The genomes of two bacteriobionts of the fruticose lichen Ramalina pollinaria, Lichenibacterium ramalinae and L. minor, were analyzed. Genetic determinants potentially determining the integration and adaptation of these bacteria in the lichen thallus were identified. This is the first report on assessment of genetic determinants of the stress reaction factors and secretion systems of lichen bacteriobionts. The genes encoding the proteins of the VapCB toxin–antitoxin (TA) systems exhibited >60% homology with the genes of the known plant symbionts Bradyrhizobium, Sinorhizobium, Agrobacterium, Mesorhizobium, and Ralstonia, as well as with those of a human pathogen Bartonella. The genes encoding the proteins of type II secretion system were found in the genomes of both species. The genes encoding type IV secretion proteins were found only in the genome of L. ramalinae; they were homologous to those of epiphytic Methylobacterium, plant pathogens Agrobacterium, and plant root symbionts Rhizobium and Neorhizobium. Homology between the genes encoding TA system and secretion system proteins and the genes of plant-associated bacteria was over 60%. This may indicate that green algae are the main target for invasion. Detection of the urease synthesis genes in the genomes of lichen bacteriobionts suggested the hypothesis that urea decomposition results in an additional supply of ammonium and bicarbonate to the symbiosis. The latter may potentially be utilized by phototrophic eukaryotes and prokaryotes as an additional carbon source. Analysis of the genomes of lichen bacteriobionts L. ramalinae and L. minor revealed the possible differences in their survival strategies, with L. ramalinae more integrated into the symbiosis, while L. minor is characterized by more autonomous features.

Modern microbialites formed in soda-saline and soda lakes are of interest as model systems for studying geobiological interactions in the Precambrian, when such geochemical settings were widespread. This work describes the structure and mineral composition of microbialites from the soda-saline Laguna de Los Cisnes (Isla Grande, Tierra del Fuego, Chile), and also characterizes the biodiversity of microorganisms involved in their formation. The microbialites consist mainly of carbonate minerals, of which monohydrocalcite is of particular interest. It was shown that the formation of microbialites occurs under alkaline conditions in the presence of taxonomically and functionally diverse microorganisms and in direct contact with exopolysaccharides produced by the microbial community.

According to 16S rRNA gene- or genome-based phylogeny, magnetotactic bacteria (MTB) belong to diverse taxonomic groups. Here we analyzed the diversity of MTB in a sample taken from the freshwater lake Beloe Bordukovskoe near Moscow, Russia, by using molecular identification based on sequencing of the 16S rRNA gene and mamK , a specific marker gene for these bacteria. A protein encoded by the mamK gene is involved in magnetosome chain arrangement inside the cell. As a result, six operational taxonomic units (OTUs) of MTB were identified. Among them, OTUs affiliated with the phylum Nitrospirae were predominant. ‘ Ca . Etaproteobacteria’ and Alphaproteobacteria represented the minor groups of MTB. We also identified a novel MTB belonging to the family Syntrophaceae of the Deltaproteobacteria class. Using a combination of fluorescence and transmission electron microscopy, the bacteria belonging to these new MTB groups were visualized. Electron microscopy revealed that Syntrophaceae MTB were rod-shaped and synthesized elongated magnetosomes, arranged as a disorganized cluster. Among the Nitrospirae group, two groups with vibrioid cell shape and one group of ovoid-shaped bacteria were identified, all of which had elongated magnetosome crystals consisting of magnetite.

Clone libraries and morphological analysis were used to investigate cyanobacterial diversity in the cyanobacterial mat and dry crust at the bottom of the shallow, saline, alkaline Lake Khilganta (Southern Siberia, Russia). Filamentous cyanobacteria belonging to Phormidium genus and Coleofasciculus chthonoplastes were found to predominate during the dry period (2006) and the wet periods (1995 and 2012), respectively. Community composition during the dry and wet periods differed significantly. While 11 operational taxonomic units of cyanobacteria were revealed, only 3 occurred during both dry and wet periods. Occurrence of cosmopolitan C. chthonoplastes, which is common in neutral saline environments, is not typical of a continental alkaline lake and may be explained by the similarity of the dominant ions composition in lake water and in seawater.

В активном иле полупромышленного биореактора, очищающего фильтрат сброженного осадка сточных вод Курьяновских очистных сооружений (г. Москва), выявлены и охарактеризованы по физиологическим, морфологическим и молекулярно-биологическим показателям представители нового вида бактерий, окисляющих аммоний нитритом в бескислородных условиях. Клетки бактерий овоидной формы, 0.5 ? 0.8 мкм, имеют внутриклеточные мембранные структуры, характерные для анаммокс-бактерий: анаммоксосому, парифоплазму, а также, в отличие от других анаммокс-бактерий, обширные внутриклеточные мембранные структуры, располагающиеся слоями параллельно цитоплазматической мембране, и никогда – в области анаммоксосомы. Клетки объединены в агрегаты диаметром 5–28 мкм, легко адгезируют к твердым поверхностям. Клетки морфологически лабильны – легко подвергаются плазмолизу, теряют содержимое. Время удвоения – 28 сут.; макс =0.025 сут-1; температурный оптимум роста 20–45°C, оптимум рН 8.0. По результатам филогенетического анализа последовательностей нуклеотидов генов, кодирующих 16S рРНК, бактерия отнесена к новому виду рода-кандидата Jettenia, принадлежащего к порядку Planctomycetales. Для новой бактерии предложено название Candidatus “Jettenia moscovienalis” sp. nov.

A new species of bacteria oxidizing ammonium with nitrite under anoxic conditions was isolated from the activated sludge of a semi-industrial bioreactor treating digested sludge of the Kuryanovo wastewater treatment plant (Moscow, Russia). Physiological, morphological, and molecular genetic characterization of the isolate was carried out. The cells were ovoid (∼0.5 × 0.8 μm), with the intracellular membrane structures characteristic of anammox bacteria (anammoxosome and paryphoplasm); unlike other anammox bacteria, it possessed extensive intracellular membrane structures located in layers parallel to the cytoplasmic membrane, but never close to the anammoxosome. The cells formed aggregates 5–28 μm in diameter and readily attached to solid surfaces. The cells were morphologically labile, easily plasmolyzed, and lost their content. Doubling time was 28 days, μmax = 0.025 day−1; optimal temperature and pH for growth were 20–45°C and 8.0, respectively. Phylogenetic analysis of the 16S rRNA gene sequences suggested its classification as a new species of the candidate genus Jettenia (order Planctomycetales). The name Candidatus “Jettenia moscovienalis” sp. nov. was proposed for the new bacterium.

Методом создания и анализа библиотек клонов гена 16S рРНК изучен видовой состав двух термотолерантных сообществ ацидофильных хемолитотрофных микроорганизмов (АХМ), выделенных из пульпы лабораторных реакторов, в которых проводились процессы окисления концентратов разных золотосодержащих руд. Первое сообщество сформировалось в процессе окисления пирит-арсенопиритного концентрата руды Кючусского месторождения. Клоны бактериального компонента первого сообщества принадлежали к родам Sulfobacillus и Leptospirillum. 32 клона Sulfobacillus были разделены на три группы: Sb. thermosulfidooxidans, Sb. benefaciens и Sb. thermotolerans. 33 клона Leptospirillum были близки к виду Leptospirillum ferriphilum. Все клоны архейного компонента соответствовали виду Ferroplasma acidiphilum. Микроорганизмы данного сообщества были использованы как инокулят для процесса биоокисления другого по составу минерального концентрата – пирротинсодержащего пирит-арсенопиритного концентрата руды Олимпиадинского месторождения, и состав сообщества, сформировавшегося в данном процессе был также исследован. Клоны бактериального компонента второго сообщества также принадлежали к родам Sulfobacillus и Leptospirillum. 14 клонов Sulfobacillus были разделены на две группы: Sb. thermosulfidooxidans (13 клонов) и Sb. thermotolerans (1 клон). 48 клонов рода Leptospirillum были близки к виду L. ferriphilum. Все клоны архейного компонента соответствовали виду F. acidiphilum. В процессе адаптации сообщества к новому окисляемому минеральному субстрату произошли изменения, как в его составе, так и в численном соотношении видов микроорганизмов.

Construction and analysis of the 16S rDNA clone libraries was used to investigate the species composition of two thermotolerant communities of acidophilic chemolithotrophic microorganisms (ACM) isolated from the pulp of laboratory reactors used for oxidation of different gold-containing ore concentrates. The first community was formed during oxidation of the pyrite-arsenopyrite ore concentrate from the Kyuchus deposit. The clones of the bacterial component of this community belonged to the genera Sulfobacillus (32 clones) and Leptospirillum (33 clones). The Sulfobacillus clones belonged to three groups: Sb. thermosulfidooxidans, Sb. benefaciens, and Sb. thermotolerans . All Leptospirillum clones were closely related to L. ferriphilum . All clones of the archaeal component belonged to Ferroplasma acidiphilum . The microorganisms of this community were used as inoculum for biooxidation of a different mineral concentrate, the pyrrhotite-containing pyrite-arsenopyrite ore concentrate from the Olympiadinskoe deposit, and the structure of the community formed in the process was investigated. The clones of the bacterial component of the second community also belonged to the genera Sulfobacillus (14 clones) and Leptospirillum (48 clones). The Sulfobacillus clones belonged to the species Sb. thermosulfidooxidans (13 clones) and Sb. thermotolerans (1 clone). All Leptospirillum clones were closely related to L. ferriphilum . All clones of the archaeal component belonged to Ferroplasma acidiphilum . During the adaptation of the community to a new oxidized mineral substrate, both the composition and the ratio of the constituent microbial species changed.

The genes encoding the key metabolic reactions are often used as functional markers for phylogenetic analysis and microbial ecology studies. The composition and structure of the genes encoding ribulose-1,5-bisphosphate carboxylase (RuBisCO) of various photoautotrophic bacteria, representatives of the order Chromatiales, including collection strains and the strains isolated from saline and soda lakes, were studied in detail. The green-like form I RuBisCO was detected in the majority of the studied strains. In some strains, the genes encoding both form I and form II RuBisCO were present, which has not been previously known for the representatives of this group of bacteria. Moreover, RuBisCO genes were used as functional markers to investigate the autotrophic microbial community inhabiting the upper horizons of bottom sediments of two saline soda lakes and two hypersaline neutral lakes of the Kulunda Steppe. In general, the diversity of autotrophic bacteria in the studied sediment horizons was low. In soda lakes, haloalkaliphilic cyanobacteria and sulfuroxidizing bacteria (SOB) of the genus Halorhodospira were predominant. In saline lakes, halophilic chemoautotrophic SOB Halothiobacillus and Thioalkalivibrio were found, as well as photoautotrophic bacteria of the genus Ectothiorhodosinus and cyanobacteria. Many phylotypes remained unidentified, which indicates the presence of groups of microorganisms with an unknown type of metabolism.

The species composition of the microbial association involved in industrial tank biooxidation of the concentrate of refractory pyrrhotite-containing pyrite-arsenopyrite gold-arsenic ore of the Olympiadinskoe deposit at 39°C was studied by cultural and molecular biological techniques. Pure microbial cultures were isolated, their physiological characteristics were investigated, and their taxonomic position was determined by 16S rRNA gene sequencing. The library of 16S rRNA gene clones obtained from the total DNA isolated from the biomass of the pulp of industrial reactors was analyzed. The diversity of microorganisms revealed by cultural techniques in the association of acidophilic chemolithotrophs (Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, Ferroplasma acidiphilum, Alicyclobacillus tolerans, and Acidiphilium cryptum) was higher than the diversity of the 16S rDNA clone library (At. ferrooxidans, L. ferriphilum, and F. acidiphilum). The combination of microbiological and molecular biological techniques for the investigation of the biodiversity in natural and anthropogenic microbial communities promotes detection of new phylogenetic microbial groups in these communities.