Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation.

The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile α-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80%). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the 'lipid fingerprint' produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.

Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane.

Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher (15)N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.

Chemical composition of gas- and aerosol-phase products from the photooxidation of naphthalene.

The current work focuses on the detailed evolution of the chemical composition of both the gas- and aerosol-phase constituents produced from the OH-initiated photooxidation of naphthalene under low- and high-NO(x) conditions. Under high-NO(x) conditions ring-opening products are the primary gas-phase products, suggesting that the mechanism involves dissociation of alkoxy radicals (RO) formed through an RO(2) + NO pathway, or a bicyclic peroxy mechanism. In contrast to the high-NO(x) chemistry, ring-retaining compounds appear to dominate the low-NO(x) gas-phase products owing to the RO(2) + HO(2) pathway. We are able to chemically characterize 53-68% of the secondary organic aerosol (SOA) mass. Atomic oxygen-to-carbon (O/C), hydrogen-to-carbon (H/C), and nitrogen-to-carbon (N/C) ratios measured in bulk samples by high-resolution electrospray ionization time-of-flight mass spectrometry (HR-ESI-TOFMS) are the same as the ratios observed with online high-resolution time-of-flight aerosol mass spectrometry (HR-ToF-AMS), suggesting that the chemical compositions and oxidation levels found in the chemically-characterized fraction of the particle phase are representative of the bulk aerosol. Oligomers, organosulfates (R-OSO(3)), and other high-molecular-weight (MW) products are not observed in either the low- or high-NO(x) SOA; however, in the presence of neutral ammonium sulfate seed aerosol, an organic sulfonic acid (R-SO(3)), characterized as hydroxybenzene sulfonic acid, is observed in naphthalene SOA produced under both high- and low-NO(x) conditions. Acidic compounds and organic peroxides are found to account for a large fraction of the chemically characterized high- and low-NO(x) SOA. We propose that the major gas- and aerosol-phase products observed are generated through the formation and further reaction of 2-formylcinnamaldehyde or a bicyclic peroxy intermediate. The chemical similarity between the laboratory SOA and ambient aerosol collected from Birmingham, Alabama (AL) and Pasadena, California (CA) confirm the importance of PAH oxidation in the formation of aerosol within the urban atmosphere.