Ha.lo.na.tro'num. Gr. n. hals, halos salt; Ar. n. natron soda; N.L. neut. n. Halonatronum an organism growing with salt and soda. Firmicutes / “Clostridia” / Halanaerobiales / Halobacteroidaceae / Halonatronum Cells are rod‐shaped , flexible , and motile by peritrichous flagella . The cell wall has a Gram‐stain‐negative structure . Strictly anaerobic . Chemo‐organotrophic with fermentative metabolism. Carbohydrates, including soluble polysaccharides, are fermented to acetate, ethanol, formate, H 2 , and CO 2 . Halophilic and alkaliphilic . Endospores produced . DNA G + C content ( mol %): 34.4 ( T m ). Type species : Halonatronum saccharophilum Zhilina, Garnova, Tourova, Kostrikina and Zavarzin 2001a, 263 VP (Effective publication: Zhilina, Garnova, Tourova, Kostrikina and Zavarzin 2001b, 71.).

Humic substances and their organic-mineral compounds are the first stage in transformation of biotic residues into stable geopolymers, which comprise the main reservoir of organic C in the biosphere. Early appearance of HS in the Earth’s history is of principal importance for the understanding of geo-biological processes on land in the past. However, there is no fossil record of HS before land colonization by lignified vegetation (400 Ma). When the first soil HS were formed? Could HS be synthesized in the Precambrian before plants and mosses terrestrialization? The formation of HS occurs in mesophilic aerobic conditions and requires presence of oxidative catalysts and production of aromatic (phenolic) precursors by biota. In this paper, humification processes in algo-myco-bacterial and lichen communities are discussed from actualistic point of view. These communities are considered as a relict ecosystem, which could dominate on land during the Neoproterozoic-Early Paleozoic (1–0.5 Ga).

In the course of an investigation of alkaliphilic iron reduction, metabiotic interactions in a binary culture reducing synthetic ferrihydrite (SF) have been studied. The binary culture contained two anaerobic bacteria: the alkaliphilic organotrophic bacillus Anaerobacillus alkalilacustris , which ferments sugars and sugar alcohols and is incapable of iron reduction, and the dissimilatory iron-reducing bacterium Geoalkalibacter ferrihydriticus , which is able to grow on acetate at the expense of anaerobic respiration. The experiments were performed under conditions of SF excess and deficiency. It was expected that G. ferrihydriticus would oxidize the acetate formed in the course of mannitol fermentation by A. alkalilacustris . The results were different from the expected ones: in the binary culture, fermentation products other than acetate were used for iron reduction; these were primarily formate and ethanol, which led to acetate accumulation rather than consumption. The reduction of SF to magnetite and/or siderite followed the earlier established regularities. The preferential order of donor utilization by G. ferrihydriticus did not conform to the energy yields of the corresponding reactions. Thus, it has been shown that there may be interactions in microbial communities that cannot be predicted from the characteristics of pure cultures. The degradation pathways of organic matter in communities may differ considerably from those observed in pure cultures, even in pure cultures of highly specialized organisms.

Fluorescent in situ hybridization (FISH) with rRNA-specific oligonucleotide probes was used to assess the numbers and phylogenetic diversity of prokaryotic microorganisms in the water of small boreal lakes and peatland catchments of the swampy upper Volga basin. The abundance of bacterioplankton in lake water was found to vary from 1.6 to 8.7 × 10 6 cells ml −1 , with the highest values detected in neutral eutrophic lakes. The total cell numbers in the peat of ombrotrophic bogs were 3.9–4.3 × 10 8 cells g −1 of wet peat. The proportion of bacteria identified by the group-specific probes decreased from 79–85% in neutral (pH 6.6–6.9) mesotrophic and eutrophic lakes to 65–69% in acidic (pH 4.4–5.5) dystrophic lakes and to 51–58% in the peat of acidic (pH 3.6–3.9) ombrotrophic bogs. The diversity of bacterial communities was highest in lakes with neutral water. These communities were dominated by members of the phylum Actinobacteria (31–44% of the total bacterial number), while the contribution of Alphaproteobacteria (16–19%), Bacteroidetes (6–16%), Betaproteobacteria (6–7%), Planctomycetes (2–8%), and Gammaproteobacteria (4–5%) was also significant. In acidic dystrophic lakes, Actinobacteria (25–35%) and Betaproteobacteria (25–34%) predominated, while peatland catchments were dominated by the Alphaproteobacteria (20–23%). The presence of acidobacteria and some planctomycetes common for bogs in the water of acidic dystrophic lakes, as well as the high proportion of bacteria (31–49%) that were not identified by the group-specific probes, suggest the impact of microbial processes in peatland catchments on the microbial composition of the receiving waters.

The origin of life belongs to urgent worldview problems; it has been in the limelight since time immemorial, pressing for an answer all through the evolution of knowledge and getting a different interpretation at each stage largely under the prevailing worldview. In recent years, Russian scientists tried to summarize up-to-date information concerning primarily the life origin problem in three collective monographs: Biosphere Origin and Evolution (2008), Biosphere Origin and Evolution Problems (2008), and Life Origin Problems (2009). These monographs served as the subject matter for a critical analysis in the article below of the most general ideas about the early evolution of geospheric and biological systems.

Theories attempting to explain the origin of life on Earth should be based on the assumption that habitability precedes habitation. The hypotheses of the first organism should be based on the evaluation of its possible life-supporting ecosystem. The ecosystem should necessarily include primary autotrophic producers, and hydrogenotrophy appears to be an adequate physiological type for primitive ecosystems. Consideration of life on Earth should differentiate between the origin of organisms in situ and the transportation of organisms from outside with cosmic bodies in the framework of life as a widespread phenomenon of the Universe. In the case of transport of life with cosmic bodies, there are no limitations on the transfer of a community rather than an individual cell. In the case of the transport of the community with a large piece of “dirty ice,” the problem lies in the correspondence between the community and its ecosystem on the parent body and the conditions on the primeval Earth rather than functional divergence from a primary ancestor. Subsequent events are within the framework of paleontologically observed evolution and can be described as biogeochemical succession without any additional speculations.

An aerobic gram-negative bacterial strain Z-0532 with ring-shaped cells forming spirals in the course of growth was isolated from the humified solution produced by spruce wood decomposition. The new isolate was a chemoorganotrophic, mesophilic, moderately acidophilic organism with the temperature range of 6–32°C (optimum at 25–28°C) and pH range from 4.7 to 7.2 (optimum at pH 5.5–6.5). A broad range of substrates was used as carbon and energy sources, including sugars, some organic acids and polyalcohols, and soluble polymeric compounds (gelatin, esculin, starch, xylan, laminarin, dextrin, casein hydrolysate, and Tween-40). According to its physiological and biochemical characteristics, strain Z-0532 is a typical member of the trophic group of oligotrophic bacteria, which utilize the products of wood hydrolysis dissipated by xylotrophic microorganisms. The G+C base content of strain Z-0532 was 52.1 mol %. Sequencing of the 16S rRNA gene of the new isolate revealed 98% similarity to Larkinella insperata LMG 22510T, which is a recently described species of the family Spirosomaceae of the phylum Bacteroidetes. The level of DNA: DNA homology between this species and strain Z-0532 was only 40%. The differences in the phenotypic and genotypic characteristics suggested classification of the isolate obtained from decomposing wood as a new species of the genus Larkinella, Larkinella arboricola sp. nov., with the type strain Z-0532T (=VKM B-2528T = DSM 21851T).

The microbial communities developing in ultrafresh stagnant water originating from rainfall comprise the group of ombrophiles. The microorganisms of the myco-bacterial community developing on coarse woody debris are involved in formation of humus-enriched dystrophic waters in the watersheds of forested wetlands. Oligotrophic acidophilic dissipotrophs participate in the transformation of organic matter in such waters. The scheme of trophic interactions in the microbial community is proposed.

Sequential stages of formation of an ombrophilic cyano-bacterial community on clay were determined in a laboratory model of a puddle community. In a suspension of washed clay obtained from loamy soil, with montmorillonite as the predominant phase, a bacterial neustonic film is initially formed; it acts as a support for cyanobacterial hormogonia. At the next stage, the upper layer of precipitated clay (about 1 mm) is reinforced by a cyano-bacterial structure of Phormidium sp. trichomes and develops a tissue-like structure. The hormogonia and sheathless cyanobacteria remain free from mineral particles. Subsequently, gas formation results in a separation of a dense cyano-bacterial film from the underlying loose suspension and in formation of gas swellings. The mineral component of the film is differentiated: mineral particles of quartz and feldspar grains are attached to Phormidium sp. trichomes, which act as a factor of mineral selection.

Communities of bacteria, the first inhabitants and creators of the earth’s biosphere, are distributed on the geographical surface of our planet according to opportunities opened by the abiotic environment. In relation to bacteria, the geosphere is primary, but bacteria change it. Which features of the geographical surface made the earth accessible for bacteria and what changes introduced by bacteria turned this surface into the biosphere? The author looks for answers to these questions.

Soda lakes are characterized by an intense sulfur cycle that begins with sulfidogenesis. Model laboratory experiments that involved combining of pure cultures showed that, during anaerobic decomposition of cellulose by Clostridium alkalicellulosi , the sulfate-reducing bacteria (SRB) of the species Desulfonatronovibrio hydrogenovorans, Desulfonatronum lacustre , and Desulfonatronum cooperativum , different in their nutritional requirements, may directly use the cellulose fermentation products for sulfidogenesis without mediatory microorganisms. In binary cocultures with SRB, the amount of the H 2 S formed constituted from one-third to two-thirds of the cellulose [H] equivalents; acetate was among the products formed. When the syntrophic Contubernalis alkalaceticum , capable of acetate oxidation, was incorporated into the trophic chain along with hydrogenotrophic SRB, the amount of the H 2 S formed exceeded by 33–42% the amount of the [H] equivalents in the utilized cellulose, water being the source of additional hydrogen. Thus, the trophic pathway from plant residues to sulfide, previously considered to be the longest in the alkaliphilic microbial community, may involve a minimal number of stages and do without intermediate participation of dissipotrophic fermenting organisms.

Strain Z-M001 of a unicellular cyanobacterium, assigned by analysis of the 16S rRNA gene sequence to the phylogenetic group of the generic level Euhalothece, was isolated from soda Lake Magadi. It was shown that strain Z-M001, unlike all other known cultured and uncultured organisms of the Euhalothece group, is extremely natronophilic, and it was named accordingly "Euhalothece natronophila". In its ecophysiological characteristics, it is comparable to extremely alkaliphilic organotrophic natronobacteria, which is essential for soda ecosystems, because cyanobacteria belong to primary producers. "E. natronophila" exhibits considerable morphological variability depending on the concentration of carbonates in the medium. The polymorphism of "E. natronophila" is primarily connected to limitation by utilizable forms of carbon.

The effect of carbonate concentration, pH of the medium, and illumination intensity on the major physiological characteristics (growth rate and the intensities of CO 2 assimilation and oxygen photoproduction) of the natronophilic cyanobacterium Euhalothece sp. Z-M001 have been studied. It was established that the investigated microorganism has at least two transport systems (TS) for CO 2 , which differ in both the pH optimum and substrate affinity: TS I has a pH opt 9.4–9.5 and a K S 0.5 of 13–17 mM, whereas TS II has a pH opt 9.9–10.2 and a K S 0.5 of 600–800 mM. The substrate affinity of these transport systems is several orders of magnitude lower than the substrate affinity of the transport systems of freshwater cyanobacteria. It is suggested that they are unique for extremely alkaliphilic cyanobacteria and reflect their adaptation to the seasonal cycles of the lake hydrochemistry.

Для содовых озер характерен интенсивный серный цикл, который начинается сульфидогенезом. В лабораторных модельных экспериментах путем комбинирования чистых культур алкалофильных микроорганизмов показано, что при анаэробном разложении целлюлозы Clostridium alkalicellulosi возможно прямое, без посредников, использование продуктов брожения целлюлозы на сульфидогенез сульфатредуцирующими бактериями (СРБ) видов Desulfonatronovibrio hydrogenovorans, Desul-fonatronum lacustre, Desulfonatronum cooperativum, различающихся пищевыми потребностями. В бинарных комбинациях с СРБ количество образованного H2S составило 1/3–2/3 эквивалентов [H] целлюлозы, а в составе продуктов оставался ацетат. При включении в трофическую цепь синтрофного Contubernalis alkalaceticum, способного к окислению ацетата в паре с гидрогенотрофными СРБ, количество образованного H2S на 33–42% превышало эквиваленты [H] использованной целлюлозы. Источником дополнительного водорода могла служить вода. Таким образом, наиболее длинный для алкалофильного микробного сообщества трофический маршрут от растительных остатков до сульфида может осуществляться в минимальное число этапов без промежуточного участия бродильщиков-диссипотрофов.

Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 × 107 cells ml−1. About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Planctomycetes. The population sizes of the Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of the Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of the Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.

The life philosophy aspects of natural sciences are discussed. The key role of prokaryotes in the origin, development, and existence of the biosphere is considered. It helps to understand how the penetration in the world of prokaryotes changes our notions of the place of biology in natural sciences.