Microorganisms of Lake Baikal and Lake Nyasa as Indicators of Anthropogenic Influence: Prospects for Use in Biotechnology

Restriction endonucleases (RENs) were detected in 650 microbial strains isolated from water columns and bottom sediments of deep rift lakes, Baikal (Russia) and Nyasa (Southeastern Africa). They enzymes included unique (Fan I, Aca I, and Sse 91) and very rare (Bsi I, and Cci N I) species not typical of aquatic ecosystems. Water columns, deep cores, and bottom sediments of pure areas of the lakes contained no microorganisms with new RENs. Thus, the inshore areas of Lake Baikal, having been exposed to anthropogenic influences, may contain mutant bacterial strains expressing RENs that have not been described previously.     

Diversity of laboratory-reared prokaryotes in the bottom sediments of the Akademichesky Ridge,Lake Baikal

Microbial communities in the bottom sediments of the Akademichesky Ridge, Lake Baikal, were studied. The samples were taken by deep drilling BDP-96 (a 100-m core). Vertical distribution of the prokaryotes with different physiological characteristics was studied for the core. The phylogenetic analysis of the organotrophic laboratory-reared microorganisms revealed the clusterization of Baikal strains and species which have not been identified yet.     

Transformation of Organic Matter by a Microbial Community in Sediments of Lake Baikal under Experimental Thermobaric Conditions of Protocatagenesis

Early diagenesis of organic matter in bottom sediments of Lake Baikal is a focus of many geochemical studies, because it is one of the few sites of petroleum formation in a nonmarine environment. Although Baikal is a rift lake and considered one of the prospective fields for deep biosphere investigations, the transformation processes of organic matter by microbial communities from deep bottom sediments and likely entering of the microorganisms from deep sediments into the near-surface sediments were not previously studied in Lake Baikal. The natural microbial community from near-surface sediments of the cold methane seep Goloustnoe (Southern Baikal Basin) was incubated with methane and the diatom Synedra acus at 80°C and 49.5 atm to simulate catagenesis. The 11-month incubation yielded the enrichment culture of viable thermophilic microorganisms. Their presence in low-temperature sediment layers may be indicative of their migration through fault zones together with gas-bearing fluids. After culturing, molecular biological methods allowed for the detection of both widespread microorganisms and unique clones whose phylogenetic status is currently unknown. The sediment after the experiment showed the formation of polycyclic aromatic hydrocarbon, retene. Retene can be either a conifer or algal biomarker, thus, interpretation of paleoclimate data is tenuous.     

Genomic and phenotypic analyses of microorganisms isolated from the sediments of Lake Baikal

Genetic and biochemical methods and morphological examination were used to study microorganisms isolated from samples of deep drilling of the Lake Baikal bottom sediments. Based on blot hybridization patterns, the strains investigated were divided into several groups according to the degree of homology of their genomic DNA. Morphological, biochemical, and ultrastructural characteristics of bacterial strains are described, and their compliance with the genomic analysis data is demonstrated.     

Genomic and Phenotypic Analyses of Microorganisms Isolated from the Sediments of Lake Baikal

Genetic and biochemical methods and morphological examination were used to study microorganisms isolated from samples of deep drilling of the Lake Baikal bottom sediments. Based on blot hybridization patterns, the strains investigated were divided into several groups according to the degree of homology of their genomic DNA. Morphological, biochemical, and ultrastructural characteristics of bacterial strains are described, and their compliance with the genomic analysis data is demonstrated.     

Sediment formation in Lake Baikal

The following stages in the formation of sediments in Lake Baikal have been distinguished. In the Middle Miocene lacustrine deposits accumulated in the southern depression. In Early and Middle Pliocene, as well as in Early-Middle Pleistocene the bottom of the southern and middle Baikal depressions was occupied by large lakes, but the northern basin was mainly dry with a system of small lakes, streams and rivers. This accounts for the great facies variety and the genetic heterogeneity of sediments in the northern depression. At the end of Middle and in the Late Pleistocene an abrupt warping of the depression took place, and a shore-line similar to the present one was formed. Sands in the upper part of the sediments are considered to be the product of intensive erosion which probably occurred in the pluvial epoch in the Late Pleistocene period.     

The biodiversity of actinomycetes in Lake Baikal

The taxonomic analysis of 107 actinomycete strains isolated from the bottom sediments and water of Lake Baikal showed that most of the water isolates belong to the genus Streptomyces and most of the sediment isolates belong to the genus Micromonospora. In the sediments, the number of actinomycetes increased with depth (down to 200 m). Eight Streptomyces isolates were identified to a species level.     

The Biodiversity of Actinomycetes in Lake Baikal

The taxonomic analysis of 107 actinomycete strains isolated from the bottom sediments and water of Lake Baikal showed that most of the water isolates belong to the genus Streptomyces and most of the sediment isolates belong to the genus Micromonospora. In the sediments, the number of actinomycetes increased with depth (down to 200 m). Eight Streptomyces isolates were identified to a species level.     

Oxygen concentration profiles in sediments of two ancient lakes: Lake Baikal (Siberia,Russia) and Lake Malawi (East Africa)

Oxygen concentration profiles have been measured, by means of with microelectrodes in sediments of Lake Baikal and Lake Malawi, along transects allowing to give a survey of two major ancient Rift lakes: Lake Baikal (Eastern Siberia) and Lake Malawi (East Africa), along depth transects in the constitutive basins of the lakes and/or of relevant depths with regard to oxygen (including including the deepest point, 1680 m, in Lake Baikal). Sediment oxygen penetration depths (SOPs) display very different patterns, depending on the lake in the two lakes. In Lake Baikal, SOPs are variable, show no significant relationship with bathymetric depth and are surprisingly deep on Akademichesky ridge (> 50.0 mm), emphasizing the distinctive feature of this region in the lake. While the Selenga river is an important source of eutrophication, the similarity of SOP-values in the Selenga shallow with those of most other sites suggests either a dilution of organic material by allochthonous matter, or a strong south-to-north transport of particles. In Lake Malawi, available oxygen is restricted to a maximum of three millimetres of the sediment, and there is a negative relationship with bathymetric depth, as a result of a steady decline of oxygen concentration with depth through the water column. Amongst the few parameters known to affect SOPs, the oxygen consumption by the sediment seems the most significant in both lakes. SOP-values furthermore confirm differences in the trophic status of Baikal and Malawi, respectively. The importance of oxygen as a factor likely to create ecological segregation for benthic organisms is discussed. Lake Malawi offers possibilities of bathymetric segregation but no vertical segregation in the sediment. In contrast, no bathymetric segregation related to oxygen is possible in Lake Baikal, but vertical segregation in the sediment is very likely. This revised version was published online in July 2006 with corrections to the Cover Date.     

Distribution of iron- and manganese-oxidizing bacteria in the bottom sediments of Lake Baikal

The specific features of the distribution, abundance, and taxonomic diversity of bacteria oxidizing iron and manganese in the bottom sediments sampled from different areas of Lake Baikal are studied. These bacteria are widespread in Baikal bottom sediments. Cultivated iron- and manganese-oxidizing microorganisms are ascribed to six genera: Metallogenium, Leptothrix, Siderocapsa, Naumaniella, Bacillus, and Pseudomonas. The surface layers of the ground and the border between oxidized and reduced sediments serve as ecological niches for iron- and manganese-oxidizing microorganisms. Redox conditions of the environment and the availability of dissolved forms of iron and manganese, as well as of organic matter, which are controlled by the conditions of sedimentation in the lake, are the main factors affecting the abundance and distribution of iron bacteria.     

Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments

Methane (CH₄) emitted from high-latitude lakes accounts for 2–6% of the global atmospheric CH₄ budget. Methanotrophs in lake sediments and water columns mitigate the amount of CH₄ that enters the atmosphere, yet their identity and activity in arctic and subarctic lakes are poorly understood. We used stable isotope probing (SIP), quantitative PCR (Q-PCR), pyrosequencing and enrichment cultures to determine the identity and diversity of active aerobic methanotrophs in the water columns and sediments (0–25 cm) from an arctic tundra lake (Lake Qalluuraq) on the north slope of Alaska and a subarctic taiga lake (Lake Killarney) in Alaska''s interior. The water column CH₄ oxidation potential for these shallow (∼2 m deep) lakes was greatest in hypoxic bottom water from the subarctic lake. The type II methanotroph, Methylocystis, was prevalent in enrichment cultures of planktonic methanotrophs from the water columns. In the sediments, type I methanotrophs (Methylobacter, Methylosoma and Methylomonas) at the sediment-water interface (0–1 cm) were most active in assimilating CH₄, whereas the type I methanotroph Methylobacter and/or type II methanotroph Methylocystis contributed substantially to carbon acquisition in the deeper (15–20 cm) sediments. In addition to methanotrophs, an unexpectedly high abundance of methylotrophs also actively utilized CH₄-derived carbon. This study provides new insight into the identity and activity of methanotrophs in the sediments and water from high-latitude lakes.     

Isolation of total bacterial DNA for ecological characterization of bottom sediments of Lake Baikal

It is known that the conventional microbiological methods of investigation reveal not more than 1% of the species of microorganisms actually inhabiting one biotope or another. The most complete characterization of the microbial community is achieved by investigating DNA isolated from the samples differing from each other in ecological conditions. The sediments of Lake Baikal are characterized by a high content of humic compounds which hinders molecular biological analyses. Because of this, the procedure of DNA isolation is a step o critical importance for the analysis of bottom sediments. In the present work we compare the methods of isolation of the whole bacterial DNA from the bottom sediments of Lake Baikal. The most efficient method allowing us to obtained DNA preparations for further molecular investigation was chosen.     

A method for cultivation of microorganisms oxidizing iron and manganese in bottom sediments of Lake Baikal

Methods for cultivation of microorganisms oxidizing iron and manganese in bottom sediments of Lake Baikal were tested. Bacteria were grown on selective media with a characteristic accumulation of metal oxides. The morphology and developmental patterns of the isolated microbial group were studied. The studied sediment core was used to isolate 42 strains of bacteria oxidizing iron and manganese. The cultivated bacteria were confined to the upper sediment layers (down to 11 cm) and their abundance depended on sediment type and redox conditions.     

Microorganisms in the Sediments of Lake Baikal,the Deepest and Oldest Lake in the World

Microbiology - The review summarizes the results of recent studies of microbial communities of the Lake Baikal sediments obtained using diverse techniques. In the sediments of the areas of stable...     

Study on the Lake Baikal microbial community in the areas of the natural oil seeps

We studied the composition of a natural microbial community, the distribution of different groups of microorganisms (including those able to degrade oil hydrocarbons) within the areas of natural oil seeps in the Lake Baikal. It was revealed that, in the bottom sediments, the oil-degrading microorganisms dominating the community have included the bacteria of g. Bacillus, while in the water column, dominating microbes are presented by species of genera Rhodococcus Pseudomonas, and Micrococcus. Under the conditions of the model experiment, the potential activity of Baikal microbes towards utilization of n-alcanes has been assessed. Under such conditions it was shown that the concentration of n-alcanes decreases to 60% during 20 days of the experiment (the initial oil concentration was 0.5 mg/l, i.e., ten maximal permissible concentrations, MPC).     

Depleted methane-derived carbon in waters of Lake Baikal,Siberia

Results of hydrochemical and stable isotope measurements during the ice-breaking period on Lake Baikal indicate an apparent lack of relationship between measured δ¹³C of dissolved inorganic carbon (DIC) and phytoplankton below the trophogenic layer. While planktonic values of −31.7 to −33.5‰ are within a typical lacustrine range, the δ¹³C values of DIC turned out to be very negative, from −28.9 to −35.6‰. These isotopic values of DIC appear to be associated with oxidation of methane that accumulated during winter ice cover period. At the time of sampling, however, the observed depletion did not affect the phytoplankton/DIC fractionation relationship, because the difference between phytoplankton and DIC (−20 to −22‰ in surface waters) lies within the expected range of the fractionation coefficient. By analogy with small lakes, we explain this lack of relationship by the time lag between peak productivity and peak methane oxidation. Our interpretation of the Baikal DIC isotopic signature is consistent with methanogenesis in bottom sediments and with the known presence of widespread unstable gas hydrates and active methane seeps on the lake floor. Our findings suggest that methane is an important component of the Baikal carbon cycle, that late winter concentrations of methane in Baikal under ice may be 3–4 orders of magnitude higher than previously reported values for summer, and that the lake may be emitting a significant amount of methane to the atmosphere.     

Study on the Lake Baikal microbial community in the areas of the natural oil seeps

We studied the composition of a natural microbial community, the distribution of different groups of microorganisms (including those able to degrade oil hydrocarbons) within the areas of natural oil seeps in the Lake Baikal. It was revealed that, in the bottom sediments, the oil-degrading microorganisms dominating the community have included the bacteria of g. Bacillus, while in the water column, dominating microbes are presented by species of genera Rhodococcus, Pseudomonas, and Micrococcus. Under the conditions of the model experiment, the potential activity of Baikal microbes towards utilization of n-alcanes has been assessed. Under such conditions it was shown that the concentration of n-alcanes decreases to 60% during 20 days of the experiment (the initial oil concentration was 0.5 mg/l, i.e., ten maximal permissible concentrations, MPC).     

Microbial decomposition of organic matter in the bottom sediments of small lakes of the urban landscape (Lithuania)

Bacterial abundance and the rates of sulfate reduction (SR) and total organic matter decomposition (D_total) were studied in the bottom sediments of nine lakes in the vicinity of Vilnius (Lithuania) during the ice-free seasons of 2006–2009. During the spring mixing of the water, aerobic processes of organic matter decomposition prevailed in the bottom sediments of most lakes, while anaerobic processes predominated (up to 80–90% D_total) in summer and early autumn. SR rates in the bottom sediments made up 0.16–2.6 and 0.09–2.0 mg S^2?/(dm³ day) for the medium-depth and shallow lakes, respectively. The highest numbers of sulfate-reducing bacteria (up to 10⁶ cells/cm³) and SR rates were observed in summer. SR rate in mediumdepth lakes increased with development of anaerobic conditions at the bottom and elevated sulfate concentrations (up to 96.0 mg/dm³). In shallow lakes, where O₂ concentration at the bottom was at least 6.7 mg/L, SR rates increased with temperature and inflow of fresh organic matter, especially during cyanobacterial blooms. The average SR rates in the bottom sediments of the lakes of urbanized areas were 4 times higher than in the shallow lakes of protected areas. Accumulation of organic matter and its intensive decomposition during summer may enhance the processes of secondary eutrophication of these small and shallow lakes.     

Application of ribulose-1,5-bisphosphate carboxylase/oxygenase genes as molecular markers for assessment of the diversity of autotrophic microbial communities inhabiting the upper sediment horizons of the saline and soda lakes of the Kulunda Steppe

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.     

Comparative aspects of adaptive radiation and speciation in Lake Baikal and the great rift lakes of Africa

Lakes Baikal, Tanganyika and Malawi have similar origins, are physiographically similar, and of similar size. The hydrological regime of Baikal is, however, very different from that which prevails in its African sisters. Apart from being much cooler, it differs fundamentally in being oxygenated to all depths while the two great African rift lakes possess only a relatively thin oxygenated surface layer and have vast oxygenless, and therefore azoic, abyssal regions. Nevertheless, like Baikal, they have rich endemic faunas.That these faunas originated largely by intralacustrine speciation and not by multiple invasion is now well established. They provide some of the world's most spectacular examples of species flocks, and some groups display what has been aptly described as explosive speciation. Certain features, and especially the adaptive radiation, of some of the groups involved, are noted. Comparisons between lakes are illuminating. Some species flocks, such as those of amphipods, sponges and turbellarians of Baikal and the atyid prawns and potamid crabs of Tanganyika, have no counterparts in the other lakes. Other groups, such as the prosobranch gastropods, ostracods and harpacticoid copepods of Baikal and Tanganyika, and the fishes of all three, involve representatives of the same major group, though often of different families or even higher taxonomic categories.That allopatric speciation has been involved is universally acknowledged but the problems posed by species multiplication in deep water in L. Baikal have led to suggestions that sympatric speciation could have played a part. Notwithstanding the difficulties, it is suggested that the process can be explained without invoking the assistance of the sympatric model.The faunas of these lakes provide immense fields for investigation and enormous intellectual challenges. While each is an entity in itself, comparative studies may be particularly enlightening.The substance of this paper was presented as a lecture at the First International Baikal Vereshchagin Conference held in Listvyanka, Irkutsk Region, U.S.S.R. in October 1989.