Lipid Biomarkers for Bacterial Ecosystems: Studies of Cultured Organisms, Hydrothermal Environments and Ancient Sediments

Summons, Roger E.; Jahnke, L. L.; Simoneit, Bernd R.T.

doi:10.1002/9780470514986.ch10

Cited by 38 publications

(38 citation statements)

References 33 publications

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“…Another concern is the differences in the lipids of FAP isolates compared to lipids that we and others have detected in Octopus Spring and Mushroom Spring mats (14,39,41,42,55,58,59). In addition to complex polar lipids (53), these mats contain abundant long-chain (C 31 to C 37 ) normal and branched wax esters (14,55,58,59) (Table 1).…”

mentioning

confidence: 80%

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

et al. 2010

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Roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in Yellowstone National Park. These strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rRNA, lipid distributions, and genomic and metagenomic sequences. Like a Japanese isolate, R. castenholzii, the Yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photoheterotrophically or chemoheterotrophically under dark aerobic conditions. The genome of one isolate, Roseiflexus sp. strain RS1, contains genes necessary to support these metabolisms. This genome also contains genes encoding the 3-hydroxypropionate pathway for CO 2 fixation and a hydrogenase, which might enable photoautotrophic metabolism, even though neither isolate could be grown photoautotrophically with H 2 or H 2 S as a possible electron donor. The isolates exhibit temperature, pH, and sulfide preferences typical of their habitat. Lipids produced by these isolates matched much better with mat lipids than do lipids produced by R. castenholzii or Chloroflexus isolates.We have investigated laminated cyanobacterial mats in alkaline siliceous hot springs of Yellowstone National Park (Octopus Spring and Mushroom Spring) as models for understanding principles of microbial community ecology (49, 51, 54) and as models of stromatolites (50, 55), which are important fossilized microbial communities of the Precambrian. These mats are dominated by unicellular cyanobacteria (Synechococcus spp.) and filamentous anoxygenic phototrophic bacteria (FAPs) (e.g., Chloroflexus spp. and Roseiflexus spp.); they also contain newly described anoxygenic phototrophic bacteria (8) and many organisms involved in mat decomposition (49). We have studied the composition and structure of the mat community using both nucleic acid and lipid biomarker approaches (50), as well as the functional contributions of and interactions among community members (34, 46, 47).A major finding from molecular analyses was that the predominant Synechococcus spp. of the mat are distantly related to readily cultivated strains (15, 49). Careful cultivation of predominant strains was necessary before we could observe phenotypic properties of Synechococcus sp. isolates that were useful for understanding the in situ ecology of native mat populations (2). Genomic analysis of relevant isolates has also vastly improved our ability to understand metagenomic Similarly, based on small-subunit rRNA (SSU rRNA) cloning and sequencing and fluorescent in situ hybridization (FISH) probing, the dominant FAPs of the community were found to be distantly related to readily cultivated Chloroflexus spp. but closely related to Roseiflexus castenholzii (35), a bacteriochlorophyll a-containing anoxygenic phototroph lacking chlorosomes, which was initially cultivated from a Japanese hot spring (20). Only one SSU rRNA sequence somewhat distantly related to that of Heliothrix oregonensis, the only ot...

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confidence: 80%

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

et al. 2010

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“…For instance, different wavelengths of light penetrate differentially, gas exchange with the atmosphere occurs at the surface, an organic carbon-based matrix provides a scaffold for growth, and sedimentation occasionally buries the surface, which is then overgrown, leading to layering. Comparisons of biosignatures in modern and fossilized mats seek to describe ancient biogeochemical cycles and the microbial activities of ancient communities (34,57,58).…”

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confidence: 99%

Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat

Ley

Harris

Wilcox

et al. 2006

Appl Environ Microbiol

427

438

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We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (>97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O 2 and H 2 S. Bacteria of the phylum Chloroflexi formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments), Chloroflexi sequences were conspicuous throughout the mat. Filamentous Chloroflexi bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium Microcoleus chthonoplastes, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity.

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“…Branched alkanes, isoprenoids and hopanoids are bacterial biomarkers (Rohmer et al, 1984;Summons et al, 2007). These compounds indicated a higher bacterial biomass around 1980 and since the end of the 1990s in core Amvr13 (Fig.…”

Section: Impact Of Eutrophication On Benthic Foraminifera and Bacterimentioning

confidence: 95%

Environmental variations in a semi-enclosed embayment (Amvrakikos Gulf, Greece) – reconstructions based on benthic foraminifera abundance and lipid biomarker pattern

et al. 2012

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The evolution of environmental changes during the last decades and the impact on the living biomass in the western part of Amvrakikos Gulf was investigated using abundances and species distributions of benthic foraminifera and lipid biomarker concentrations. These proxies indicated that the gulf has markedly changed due to eutrophication. Eutrophication has led to a higher productivity, a higher bacterial biomass, shifts towards opportunistic and tolerant benthic foraminifera species (e.g. Bulimina elongata, Nonionella turgida, Textularia agglutinans, Ammonia tepida) and a lower benthic species density. Close to the Preveza Strait (connection between the gulf and the Ionian Sea), the benthic assemblages were more diversified under more oxygenated conditions. Sea grass meadows largely contributed to the organic matter at this sampling site. The occurrence of isorenieratane, chlorobactane and lycopane supported by oxygen monitoring data indicated that anoxic (and partly euxinic) conditions prevailed seasonally throughout the western part of the gulf with more severe oxygen depletion towards the east. Increased surface water temperatures have led to a higher stratification, which reduced oxygen resupply to bottom waters. Altogether, these developments led to mass mortality events and ecosystem decline in Amvrakikos Gulf

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Lipid Biomarkers for Bacterial Ecosystems: Studies of Cultured Organisms, Hydrothermal Environments and Ancient Sediments

Cited by 38 publications

References 33 publications

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat

Environmental variations in a semi-enclosed embayment (Amvrakikos Gulf, Greece) – reconstructions based on benthic foraminifera abundance and lipid biomarker pattern

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