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).     

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.     

Seasonal variability in bacterial and fungal diversity and community composition of the near-surface atmosphere in coastal megacity

Bacteria and fungi are ubiquitous in the near-surface atmosphere where they may impact on the surrounding environment and human health, especially in coastal megacities. However, the diversity, composition, and seasonal variations of these airborne microbes remain limited. This study investigated the airborne microbes of the near-surface atmosphere in coastal megacity Qingdao over one year. It was found that the sample in summer displayed the highest bacterial and fungal diversity, while sample in winter exhibited the lowest bacterial and fungal diversity. Proteobacteria was the dominating bacteria, and Dothideomycetes was the most dominating fungi in the near-surface atmosphere, which took up 53–76 and 49–78% relative abundance, respectively. However, the bacterial diversity and community composition had significant seasonal variations. These data suggest that a complex set of environmental factors, including landscaping ratio, solar radiation temperature, and marine microorganisms, can affect the composition of airborne microbes in the near-surface atmosphere in coastal megacity. The analysis of the pathogenic microorganisms or opportunistic pathogenic microorganisms existed in the near-surface atmosphere revealed that the relative abundance of pathogenic microorganisms in autumn was the highest. The main pathogenic microorganisms or opportunistic pathogenic microorganisms were Acinetobacter baumannii (accounting for up to 9.93% relative abundance), Staphylococcus epidermidis (accounting for up to 11.26% relative abundance), Mycobacterium smegmatis (accounting for up to 3.68% relative abundance), Xanthomonas oryzae pv. oryzae (accounting for up to 5.36% relative abundance), which may be related to certain human or plant diseases in specific environments or at certain seasons. Therefore, the investigation of airborne microbial communities of near-surface atmosphere in coastal megacities is very important to both the understanding of airborne microbes and public health.     

Microbial communities and their ability to oxidize n-alkanes in the area of release of gas- and oil-containing fluids in Mid-Baikal (Cape Gorevoi Utes)

The microbial community in the area of oil seep in Mid-Baikal (Cape Gorevoi Utes) was studied. The number of microorganisms that oxidize normal hydrocarbons, petroleum, and easily accessible organic matter in the water mass of the lake, bottom sediments, and bitumen structures was studied in 2005?C2009. The high heterogeneity of the distribution of microorganisms associated with the deparaffination of oil in the areas of oil seeps was noted. The maximum concentrations of hydrocarbon-oxidizing microorganisms in the samples of bottom water above bitumen structures (up to 2200 ± 175 CFU/mL) and in bitumen structures themselves (up to 170 000 ± 13 000 CFU/g) were determined. A model experiment showed that in the conditions of low temperatures (4°C) the degradation of the fraction of oil n-alkanes by the natural microbial community reaches 90% over a period of 60 days.     

Description of the lake baikal microorganism communities growing on a steel plate and in the natural water surrounding this substratum

This article presents an analysis of the microbial community growing on a stainless steel plate. A sample from this plate has been tested for the rpoC gene. Dominant biofilm species (clones) were identified with the help of molecular cloning and nucleotide sequencing of a 16S rRNA gene fragment. The activities of planktonic microorganisms and biofilm microorganisms attached to the plate were compared. Seven of nineteen sequences (37%) were found to belong to the Sphingobacteria group. Analysis of 16S rRNA gene sequences cloned from natural biofilms sampled from Lake Baikal showed a great variety of microorganisms in the biofilm. The following taxonomic groups were revealed among them: sphingobacteria, α-proteobacteria, cyanobacteria, verrucomicrobia, bacilli, γ-proteobacteria, flavobacteria, and β-proteobacteria. This kind of analysis was done in Lake Baikal for the first time.     

模拟油藏条件下内源微生物群落空间分布规律

【背景】油藏内源微生物群落是开展内源微生物驱油技术的物质基础,由于油藏多孔介质取样技术难度大、成本高,实施内源微生物驱油后从注入端到产出端多孔介质中的内源微生物空间分布规律尚不明确。【目的】通过室内长岩心连续驱替实验模拟油藏内源微生物驱油过程,分析实施后不同空间位点油砂上吸附的内源微生物群落结构,揭示从注入端到产出端内源微生物群落的空间分布规律。【方法】借助高通量测序技术及荧光定量PCR技术解析不同空间位点油砂原位微生物群落信息。【结果】注入端到产出端不同空间位点生态环境的差异及菌属间的相互作用造成油藏内源微生物群落空间分布差异,存在明显的好氧、厌氧空间演替变化规律。岩心前端主要存在一些好氧类的产生物表面活性剂类微生物如假单胞菌属,岩心中部主要存在兼性和厌氧类的微生物如地芽孢杆菌、厌氧杆菌属,岩心末端主要分布严格厌氧类细菌和产甲烷古菌,厌氧类微生物代谢产生的H2、CO2和乙酸分子可以为产甲烷古菌提供代谢底物。【结论】通过室内物模油砂研究,首次明确了内源微生物群落在多孔介质中从注入端到产出端的空间分布规律,证实油藏内源微生物的好氧、厌氧空间接替分布规律,深化了对油藏内源微生物的认识。     

Comparative characterization of microbial communities in two regions of natural oil seepage in Lake Baikal

Microbial communities and hydrocarbon contents have been studied in two regions of natural oil seepage in Lake Baikal: (1) opposite the Bol’shaya Zelenovskaya River mouth (studied previously) and (2) near Cape Gorevoi Utes (discovered in 2005). The abundance of both heterotrophic and hydrocarbon-oxidizing microorganisms is significantly higher in water samples from the first region, where the oil is biologically degraded. In the surface soil layer at stations located in the immediate vicinity of oil seepage site, the abundance of n-alkane-oxidizing microorganisms reaches 2000 cells/ml, and that of oil-oxidizing microorganisms reaches 2600 cells/ml. In water samples from near Cape Gorevoi Utes, the abundance of these groups of microorganisms does not exceed 190 and 500 cells/ml, respectively.     

Microbial Biodiversity in the Water of Lake Baikal

An investigation of the microbial community of Lake Baikal by the methods of general and molecular microbiology showed that culturable bacterial strains are represented by various known genera. The lake water contains a great number of bacterial morphotypes, as revealed by electron microscopy, and a great diversity of nonculturable microorganisms belonging to different phylogenetic groups, as revealed by 16S rRNA gene fragment sequencing. The inference is made that the microbial community of Lake Baikal contains not only known species but also new bacterial species that are possibly endemic to the lake.     

Microbial biodiversity in the Lake Baikal water

The investigation of the microbial community of Lake Baikal by the methods of general and molecular microbiology showed that culturable bacterial strains were represented by various known genera. The lake water contains a great number of bacterial morphotypes, as revealed by electron microscopy, and a great diversity of nonculturable microorganisms belonging to different phylogenetic groups, as revealed by 16S rRNA gene fragment sequencing. The inference is made that the microbial community of Lake Baikal contains not only the known species but also new, possibly endemic to the lake, bacterial species.     

A transcriptome-wide assessment of differentially expressed genes among two highly divergent,yet sympatric,lineages of the freshwater Atyid shrimp, <Emphasis Type="Italic">Paratya australiensis</Emphasis>

The current study evaluated the possible toxic effects of the water-soluble fraction of crude oil on the general cellular stress-response mechanisms of two dominant representatives of Lake Baikal’s littoral community, the endemic amphipod species Eulimnogammarus verrucosus and E. cyaneus. The acute toxicity effects on the cellular stress-response mechanisms of amphipods were studied in the laboratory by exposing amphipods in water from Lake Baikal to addition of a water-soluble fraction of crude oil at concentrations considered safe for the aquatic environment. The present study found that even short-term exposure to a water-soluble fraction of crude oil at concentration of 50 µg/L, established as the threshold limit for fishery and aquaculture water reservoirs in the Russian Federation, directly affected the general stress-response markers HSP70 and lipid peroxidation and significantly changed the activity of antioxidant enzymes in both studied species. This result confirms the high sensitivity of Baikal endemics to crude oil. Thus, it also indicates that established standards and threshold limit values of oil concentrations estimated for ecological monitoring of general water reservoirs cannot be applied directly to the unique Lake Baikal ecosystem.     

Microdroplet-enabled highly parallel co-cultivation of microbial communities

Microbial interactions in natural microbiota are, in many cases, crucial for the sustenance of the communities, but the precise nature of these interactions remain largely unknown because of the inherent complexity and difficulties in laboratory cultivation. Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities. In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes. Using aqueous micro-droplets dispersed in a continuous oil phase, the device could readily encapsulate and co-cultivate subsets of a community. A large number of droplets, up to ～1,400 in a 10 mm × 5 mm chamber, were generated with a frequency of 500 droplets/sec. A synthetic model system consisting of cross-feeding E. coli mutants was used to mimic compositions of symbionts and other microbes in natural microbial communities. Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.     

Micro-ecological aspects of studies on the effect of antibacterial drugs on intestinal microflora

Possible characterization of intestinal microflora as an integral system after exposure to antibacterial drugs was studied. Microflora of the contents and mucosa of the jejunum and large intestine in control rats and in rats exposed to metronidazole was studied and numerical indicators characterizing ratios of dominating and accompanying microbial groups in the intestine biotope++ were developed. With this purpose the proportion of the microbial groups in the total quantity of the microbes of a microbiocenosis was determined by the data on microflora quantitative composition. On the basis of detected wide species variety of microorganisms potentially dominating by their biotope numerical limits of the norm were determined only for the microbial groups of the accompanying microflora. The total proportion of the accompanying microbial populations under the normal conditions and the detected measure of deviation (reverse, partial) from the ratio of the dominating and accompanying microorganisms peculiar of the given biotope++ in separate subjects promoted estimation of microbiocenoses of definite biotope of the intestine as a whole.     

采油微生物在微驱过程中的生长、运移及分布规律

[目的]深入了解现场微生物驱油机理、效果评价标准及影响因素.[方法]结合现场微生物驱油过程产出液的跟踪监测及室内物模实验对微生物在地层中的生长繁殖、运移及分布规律进行研究.[结果]结果表明,通过从水井注入的外源微生物在油藏中能够有效生长繁殖,而且注入的营养液也能够激活内源微生物,但由于地层渗透率及营养液浓度的影响,产出液菌浓要比注入菌浓低1-2个数量级;葡萄糖的快速降解以及地层对微生物的过滤及吸附作用使大量的微生物停留在近井地带,仅有部分微生物能够从生产井采出,而且其运移速度要比营养液慢.[结论]地层渗透率和产出液中营养物浓度是影响微生物数量及分布的两个关键因素,现场微生物驱油产出液中的菌浓一般很难达到106个/mL以上,该研究结果对微生物驱油技术的发展和应用具有重要意义.     

Generation time of pure cultures of heterotrophic microorganisms isolated from Lake Ba?kal]

Generation time was determined in pure cultures of heterotrophic microorganisms in the conditions similar to those of Baikal in June--July of 1972. Generation time was found to be 37+/-7, 16+/-2.5, 16+/-3.2, and 10+/-2.5 hours, respectively, when the cultures had been diluted with Baikal water in the following rations: 1 : 0,1 : 5,1 : 10, and 1 : 20. No differences in the growth rate were found among 11 cultures of heterotrophic microorganisms isolated from Baikal. Conditions limiting the microbial growth improve from the dilution of 1 : 0 to the dilution of 1 : 5. The mean time of generation is 27 hours for June--July. Generation time determined for pure cultures of heterotrophic microorganisms in the conditions similar to natural can be used to calculate production of the bacterial biomass for a definite period of the year.     

Biodiversity and Activity of the Microbial Community in the Kotelnikovsky Hot Springs (Lake Baikal)

Complex microbiological and chemical analyses of water and bacterial mats were performed in the Kotelnikovsky Hot Springs (Lake Baikal). Transmission electron microscopy demonstrated that short rods about 1.2–2 μm in diameter predominated in the natural microbial community. Scanning electron microscopy coupled with chemical analysis revealed a characteristic P peak in the bacteria-like mineral particles, which suggests their biogenic origin. Most strains of the thermophilic microorganisms were gram-positive spore-forming rods and can be assigned to the genus Bacillus. Assays for potential enzyme activity demonstrated that most of the strains tested were active at high temperature. The data obtained suggest high activity of the bacterial community in situ and its particular role in the functioning of the hydrothermal ecosystem. __________ Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 6, 2005, pp. 664–671. Original Russian Text Copyright ? 2005 by Bel'kova, Parfenova, Suslova, Ahn, Tazaki.     

Taxonomic composition of Lake Baikal bacterioneuston communities

The taxonomic composition of microbial communities of Lake Baikal surface microlayer was studied by pyrosequencing of the 16S rDNA amplicons. Statistically reliable differences were found between bacterioneuston of the shallow and deep-water stations. The shallow station community was characterized by higher diversity than the deep-water one. While bacterioneuston communities were shown to be less diverse than the water column communities, their diversity was comparable to that of other biofilm associations. Microbial communities of Lake Baikal surface microlayer were shown to be similar to those of the water column in the composition of predominant phyla, while differing considerably at the genus level. Bacterioneuston of Lake Baikal was comparable to microbial communities of the surface microlayer of other freshwater basins, although it was characterized by high abundance of the Alphaproteobacteria and Verrucomicrobia. High abundance of photoheterotrophs compared to the water column communities of other freshwater basins was another distinctive feature of Lake Baikal bacterioneuston. Our results showed the Lake Baikal surface microlayer to be a specific microbial community with low species diversity and relatively high abundance of photoheterotrophic microorganisms.     

黄土高原石油污染土壤微生物群落结构及其代谢特征

针对污染胁迫下土壤微生物群落变化和代谢变异等问题,基于平板稀释法和Biolog微平板分析方法,研究了陕北黄土高原石油污染土壤微生物群落结构、代谢特征及其功能多样性。结果表明,不同类群的土壤微生物对石油污染胁迫的响应不同,污染土壤细菌和真菌数量高出清洁土壤1个数量级,而污染土壤的放线菌数量极显著减少(P0.01);污染土壤和清洁土壤微生物对糖类和多聚物类碳源较易利用,污染土壤微生物总体上代谢碳源的种类和活性均低于清洁土壤。微生物群落主成分分析(PCA)表明,石油污染土壤和清洁土壤的微生物群落存在显著差异(P0.01),起分异作用的碳源主要为糖类,其次是羧酸类和氨基酸类;随着土壤石油含量增加,典型变量值变异(离散)增大,土壤微生物群落结构稳定性降低。微生物群落多样性分析表明,Shannon丰富度指数(H)、McIntosh均一度指数(U)和Simpson优势度指数(1/D)均达到极显著差异(P0.01),污染土壤微生物群落H和U低于清洁土壤,但是一定浓度的石油污染可以刺激土壤微生物群落中优势种群的生长,1/D增高。研究结果为陕北黄土高原石油污染区土壤微生物修复提供理论基础。     

A Mesocosm Study of the Changes in Marine Flagellate and Ciliate Communities in a Crude Oil Bioremediation Trial

Protozoan grazers play an important role in controlling the density of crude-oil degrading marine communities as has been evidenced in a number of microcosm experiments. However, small bioreactors contain a low initial titre of protozoa and the growth of hydrocarbon-depleting bacteria is accompanied by the fast depletion of mineral nutrients and oxygen, which makes microcosms rather unsuitable for simulating the sequence of events after the oil spill in natural seawater environment. In the present study, the population dynamics of marine protozoan community have been analysed in a 500 l mesocosm experiment involving bioaugmented oil booms that contained oil sorbents and slow-release fertilisers. A significant increase in numbers of marine flagellates and ciliates on biofilms of oil-degrading microbes was microscopically observed as early as 8 days after the start of the experiment, when protozoa exhibited a population density peak making up to 3,000 cells ml⁻¹. Further, the protozoan density varied throughout the experiment, but never dropped below 80 cells ml⁻¹. An 18S rRNA gene-based fingerprinting analysis revealed several changes within the eukaryotic community over the whole course of the experiment. Initial growth of flagellates and small ciliates was followed by a predominance of larger protozoa. According to microscopic observations and SSU rRNA molecular analyses, most predominant were the ciliates belonging to Euplotidae and Scuticociliatia. This is the first study to characterise the eukaryotic communities specifically in a large-scale oil bioremediation trial using both microscopy-based and several molecular techniques.