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Роль микробных сообществ в водных экосистемах

Журнальные статьи

1.U32980
Aquilina A.,Knab N.J. et al. BIOMARKER INDICATORS FOR ANAEROBIC OXIDIZERS OF METHANE IN BRACKISH-MARINE SEDIMENTS WITH DIFFUSIVE //Organic Geochemistry(GBR). 2010 г., т. 41, N 4. P.414-426.

2.U45336
Belila, Abdelaziz; Abbas, Ben; Fazaa, Imed et al. Sulfur bacteria in wastewater stabilization ponds periodically affected by the 'red-water' phenomenon //APPLIED MICROBIOLOGY AND BIOTECHNOLOGY .– 2013.Vol. 97. Iss.1. Pag. 379-394.

. Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the 'red-water' phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menzeh WSP and focused in particular on the different functional groups of sulfur bacteria. For this purpose, we used denaturing gradient gel electrophoresis of PCR-amplified fragments of the 16S rRNA gene and of different functional genes involved in microbial sulfur metabolism (dsrB, aprA, and pufM). Analyses of the 16S rRNA revealed a relatively high microbial diversity where Proteobacteria, Chlorobi, Bacteroidetes, and Cyanobacteria constitute the major bacterial groups. The dsrB and aprA gene analysis revealed the presence of deltaproteobacterial sulfate-reducing bacteria (i.e., Desulfobacter and Desulfobulbus), while the analysis of 16S rRNA, aprA, and pufM genes assigned the sulfur-oxidizing bacteria community to the photosynthetic representatives belonging to the Chlorobi (green sulfur bacteria) and the Proteobacteria (purple sulfur and non sulfur bacteria) phyla. These results point on the diversity of the metabolic processes within this wastewater plant and/or the availability of sulfate and diverse electron donors

3.U08182
Cangemi M.,Leonardo R.D.et al. GEOCHEMISTRY AND MINERALOGY OF SEDIMENTS AND AUTHIGENIC CARBONATES FROM THE MALTA PLATEAU, STRAIT OF //Chemical Geology(NLD). 2010 г., т. 276, N 3.P.294-308.

4.U47100
Clara Ruiz-Gonzales et al. EFFECTS OF LARGE RIVER DAM REGULATION ON BACTERIOPLANKTON COMMUNITY STRUCTURE //FEMS Microbiology Ecology(NLD). 2013 г., т. 84, N 2, P.316-331.

5.U03047
Erwin, Patrick M.; Pita, Lucia; Lopez-Legentil, Susanna et al. Stability of Sponge-Associated Bacteria over Large Seasonal Shifts in Temperature and Irradiance // APPLIED AND ENVIRONMENTAL MICROBIOLOGY .-2012, Volume: 78 Issue: 20 Pages: 7358-7368

Complex microbiomes reside in marine sponges and consist of diverse microbial taxa, including functional guilds that may contribute to host metabolism and coastal marine nutrient cycles. Our understanding of these symbiotic systems is based primarily on static accounts of sponge microbiota, while their temporal dynamics across seasonal cycles remain largely unknown. Here, we investigated temporal variation in bacterial symbionts of three sympatric sponges (Ircinia spp.) over 1.5 years in the northwestern (NW) Mediterranean Sea, using replicated terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of bacterial 16S rRNA gene sequences. Bacterial symbionts in Ircinia spp. exhibited host species-specific structure and remarkable stability throughout the monitoring period, despite large fluctuations in temperature and irradiance. In contrast, seawater bacteria exhibited clear seasonal shifts in community structure, indicating that different ecological constraints act on free-living and on symbiotic marine bacteria. Symbiont profiles were dominated by persistent, sponge-specific bacterial taxa, notably affiliated with phylogenetic lineages capable of photosynthesis, nitrite oxidation, and sulfate reduction. Variability in the sponge microbiota was restricted to rare symbionts and occurred most prominently in warmer seasons, coincident with elevated thermal regimes. Seasonal stability of the sponge microbiota supports the hypothesis of host-specific, stable associations between bacteria and sponges. Further, the core symbiont profiles revealed in this study provide an empirical baseline for diagnosing abnormal shifts in symbiont communities. Considering that these sponges have suffered recent, episodic mass mortalities related to thermal stresses, this study contributes to the development of model sponge-microbe symbioses for assessing the link between symbiont fluctuations and host health

6.U12332
Henrik Drake, Mats E. Astrom, Eva-Lena Tullborg, Martin Whitehouse, Anthony E. Fallick . Variability of sulphur isotope ratios in pyrite and dissolved sulphate in granitoid fractures down to 1 km depth – Evidence for widespread activity of sulphur reducing bacteria //Geochimica et Cosmochimica Acta, Volume 102, 1 February 2013, Pag.143-161

. Euhedral pyrite crystals in 46 open bedrock (granitoid) fractures at depths down to nearly 1 km were analysed for sulphur isotope ratios (?34S) by the in situ secondary ion mass spectrometry (SIMS) technique and by conventional bulk-grain analysis, and were compared with groundwater data. Twenty nine of the fractures sampled for pyrite had corresponding data for groundwater, including chemistry and isotopic ratios of sulphate, which provided a unique opportunity to compare the sulphur-isotopic ratios of pyrite and dissolved sulphate both at site and fracture-specific scales. Assessment of pyrite age and formation conditions were based on the geological evolution of the area (Laxemar, SE Sweden), and on data on co-genetic calcite as follows: (1) the isotopic ratios of the calcite crystals (?18O, ?13C, 87Sr/86Sr) were compared with previously defined isotopic features of fracture mineral assemblages precipitated during various geological periods, and (2) the ?18O of the calcites were compared with the ?18O of groundwater in fractures corresponding to those where the calcite/pyrite assemblages were sampled. Taken together, the data show that all the sampled fractures carried pyrite/calcite that are low-temperature and precipitated from the current groundwater or similar pre-existing groundwater, except at depths of ?300 to ?600 m where water with a glacial component dominates and the crystals are from pre-modern fluids. An age of <10 Ma are anticipated for the pre-modern fluids. The ?34Spyr showed huge variations across individual crystals (such as ?32 to +73‰) and extreme minimum (?50‰) and maximum (+91‰) values. For this kind of extreme S-isotopic variation at earth-surface conditions there is no other explanation than activity of sulphur reducing bacteria coupled with sulphate-limited conditions. Indeed, the most common subgrain feature was an increase in ?34Spyr values from interior to rim of the crystal, which we interpret are related to successively higher ?34S values of the dissolved source SO42? caused by ongoing bacterial sulphate reduction in fractures with low-flow or stagnant waters. The measured groundwater had ?34SSO4 values of +9‰ to +37‰, with the highest values associated with low sulphate concentrations. These values are overall, and especially in the sulphate-poor waters down to ?400 m, somewhat higher than the anticipated initial values, and can thus, like for the 34S-enriched pyrites, be explained by a Rayleigh distillation process driven by microbial sulphate reduction.

7.U03047
Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L.et al. Microbial Community Dynamics of an Urban Drinking Water Distribution System Subjected to Phases of Chloramination and Chlorination Treatments//APPLIED AND ENVIRONMENTAL MICROBIOLOGY.-2012, Volume: 78 Issue: 22 Pages: 7856-7865 .

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population congruent to 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations, Cyanobacteria, Methylobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae were more abundant in chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine

8.U15400
Hyun-Myung Oh. ,Linam Kang et al. COMPLETE GENOME SEQUENCE OF STRAIN HTCC2170, A NOVEL MEMBER OF THE GENUS MARIBACTER IN THE FAMILY FLAVOBACTERIACEAE //J.of Bacteriology.-2011,vol.193,№1, p.303-304.

Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution-to-extinction culturing. Here, we present the finished genome sequence of a marine bacterium, Maribacter sp. strain HTCC2170. Strain sp. HTCC2170 is predicted to be a facultatively aerobic chemoorganotroph that, based on genomic sequence analysis, is capable of macromolecule degradation and anaerobic respiration. Copyright © 2011, American Society for Microbiology. All Rights Reserved

9.U12332
Jaeschle A.,Rooks C. et al. COMPARISON OF LADDERANE PHOSPHOLIPID AND CORE LIPIDS AS INDICATORS FOR ANAEROBIC AMMONIUM OXIDATION //Geochimica et Cosmochimica Acta(GBR). 2009 г., т. 73, N 7. P.2077-2088.

10.U60726
Kadnikov V.V.,Lomakina A.V.et al. COMPOSITION OF THE MICROBIAL COMMUNITIES OF BITUMINOUS CONSTRUCTIONS AT NATURAL OIL SEEPS AT THE BOT //Microbiology (Mikrobiologiya)(DEU). 2013 г., т. 82, N 3. P.373-382.

11.U60726
Krevs A..Kucinskiene A. et al. MICROBIAL DECOMPOSITION OF ORGANIC MATTER IN THE BOTTOM SEDIMENTS OF SMALL LAKES OF THE URBAN LANDSC //Microbiology (Mikrobiologiya)(DEU). 2012 г., т. 81, N 4.P.477-483.

12.U11147
Lew, S., Lew, M., Biedunkiewicz, A. et al ANAEROBIC FE(II)-OXIDIZING BACTERIA SHOW AS RESISTANCE AND IMMOBILIZE AS DURING FE(III) MINERAL PRECIPITATION//Environmental Science and Technology. 2010. Т. 44. № 1. P.94-101.

More than 100 million individuals worldwide are exposed to arsenic-contaminated water, making the investigation of arsenic mobility in aquatic systems of utmost importance. Iron (hydr)oxides play a key role in preventing arsenic release in aquifers and soils due to their strong arsenic sorption and are even used to remove arsenic in water treatment. Neutrophilic Fe(II)-oxidizing bacteria produce Fe(III) minerals and therefore have the potential to affect arsenic mobility. In the present study, we demonstrate that the metabolism of anaerobic nitrate-reducing and phototrophic Fe(II)-oxidizing bacteria is not significantly affected by arsenate concentrations of up to 500 ? M (37.5 mg/L). Even in the presence of the more toxic arsenic species, arsenite, cell metabolism was significantly impaired only at the highest arsenite concentration (500 ? M) for one of the Fe(II)-oxidizers. All Fe(II)-oxidizing bacteria tested effectively immobilized arsenic during Fe(II) oxidation (>96%), lowering the remaining dissolved arsenic concentrations to values close to or even lower than the current drinking water limit of 10 ? g/L. Since the minerals formed by these bacteria included highly crystalline Fe(III) minerals that are hardly reducible by Fe(III)-reducing bacteria, stimulation of arsenic immobilization by Fe(II)-oxidizing bacteria can potentially support water treatment systems or even be applied as an effective remediation strategy

13.U03390
Lew, S.; Lew, M.; Biedunkiewicz, A.; et al . Impact of Pesticide Contamination on Aquatic Microorganism Populations in the Littoral Zone // ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY.-2013, Volume: 64 Issue: 3 Pages: 399-409

The effect of pesticide contamination of the littoral zone on the population of bacteria and fungi was analyzed using the example of a eutrophic water reservoir exposed for > 30 years to the influence of expired crop-protection chemicals, mainly DDT. For three consecutive years, quantity analyses of bacteria and fungi were conducted and the composition of the microorganism population analyzed against seasonal dynamics. Mold and yeast-like fungi were also isolated and identified. Within the Bacteria domain, in addition to the large groups of microorganisms (Alphaprotobacteria, Betaprobacteria, and Gammaproteobacteria, Actinobacteria, and Cytophaga-Flavobacterium), the analysis also involved the presence of bacteria predisposed to degraded pesticides in natural environments: Pseudomonas spp. and Alcaligenes spp. The quantity dynamics of aquatic microorganisms indicated that bacteria and fungi under the influence of long-term exposure to DDT can adapt to the presence of this pesticide in water. No modifying effect of DDT was observed on the quantity of microorganisms or the pattern of seasonal relationships in the eutrophic lake. Changes were shown in the percentage share of large groups of bacteria in the community of microorganisms as was an effect of contamination on the species diversity of fungi. The data show the effectiveness of aquatic microorganism-community analyses as a tool for indicating changes in the water environment caused by pesticide contamination

14.U12332
Marshall W.Bowles ,Samarkin V.A. et. al. WEAK COUPLING BETWEEN SULFATE REDUCTION AND THE ANAEROBIC OXIDATION OF METHANE IN METHANE-RICH SEAFL//Geochimica et Cosmochimica Acta(GBR). 2011 г., т. 75, N 2. P.500-519.

15.U12332
Michelle Y. Brabec, Timothy W. Lyons, Kevin W. Mandernack. Oxygen and sulfur isotope fractionation during sulfide oxidation by anoxygenic phototrophic bacteria //Geochimica et Cosmochimica Acta, Volume 83, 15 April 2012, Pages 234-251

Sulfide-mediated anoxygenic photosynthesis (SMAP) carried out by anaerobic phototrophic bacteria may have played an important role in sulfur cycling, formation of sulfate, and, perhaps, primary production in the Earth’s early oceans. Determination of ?34SSO4-Sulfide-SSO4-Sulfide- and ?18OSO4-H2OOSO4-H2O values for bacterial sulfide oxidation will permit more refined interpretation of the ?34S and ?18OSO4OSO4 values measured in modern anoxic environments, such as meromictic lakes where sulfide commonly extends into the photic zone, and in the ancient rock record, particularly during periods of the Precambrian when anoxic and sulfidic (euxinic) conditions were believed to be more pervasive than today. Laboratory experiments with anaerobic purple and green sulfur phototrophs, Allochromatium vinosum and Chlorobaculum tepidum, respectively, were conducted to determine the sulfur and oxygen isotope fractionation during the oxidation of sulfide to sulfate. Replicate experiments were conducted at 25 °C for A. vinosum and 45 °C for C. tepidum, and in duplicate at three different starting oxygen isotope values for water to determine sulfate-water oxygen isotope fractionations accurately (?18OSO4-H2OOSO4-H2O). ?18OSO4-H2OOSO4-H2O values of 5.6 ± 0.2‰ and 5.4 ± 0.1‰ were obtained for A. vinosum and C. tepidum, respectively. Temperature had no apparent effect on the ?18OSO4-H2OOSO4-H2O values. By combining all data from both cultures, an average ?18OSO4-H2OOSO4-H2O value of 5.6 ± 0.3‰ was obtained for SMAP. This value falls between those previously reported for bacterial oxidation of sphalerite and elemental sulfur (7–9‰) and abiotic and biotic oxidation of pyrite and chalcopyrite (2–4‰). Sulfur isotope fractionation between sulfide and sulfate formed by A.vinosum was negligible (0.1 ± 0.2‰) during all experiments. For C. tepidum an apparent fractionation of ?2.3 ± 0.5‰ was observed during the earlier stages of oxidation based on bulk ?34S measurements of sulfate and sulfide and became smaller (?0.7 ± 0.3‰) when sulfate concentrations rose above 0.5 mM and sulfide concentrations had became negligible

16.U17232
Norifumi Muraki, Daisuke Seo, Tomoo Shiba, Takeshi Sakurai, Genji Kurisu Asymmetric Dimeric Structure of Ferredoxin-NAD(P)+ Oxidoreductase from the Green Sulfur Bacterium Chlorobaculum tepidum: Implications for Binding Ferredoxin and NADP //Journal of Molecular Biology.- 2010. Volume 401, Issue 3,Pag. 403-414

. Ferredoxin-NAD(P)+ oxidoreductase (FNR) catalyzes the reduction of NAD(P)+ to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum is functionally analogous to plant-type FNR but shares a structural homology to NADPH-dependent thioredoxin reductase (TrxR). Here, we report the crystal structure of C. tepidum FNR to 2.4 A resolution, which reveals a unique structure–function relationship. C. tepidum FNR consists of two functional domains for binding FAD and NAD(P)H that form a homodimer in which the domains are arranged asymmetrically. One NAD(P)H domain is present as the open form, the other with the equivalent NAD(P)H domain as the relatively closed form. We used site-directed mutagenesis on the hinge region connecting the two domains in order to investigate the importance of the flexible hinge. The asymmetry of the NAD(P)H domain and the comparison with TrxR suggested that the hinge motion might be involved in pyridine nucleotide binding and binding of Fd. Surprisingly, the crystal structure revealed an additional C-terminal sub-domain that tethers one protomer and interacts with the other protomer by ?-? stacking of Phe337 and the isoalloxazine ring of FAD. The position of this stacking Phe337 is almost identical with both of the conserved C-terminal Tyr residues of plant-type FNR and the active site dithiol of TrxR, implying a unique structural basis for enzymatic reaction of C. tepidum FNR

17.U60726
Nozhevnikova A.N.,Litti Yu.V. et al. ANAEROBIC AMMONIUM OXIDATION (ANAMMOX) IN IMMOBILIZED ACTIVATED SLUDGE BIOFILMS DURING THE TREATMENT.// Microbiology (Mikrobiologiya)(DEU). 2012 г., т. 81, N 1, P.25-34.

18.U57174
Orcutt Beth N.,Joye S.B.et al. IMPACT OF NATURAL OIL AND HIGHER HYDROCARBONS ON MICROBIAL DIVERSITY, DISTRIBUTION, AND ACTIVITY IN .//Deep-Sea Research. Pt.II. Topical Studies in Oceanography(GBR). 2010 г., т. 57, N 21. P.2008-2011.

19.U11147
Ramos-Padron E.,Bordenave Silvain et al. CARBON AND SULFUR CYCLING BY MICROBIAL COMMUNITIES IN A GYPSUM-TREATED OIL SANDS TAILINGS POND. // Environmental Science and Technology(USA). 2011 г., т. 45, N 2.P.439-446.

20.U03047
Rattray J.E.,Van Vos et al. IMPACT OF TEMPERATURE ON LADDERANE LIPID DISTRIBUTION IN ANAMMOX BACTERIA . //Applied and Environmental Microbiology,2010. Vol.76,№5, P.1596-1603.

Anaerobic ammonium-oxidizing (anammox) bacteria have the unique ability to synthesize fatty acids containing linearly concatenated cyclobutane rings, termed "ladderane lipids." In this study we investigated the effect of temperature on the ladderane lipid composition and distribution in anammox enrichment cultures, marine particulate organic matter, and surface sediments. Under controlled laboratory conditions we observed an increase in the amount of C20 [S]-ladderane fatty acids compared with the amount of C 18 [5]-ladderane fatty acids with increasing temperature and also an increase in the amount of C18 [5]-ladderane fatty acids compared with the amount of C20 [5]-ladderane fatty acids with decreasing temperature. Combining these data with results from the natural environment showed a significant (R2 = 0.85, P = < 0.0001, n = 121) positive sigmoidal relationship between the amounts of C18 and C20 [5]-ladderane fatty acids and the in situ temperature; i.e., there is an increase in the relative abundance of C18 [5]-ladderane fatty acids at lower temperatures and vice versa, particularly at temperatures between 12°C and 20°C. Novel shorter (C16) and longer (C22 to C24) ladderane fatty acids were also identified, but their relative amounts were small and did not change with temperature. The adaptation of ladderane fatty acid chain length to temperature changes is similar to the regulation of common fatty acid composition in other bacteria and may be the result of maintaining constant membrane fluidity under different temperature regimens (homeoviscous adaptation). Our results can potentially be used to discriminate between the origins of ladderane lipids in marine sediments, i.e., to determine if ladderanes are produced in situ in relatively cold surface sediments or if they are fossil remnants originating from the warmer upper water column

21.U60726
Rogozin D.Yu.,Zukov V.V.et al. ECOLOGY OF PURPLE SULFUR BACTERIA IN THE HIGHLY STRATIFIED MEROMICTIC LAKE SHUNET//Microbiology (Mikrobiologiya)(DEU).- 2012 г., т. 81, N 6,P.727-735

Phototrophic sulfur bacteria form dense accumulations in the chemocline zone of stratified lakes where light reaches in the sulfide-containing layers of water. Many works are dedicated to the ecophysiology of these microorganisms in meromictic lakes.

22.U03047
Sharon Avrahami,Zhongjum Jia et al. ACTIVE AUTOTROPHIC AMMONIA-OXIDIZING BACTERIA IN BIOFILM ENRICHMENTS FROM SIMULATED CREEK ECOSYSTEMS //Applied and Environmental Microbiology(USA). 2011 . т. 77, N 20. P.7329-7338.

23.U03047
Thomas, Matthew C.; Selinger, L. Brent; Inglis, G. Douglas . Seasonal Diversity of Planktonic Protists in Southwestern Alberta Rivers over a 1-Year Period as Revealed by Terminal Restriction Fragment Length Polymorphism and 18S rRNA Gene Library Analyses // APPLIED AND ENVIRONMENTAL MICROBIOLOGY .-2012, Volume: 78 Issue: 16 Pages: 5653-5660

The temporal dynamics of planktonic protists in river water have received limited attention despite their ecological significance and recent studies linking phagotrophic protists to the persistence of human-pathogenic bacteria. Using molecular-based techniques targeting the 18S rRNA gene, we studied the seasonal diversity of planktonic protists in Southwestern Alberta rivers (Oldman River Basin) over a 1-year period. Nonmetric multidimensional scaling analysis of terminal restriction fragment length polymorphism (T-RFLP) data revealed distinct shifts in protistan community profiles that corresponded to season rather than geographical location. Community structures were examined by using clone library analysis; HaeIII restriction profiles of 18S rRNA gene amplicons were used to remove prevalent solanaceous plant clones prior to sequencing. Sanger sequencing of the V1-to-V3 region of the 18S rRNA gene libraries from spring, summer, fall, and winter supported the T-RFLP results and showed marked seasonal differences in the protistan community structure. The spring library was dominated by Chloroplastidae (29.8%), Centrohelida (28.1%), and Alveolata (25.5%), while the summer and fall libraries contained primarily fungal clones (83.0% and 88.0%, respectively). Alveolata (35.6%), Euglenozoa (24.4%), Chloroplastida (15.6%), and Fungi (15.6%) dominated the winter library. These data demonstrate that planktonic protists, including protozoa, are abundant in river water in Southwestern Alberta and that conspicuous seasonal shifts occur in the community structure

24.U03047
Vargas Walter A.,Weyman Philip D. et al. ([NIFE] HYDROGENASE FROM ALTEROMONAS MACLEODII WITH UNUSUAL STABILITY IN THE PRESENCE OF OXYGEN AND H. //Applied and Environmental Microbiology(USA). 2011 г., т. 77, N 6. P.1990-1998.

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