbiomes of the soils buried under earthwork structures of different age (burial mounds and defensive earth walls) and of surface soils were investigated. Microbial DNA was analyzed by quantitative PCR and sequencing of the 16S rRNA gene amplicons. Both microbial abundance and diversity in buried soils were found to be lower. The taxonomic structure of the buried soil microbiomes differed significantly from that of surface soils: the share of the bacterial phylum Verrucomicrobia was very low. The thickness of the earthwork structure should be sufficient to isolate soil from the effect of plant roots; otherwise, the microbiome may exhibit virtually no difference from that of surface soils. The degree of mineralization of stored organic matter (in the absence of inflow of fresh organic compounds) is probably the main factor affecting the structure of microbial communities in buried soils. The study did not reveal any properties of the microbiomes usable as markers of the type of buried soils.

Arsenite (As(III)) induced changes were investigated in the diazotrophic cyanobacterium Anabaena PCC 7120. The cells of Anabaena sp. strain PCC 7120 exposed to As(III) produced H₂O₂ and its production increased with increase in As(III) concentration. As a part of resistant mechanism and also to counteract the deleterious effect of H₂O₂, the cells of Anabaena sp. strain PCC 7120 produced more ascorbate peroxidase (APx) whose level also increased in response to As(III) concentrations. The increase in APx activity was directly proportional to the increase in H₂O₂ production and maximum APx activity was recorded at 40 ppm of As(III). In contrast, glutathione reductase (GR) activity decreases with increase in As(III) concentrations and attained its minimum level at 40 ppm of As(III). Lipid peroxidation increased with increase in As(III) concentration and maximum peroxidation (which was about two fold higher than that of the untreated control cells) was recorded at 40 ppm of As(III). Exposure of the Anabaena sp. strain PCC 7120cells to As(III) has also resulted in a significant increase in ascorbate and dehydro-ascorbate contents which was about 6.44 and 1.97 fold higher than that of the untreated control cells, respectively at 40 ppm of As(III).