Walter Michaelis

The molecularly-uncharacterized component of nonliving organic matter in natural environments.

Molecularly-uncharacterized organic matter comprises most reduced carbon in soils, sediments and natural waters. The origins, reactions and fates of these ubiquitous materials are relatively obscure, in large part because the rich vein of geochemical information that typically derives from detailed structural and stereochemical analysis is yet to be tapped. This discussion highlights current knowledge about the origins and characteristics of molecularly uncharacterized organic matter in the environment and outlines possible means by which this structurally uncharted frontier might best be explored.

Methane formation from long-chain alkanes by anaerobic microorganisms

Biological formation of methane is the terminal process of biomass degradation in aquatic habitats where oxygen, nitrate, ferric iron and sulphate have been depleted as electron acceptors. The pathway leading from dead biomass to methane through the metabolism of anaerobic bacteria and archaea is well understood for easily degradable biomolecules such as carbohydrates, proteins and lipids. However, little is known about the organic compounds that lead to methane in old anoxic sediments where easily degradable biomolecules are no longer available. One class of naturally formed long-lived compounds in such sediments is the saturated hydrocarbons (alkanes). Alkanes are usually considered to be inert in the absence of oxygen, nitrate or sulphate, and the analysis of alkane patterns is often used for biogeochemical characterization of sediments. However, alkanes might be consumed in anoxic sediments below the zone of sulphate reduction, but the underlying process has not been elucidated. Here we used enrichment cultures to show that the biological conversion of long-chain alkanes to the simplest hydrocarbon, methane, is possible under strictly anoxic conditions.

Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria

The short-chain hydrocarbons ethane, propane and butane are constituents of natural gas. They are usually assumed to be of thermochemical origin, but biological formation of ethane and propane has been also observed. Microbial utilization of short-chain hydrocarbons has been shown in some aerobic species but not in anaerobic species of bacteria. On the other hand, anaerobic utilization of short-chain hydrocarbons would in principle be expected because various anaerobic bacteria grow with higher homologues (≥C6). Indeed, chemical analyses of hydrocarbon-rich habitats with limited or no access of oxygen indicated in situ biodegradation of short-chain hydrocarbons. Here we report the enrichment of sulphate-reducing bacteria (SRB) with such capacity from marine hydrocarbon seep areas. Propane or n-butane as the sole growth substrate led to sediment-free sulphate-reducing enrichment cultures growing at 12, 28 or 60 °C. With ethane, a slower enrichment with residual sediment was obtained at 12 °C. Isolation experiments resulted in a mesophilic pure culture (strain BuS5) that used only propane and n-butane (methane, isobutane, alcohols or carboxylic acids did not support growth). Complete hydrocarbon oxidation to CO2 and the preferential oxidation of 12C-enriched alkanes were observed with strain BuS5 and other cultures. Metabolites of propane included iso- and n-propylsuccinate, indicating a subterminal as well as an unprecedented terminal alkane activation with involvement of fumarate. According to 16S ribosomal RNA analyses, strain BuS5 affiliates with Desulfosarcina/Desulfococcus, a cluster of widespread marine SRB. An enrichment culture with propane growing at 60 °C was dominated by Desulfotomaculum-like SRB. Our results suggest that diverse SRB are able to thrive in seep areas and gas reservoirs on propane and butane, thus altering the gas composition and contributing to sulphide production.

Molecular signals for anaerobic methane oxidation in Black Sea seep carbonates and a microbial mat

Linked to gas seeps on the Ukrainian shelf (northwestern Black Sea), massive authigenic carbonates form as a result of anaerobic methane oxidation. Lipid distributions in these ‘cold seep’ carbonates and an associated microbial mat were investigated for process markers reflecting the presence and metabolic activity of distinctive methane-related biota. The samples contain free, irregular isoprenoid hydrocarbons, namely the tail-to-tail linked acyclic C20-isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane), its C25-homologue 2,6,10,15,19-pentamethylicosane (PMI), and several unsaturated derivatives thereof. Furthermore, specific acyclic and cyclic C40-isoprenoids were released upon ether cleavage of the polar fraction from the carbonate. The abundance of these compounds indicates a pronounced role of particular Archaea in the biogeochemical cycling of carbon at methane seeps. Stable carbon isotopic analyses of these lipids reveal extraordinary depletions in 13C corresponding to δ-values in the range of −100±30‰ PDB, whereas other compounds show isotopic compositions normally observed for marine lipids (around −30‰ PDB). The isotope data imply that the biosynthesis of the archaeal isoprenoids occurred in situ and involved the utilization of isotopically depleted, i.e. methane-derived, carbon. Apart from archaeal markers, the carbonate and the mat contain authigenic, framboidal pyrite and isotopically depleted fatty acids, namely iso-, and anteiso-branched compounds most likely derived from sulphate-reducing bacteria (SRB). The indications for a tight association of these normally competitive organisms support a model invoking a syntrophic relationship of SRB with Archaea responsible for the anaerobic oxidation of methane. The biomarker patterns obtained from the Black Sea samples were further compared to those from a Oligocene seep carbonate (Lincoln Creek Formation, WA, USA) in order to evaluate their biomarker potential for ancient settings. The prominent occurrence of isotopically light crocetane (−112‰) and PMI (−120‰) meets the findings for the contemporary materials. Thus, isotopically depleted isoprenoids provide diagenetically stable fingerprints for the reconstruction of carbon cycling in both, modern and ancient methane seep systems.

Highly isotopically depleted isoprenoids: molecular markers for ancient methane venting

Abstract We propose that organic compounds found in a Miocene limestone from Marmorito (Northern Italy) are source markers for organic matter present in ancient methane vent systems (cold seeps). The limestone contains high concentrations of the tail-to-tail linked, acyclic C20 isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane), a C25 homolog 2,6,10,15,19-pentamethylicosane (PME), and a distinctive glycerol ether lipid containing 3,7,11,15-tetramethylhexadecyl (phytanyl-) moieties. The chemical structures of these biomarkers indicate a common origin from archaea. Their extremely 13C-depleted isotope compositions (δ13C ≈ −108 to −115.6‰ PDB) suggest that the respective archaea have directly or indirectly introduced isotopically depleted, methane-derived carbon into their biomass. We postulate that a second major cluster of biomarkers showing heavier isotope values (δ13C ≈ −88‰) is derived from sulfate-reducing bacteria (SRB). The observed biomarkers sustain the idea that methanogenic bacteria, in a syntrophic community with SRB, are responsible for the anaerobic oxidation of methane in marine sediments. Marmorito may thus represent a conceivable ancient scenario for methane consumption performed by a defined, two-membered bacterial consortium: (1) archaea that perform reversed methanogenesis by oxidizing methane and producing CO2 and H2; and (2) SRB that consume the resulting H2. Furthermore, the respective organic molecules are, unlike other compounds, tightly bound to the crystalline carbonate phase. The Marmorito carbonates can thus be regarded as “cold seep microbialites” rather than mere “authigenic” carbonates.

Anaerobic Naphthalene Degradation by a Sulfate-Reducing Enrichment Culture

ABSTRACT Anaerobic naphthalene degradation by a sulfate-reducing enrichment culture was studied by substrate utilization tests and identification of metabolites by gas chromatography-mass spectrometry. In substrate utilization tests, the culture was able to oxidize naphthalene, 2-methylnaphthalene, 1- and 2-naphthoic acids, phenylacetic acid, benzoic acid, cyclohexanecarboxylic acid, and cyclohex-1-ene-carboxylic acid with sulfate as the electron acceptor. Neither hydroxylated 1- or 2-naphthoic acid derivatives and 1- or 2-naphthol nor the monoaromatic compounds ortho-phthalic acid, 2-carboxy-1-phenylacetic acid, and salicylic acid were utilized by the culture within 100 days. 2-Naphthoic acid accumulated in all naphthalene-grown cultures. Reduced 2-naphthoic acid derivatives could be identified by comparison of mass spectra and coelution with commercial reference compounds such as 1,2,3,4-tetrahydro-2-naphthoic acid and chemically synthesized decahydro-2-naphthoic acid. 5,6,7,8-Tetrahydro-2-naphthoic acid and octahydro-2-naphthoic acid were tentatively identified by their mass spectra. The metabolites identified suggest a stepwise reduction of the aromatic ring system before ring cleavage. In degradation experiments with [1-13C]naphthalene or deuterated D8-naphthalene, all metabolites mentioned derived from the introduced labeled naphthalene. When a [13C]bicarbonate-buffered growth medium was used in conjunction with unlabeled naphthalene, 13C incorporation into the carboxylic group of 2-naphthoic acid was shown, indicating that activation of naphthalene by carboxylation was the initial degradation step. No ring fission products were identified.

An Anaerobic World in Sponges

Abstract Associated microorganisms have been described in numerous marine sponges. Their metabolic activity, however, has not yet been investigated in situ. We quantified for the first time microbial processes in a living sponge. Sulfate reduction rates of up to 1200 nmol cm−3d−1 were measured in the cold-water bacteriosponge Geodia barretti . Oxygen profiles and chemical analysis of sponge tissue and canal water revealed steep oxygen gradients and a rapid turnover of oxygen and sulfide, dependent on the pumping activity of the sponge. Identification of the microbial community with fluorescently labelled oligonucleotide probes (FISH) indicates the presence of sulfate-reducing bacteria belonging to the Desulfoarculus/Desulfomonile/Syntrophus -cluster in the choanosome of this sponge. Analysis of lipid biomarkers indicates biomass transfer from associated sulfate-reducing bacteria or other anaerobic microbes to sponge cells. These results show the presence of an anoxic micro-ecosystem in the sponge G. barretti, and imply mutualistic interactions between sponge cells and anaerobic microbes. Understanding the importance of anaerobic processes within the sponge/microbe system may help to answer unsolved questions in sponge ecology and biotechnology.

Polar Lipids of Archaebacteria in Sediments and Petroleums

Glycerol tetraethers with head-to-head isoprenoid 40-carbon chains that are typical of archaebacteria, in particular of methanogens, were identified in the polar lipids of sediments and petroleums. These structures are at least partially preserved in the subsurface beyond the stage of petroleum formation. Their identification provides further evidence that a significant part of geological organic matter derives from the lipids of membranes of microorganisms.

Naphthalene Degradation and Incorporation of Naphthalene- Derived Carbon into Biomass by the Thermophile Bacillus thermoleovorans

ABSTRACT The thermophilic aerobic bacterium Bacillus thermoleovorans Hamburg 2 grows at 60°C on naphthalene as the sole source of carbon and energy. In batch cultures, an effective substrate degradation was observed. The carbon balance, including naphthalene, metabolites, biomass, and CO2, was determined by the application of [1-13C]naphthalene. The incorporation of naphthalene-derived carbon into the bulk biomass as well as into specified biomass fractions such as fatty acids and amino acids was confirmed by coupled gas chromatography-mass spectrometry (GC-MS) and isotope analyses. Metabolites were characterized by GC-MS; the established structures allow tracing the degradation pathway under thermophilic conditions. Apart from typical metabolites of naphthalene degradation known from mesophiles, intermediates such as 2,3-dihydroxynaphthalene, 2-carboxycinnamic acid, and phthalic and benzoic acid were identified for the pathway of this bacterium. These compounds indicate that naphthalene degradation by the thermophilicB. thermoleovorans differs from the known pathways found for mesophilic bacteria.

Biofilm exopolymers control microbialite formation at thermal springs discharging into the alkaline Pyramid Lake, Nevada, USA

Calcium carbonate precipitation and microbialite formation at highly supersaturated mixing zones of thermal spring waters and alkaline lake water have been investigated at Pyramid Lake, Nevada. Without precipitation, pure mixing should lead to a nearly 100-fold supersaturation at 40oC. Physicochemical precipitation is modified or even inhibited by the properties of biofilms, dependent on the extent of biofilm development and the current precipitation rate. Mucus substances (extracellular polymeric substances, EPS, e.g., of cyanobacteria) serve as effective Ca 2C -buffers, thus preventing seed crystal nucleation even in a highly supersaturated macroenvironment. Carbonate is then preferentially precipitated in mucus-free areas such as empty diatom tests or voids. After the buffer capacity of the EPS is surpassed, precipitation is observed at the margins of mucus areas. Hydrocarbon biomarkers extracted from (1) a calcifying Phormidium-biofilm, (2) the stromatolitic carbonate below, and (3) a fossil ‘tufa’ of the Pleistocene pinnacles, indicate that the cyanobacterial primary producers have been subject to significant temporal changes in their species distribution. Accordingly, the species composition of cyanobacterial biofilms does not appear to be relevant for the formation of microbial carbonates in Pyramid Lake. The results demonstrate the crucial influence of mucus substances on carbonate precipitation in highly supersaturated natural environments.