Sun, 06 Jul 2008 02:20:14 BST CiteULike: vrich's lipids http://www.citeulike.org/user/vrich/tag/lipids CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/vrich/article/2785943 <i>Proceedings of the National Academy of Sciences, Vol. 104, No. 38. (18 September 2007), pp. 15099-15104.</i><br /><br />Sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-MeBHPs). Here, we report the identification of significant quantities of 2-MeBHP in two strains of the anoxygenic phototroph Rhodopseudomonas palustris. Biosynthesis of 2-MeBHP can occur in the absence of O2, deriving the C-2 methyl group from methionine. The relative abundance of 2-MeBHP varies considerably with culture conditions, ranging from 13.3% of total bacteriohopanepolyol (BHP) to trace levels of methylation. Analysis of intact BHPs reveals the presence of methylated bacteriohopane-32,33,34,35-tetrol but no detectable methylation of 35-aminobacteriohopane-32,33,34-triol. Our results demonstrate that an anoxygenic photoautotroph is capable of generating 2-MeBHPs and show that the potential origins of sedimentary 2-methylhopanoids are more diverse than previously thought. 10.1073/pnas.0704912104 Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph Sky Rashby Alex Sessions Roger Summons Dianne Newman doi:10.1073/pnas.0704912104 Proceedings of the National Academy of Sciences, Vol. 104, No. 38. (18 September 2007), pp. 15099-15104. 2008-05-11T23:09:04-00:00 2007 Proceedings of the National Academy of Sciences 104 38 15099 15104 lipids http://www.citeulike.org/user/vrich/article/2785934 <i>Journal of Industrial Microbiology and Biotechnology, Vol. 17, No. 3. (1996), pp. 185-196.</i><br /><br />Microscopic examinations have convinced microbial ecologists that the culturable microbes recovered from environmental samples represent a tiny proportion of the extant microbiota. Methods for recovery and enzymatic amplification of nucleic acids from environmental samples have shown that a huge diversity existsin situ, far exceeding any expectations which were based on direct microscopy. It is now theoretically possible to extract, amplify and sequence all the nucleic acids from a community and thereby gain a comprehensive measure of the diversity as well as some insights into the phylogeny of the various elements within this community. Unfortunately, this analysis becomes economically prohibitive if applied to the multitude of niches in a single biome let alone to a diverse set of environments. It is also difficult to utilize PCR amplification on nucleic acids from some biomes because of coextracting enzymatic inhibitors. Signature biomarker analysis which potentially combines gene probe and lipid analysis on the same sample, can serve as a complement to massive environmental genome analysis in providing quantitative comparisons between microniches in the biome under study. This analysis can also give indications of the magnitude of differences in biodiversity in the blome as well as provide insight into the phenotypic activities of each community in a rapid and cost-effective manner. Applications of signature lipid biomarker analysis to define quantitatively the microbial viable biomass of portions of an Eastern USA deciduous forest, are presented. Quantitative comparisons ofin situ microbial biodiversity by signature biomarker analysis DC White JO Stair DB Ringelberg doi:10.1007/BF01574692 Journal of Industrial Microbiology and Biotechnology, Vol. 17, No. 3. (1996), pp. 185-196. 2008-05-11T23:05:57-00:00 1996 Journal of Industrial Microbiology and Biotechnology 17 3 185 196 lipids http://www.citeulike.org/user/vrich/article/2785931 <i>Deep Sea Research Part I: Oceanographic Research Papers, Vol. 42, No. 10. (October 1995), pp. 1749-1771.</i><br /><br />The fatty acid, sterol and hydrocarbon composition of suspended particles from the central North Pacific VERTEX IV site and from the Black Sea were used to investigate the abundance of biomarkers produced by heterotrophic alteration of particulate organic matter (POM). At the oceanic VERTEX site, bacterial alteration of organic matter did not contribute significant amounts of diagnostic lipids to particles, whereas zooplankton did leave a marked imprint on particulate lipids. In contrast, in the anoxic zone of the Black Sea there were significant lipid indicators of bacterial decomposition of POM. Most of these were derived from anaerobic sulfate-reducing and phototrophic sulfur bacteria. A comparison of the two sites and their lipid distributions indicates that it may be difficult to use lipid biomarkers to assess the importance of bacterial decomposition of organic matter in the open ocean, as lipids from these bacteria are not readily distinguished from the more abundant planktonic lipids. Lipid biomarkers for heterotrophic alteration of suspended particulate organic matter in oxygenated and anoxic water columns of the ocean Stuart Wakeham doi:10.1016/0967-0637(95)00074-G Deep Sea Research Part I: Oceanographic Research Papers, Vol. 42, No. 10. (October 1995), pp. 1749-1771. 2008-05-11T23:05:00-00:00 1995 Deep Sea Research Part I: Oceanographic Research Papers 42 10 1749 1771 lipids http://www.citeulike.org/user/vrich/article/2785930 <i>Biogeochemistry, Vol. 73, No. 2. (5 April 2005), pp. 395-415.</i><br /><br />To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbondioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO2 production and soil NH4+  concentration, while microbial community characteristics correlated with N2O production, nitrification potential, gross N-mineralization, and soil NO3- concentration, independent of environmentalcontrollers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes,particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2 years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology. Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest Teri Balser Mary Firestone doi:10.1007/s10533-004-0372-y Biogeochemistry, Vol. 73, No. 2. (5 April 2005), pp. 395-415. 2008-05-11T23:04:30-00:00 2005 Biogeochemistry 73 2 395 415 lipids http://www.citeulike.org/user/vrich/article/933650 <i>Appl. Environ. Microbiol., Vol. 70, No. 11. (1 November 2004), pp. 6920-6926.</i><br /><br />A combined lipid biomarker-16S rRNA gene denaturing gradient gel electrophoresis analysis was used to monitor changes in the physiological status, biomass, and microbial composition of a microbial mat. In the morning hours, an increase in the biomass of layers containing a high density of phototrophs and a decrease in the growth rate in the deep layers were observed. The combined approach also revealed differences in major groups of microorganisms, including green nonsulfur, gram-positive, and heterotrophic bacteria. Combined Phospholipid Biomarker-16S rRNA Gene Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Diversity and Physiological Status in an Intertidal Microbial Mat Laura Villanueva Antoni Navarrete Jordi Urmeneta David White Ricardo Guerrero doi:10.1128/AEM.70.11.6920 Appl. Environ. Microbiol., Vol. 70, No. 11. (1 November 2004), pp. 6920-6926. 2006-11-06T16:34:12-00:00 2004 Appl. Environ. Microbiol. 70 11 6920 6926 lipids http://www.citeulike.org/user/vrich/article/1167743 <i>Microb Ecol (9 March 2007)</i><br /><br />Microbial mats are highly productive microbial systems and a source of not-yet characterized microorganisms and metabolic strategies. In this article, we introduced a lipid biomarker/microbial isolation approach to detect short-term variations of microbial diversity, physiological and redox status, and also characterize lipid biomarkers from specific microbial groups that can be further monitored. Phospholipid fractions (PLFA) were examined for plasmalogens, indicative of certain anaerobes. The glycolipid fraction was processed for polyhydroxyalkanoates (PHA) and the neutral lipid fraction was used to evaluate respiratory quinone content. Data demonstrate an increase in the metabolic stress, unbalanced growth, proportion of anaerobic bacteria and respiratory rate after the maximal photosynthetic activity. Higher accumulation of polyhydroxyalkanoates at the same sampling point also suggested a situation of carbon storage by heterotrophs closely related to photosynthetic microorganisms. Besides, the characterization of lipid biomarkers (plasmalogens, sphingolipids) from specific microbial groups provided clues about the dynamics and diversity of less-characterized mat members. In this case, lipid analyses were complemented by the isolation and characterization of anaerobic spore formers and sulfate reducers to obtain insight into their affiliation and lipid composition. The results revealed that temporal shifts in lipid biomarkers are indicative of an intense change in the physiology, redox condition, and community composition along the diel cycle, and support the hypothesis that interactions between heterotrophs and primary producers play an important role in the carbon flow in microbial mats. Monitoring Diel Variations of Physiological Status and Bacterial Diversity in an Estuarine Microbial Mat: An Integrated Biomarker Analysis. Laura Villanueva Antoni Navarrete Jordi Urmeneta Roland Geyer David White Ricardo Guerrero doi:10.1007/s00248-007-9224-3 Microb Ecol (9 March 2007) 2007-03-16T15:51:29-00:00 2007 Microb Ecol 0095-3628 lipids http://www.citeulike.org/user/vrich/article/2752531 <i>Microbial Ecology, Vol. 55, No. 3. (April 2008), pp. 500-511.</i> PLFA Profiling of Microbial Community Structure and Seasonal Shifts in Soils of a Douglas-fir Chronosequence Moore-Kucera Jennifer Dick Richard doi:10.1007/s00248-007-9295-1 Microbial Ecology, Vol. 55, No. 3. (April 2008), pp. 500-511. 2008-05-04T02:11:13-00:00 2008 Microbial Ecology 0095-3628 55 3 500 511 Springer lipids http://www.citeulike.org/user/vrich/article/1132903 <i>Geobiology, Vol. 5, No. 1. (March 2007), pp. 75-83.</i> Analysis of archaeal core ether lipids using Time of FlightSecondary Ion Mass Spectrometry (ToF-SIMS): Exploring a new prospect for the study of biomarkers in geobiology V Thiel J Toporski G Schumann P Sjovall J Lausmaa doi:10.1111/j.1472-4669.2006.00093.x Geobiology, Vol. 5, No. 1. (March 2007), pp. 75-83. 2007-03-01T02:44:20-00:00 2007 Geobiology 1472-4677 5 1 75 83 Blackwell Publishing lipids http://www.citeulike.org/user/vrich/article/2785889 <i>J Environ Qual, Vol. 34, No. 5. (8 September 2005), pp. 1789-1800.</i><br /><br />Heavy metal pollution of soil is of concern for human health and ecosystem function. The soil microbial community should be a sensitive indicator of metal contamination effects on bioavailability and biogeochemical processes. Simple methods are needed to determine the degree of in situ pollution and effectiveness of remediating metal-contaminated soils. Currently, phospholipid-linked fatty acids (PLFAs) are preferred for microbial profiling but this method is time consuming, whereas direct soil extraction and transesterification of total ester-linked fatty acids (ELFAs) is attractive because of its simplicity. The 1998 mining acid-metal spill of >4000 ha in the Guadiamar watershed (southwestern Spain) provided a unique opportunity to study these two microbial lipid profiling methods. Replicated treatments were set up as nonpolluted, heavy metal polluted and reclaimed, and polluted soils. Inferences from whole community-diversity analysis and correlations of individual fatty acids with metals suggested Cu, Cd, and Zn were the most important in affecting microbial community structure, along with pH. The microbial stress marker, monounsaturated fatty acids, was significantly lower for reclaimed and polluted soil over nonpolluted soils for both PLFA and ELFA extraction. Another stress marker, the monounsaturated to saturated fatty acids ratio, only showed this for the PLFA. The general fungal marker (18:2omega6c), the arbuscule mycorrhizae marker (16:1omega5c), and iso- and anteiso-branched PLFAs (Gram positive bacteria) were suppressed with increasing pollution whereas 17:0cy (Gram negative bacteria) increased with metal pollution. For both extraction methods, richness and diversity were greater in nonpolluted soils and lowest in polluted soils. The ELFA method was sensitive for reflecting metal pollution on microbial communities and could be suitable for routine use in ecological monitoring and risk assessment programs because of its simplicity and reproducibility. 10.2134/jeq2004.0470 Microbial Response to Heavy Metal-Polluted Soils: Community Analysis from Phospholipid-Linked Fatty Acids and Ester-Linked Fatty Acids Extracts Belen Hinojosa Jose Carreira Roberto Garcia-Ruiz Richard Dick doi:10.2134/jeq2004.0470 J Environ Qual, Vol. 34, No. 5. (8 September 2005), pp. 1789-1800. 2008-05-11T22:10:50-00:00 2005 J Environ Qual 34 5 1789 1800 lipids http://www.citeulike.org/user/vrich/article/2785881 <i>Soil Sci Soc Am J, Vol. 64, No. 5. (1 September 2000), pp. 1659-1668.</i><br /><br />Fatty acid profiling is a popular method for characterizing microbial communities of natural systems. Direct extraction of microbial fatty acids in situ would be useful compared with methods that extract lipids first and subsequently release fatty acids from lipids. In this study, two methods for the direct extraction of fatty acids from soils were compared for three cultivated silt loams and one forested sandy clay loam. Fresh soils were analyzed for their fatty acid methyl ester (FAME) profiles by an ester-linked (EL) method and the method of MIDI (Microbial ID, Inc., Newark, DE). Soils were stored four different ways (moist at 4degreesC, moist at -20degreesC, air-dried at 25degreesC, and partially dry at 4degreesC) and analyzed for FAME profile changes after 30 and 90 d of storage. Eleven and 17 FAMEs were unique to the EL and MIDI method, respectively, but unique FAMEs generally were found in only minute amounts. Soils extracted with the MIDI method yielded more hydroxy FAMEs and short-chain saturated and branched FAMEs. Conversely, EL-extracted soils generally produced more long-chain saturated and branched FAMEs, unsaturated FAMEs, and FAMEs with cyclopropane and methyl groups. Both extraction methods were able to differentiate among communities of different soil types, regardless if soils were fresh or stored. Changes in FAME profiles did occur in stored soils, but the effectiveness of each storage protocol for preserving FAME patterns over time was different among the four soils. While community analyses should be conducted on fresh soil, overall effects of storage were slight compared with those of extraction method and soil type. Comparison of Fatty Acid Methyl Ester (FAME) Methods for Characterizing Microbial Communities Mary Schutter Richard Dick Soil Sci Soc Am J, Vol. 64, No. 5. (1 September 2000), pp. 1659-1668. 2008-05-11T22:00:24-00:00 2000 Soil Sci Soc Am J 64 5 1659 1668 lipids http://www.citeulike.org/user/vrich/article/1562292 <i>Proc Natl Acad Sci U S A, Vol. 103, No. 17. (25 April 2006), pp. 6442-6447.</i><br /><br />An ammonia-oxidizing, carbon-fixing archaeon, Candidatus "Nitrosopumilus maritimus," recently was isolated from a salt-water aquarium, definitively confirming that chemoautotrophy exists among the marine archaea. However, in other incubation studies, pelagic archaea also were capable of using organic carbon. It has remained unknown what fraction of the total marine archaeal community is autotrophic in situ. If archaea live primarily as autotrophs in the natural environment, a large ammonia-oxidizing population would play a significant role in marine nitrification. Here we use the natural distribution of radiocarbon in archaeal membrane lipids to quantify the bulk carbon metabolism of archaea at two depths in the subtropical North Pacific gyre. Our compound-specific radiocarbon data show that the archaea in surface waters incorporate modern carbon into their membrane lipids, and archaea at 670 m incorporate carbon that is slightly more isotopically enriched than inorganic carbon at the same depth. An isotopic mass balance model shows that the dominant metabolism at depth indeed is autotrophy (83%), whereas heterotrophic consumption of modern organic carbon accounts for the remainder of archaeal biomass. These results reflect the in situ production of the total community that produces tetraether lipids and are not subject to biases associated with incubation and/or culture experiments. The data suggest either that the marine archaeal community includes both autotrophs and heterotrophs or is a single population with a uniformly mixotrophic metabolism. The metabolic and phylogenetic diversity of the marine archaea warrants further exploration; these organisms may play a major role in the marine cycles of nitrogen and carbon. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. AE Ingalls SR Shah RL Hansman LI Aluwihare GM Santos ER Druffel A Pearson doi:10.1073/pnas.0510157103 Proc Natl Acad Sci U S A, Vol. 103, No. 17. (25 April 2006), pp. 6442-6447. 2007-08-15T09:42:31-00:00 2006 Proc Natl Acad Sci U S A 0027-8424 103 17 6442 6447 archaea lipids pacific http://www.citeulike.org/user/vrich/article/2776714 <i>Proceedings of the National Academy of Sciences, Vol. 103, No. 10. (7 March 2006), pp. 3846-3851.</i><br /><br />Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea. 10.1073/pnas.0600035103 Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru Jennifer Biddle Julius Lipp Mark Lever Karen Lloyd Ketil Sorensen Rika Anderson Helen Fredricks Marcus Elvert Timothy Kelly Daniel Schrag Mitchell Sogin Jean Brenchley Andreas Teske Christopher House Kai-Uwe Hinrichs doi:10.1073/pnas.0600035103 Proceedings of the National Academy of Sciences, Vol. 103, No. 10. (7 March 2006), pp. 3846-3851. 2008-05-09T21:43:30-00:00 2006 Proceedings of the National Academy of Sciences 103 10 3846 3851 16srrna archaea fish lipids http://www.citeulike.org/user/vrich/article/1557218 <i>Appl Environ Microbiol, Vol. 71, No. 4. (April 2005), pp. 1677-1684.</i> Biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria. MC Schmid B Maas A Dapena K van de Pas-Schoonen J van de Vossenberg B Kartal L van Niftrik I Schmidt I Cirpus JG Kuenen M Wagner JS Sinninghe Damsté M Kuypers NP Revsbech R Mendez MS Jetten M Strous doi:10.1128/AEM.71.4.1677-1684.2005 Appl Environ Microbiol, Vol. 71, No. 4. (April 2005), pp. 1677-1684. 2007-08-13T09:07:42-00:00 2005 Appl Environ Microbiol 0099-2240 71 4 1677 1684 lipids http://www.citeulike.org/user/vrich/article/80546 <i>BioScience, Vol. 39, No. 8. (September 1989), pp. 535-541.</i> Lipid Analysis in Microbial Ecology Robie BioScience, Vol. 39, No. 8. (September 1989), pp. 535-541. 2005-01-20T00:29:54-00:00 1989 BioScience 39 8 535 541 lipids