Microbial Alkalinity Production and Silicate Alteration in Methane Charged Marine Sediments: Implications for Porewater Chemistry and Diagenetic Carbonate Formation

A numerical reaction-transport model was developed to simulate the effects of microbial activity and mineral reactions on the composition of porewater in a 230-m-thick Pleistocene interval drilled in the Peru-Chile Trench (Ocean Drilling Program, Site 1230). This site has porewater profiles similar to those along many continental margins, where intense methanogenesis occurs and alkalinity surpasses 100 mmol/L. Simulations show that microbial sulphate reduction, anaerobic oxidation of methane, and ammonium release from organic matter degradation only account for parts of total alkalinity, and excess CO2 produced during methanogenesis leads to acidification of porewater. Additional alkalinity is produced by slow alteration of primary aluminosilicate minerals to kaolinite and SiO2. Overall, alkalinity production in the methanogenic zone is sufficient to prevent dissolution of carbonate minerals; indeed, it contributes to the formation of cemented carbonate layers at a supersaturation front near the sulphate-methane transition zone. Within the methanogenic zone, carbonate formation is largely inhibited by cation diffusion but occurs rapidly if cations are transported into the zone via fluid conduits, such as faults. The simulation presented here provides fundamental insight into the diagenetic effects of the deep biosphere and may also be applicable for the long-term prediction of the stability and safety of deep CO2 storage reservoirs.

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

Meta-Omics Approaches Reveal Unique Small RNAs Exhibited by the Uncultured Microorganisms Dwelling Deep-Sea Hydrothermal Sediment in Guaymas Basin

Small regulatory RNAs (sRNAs) are present in almost all investigated microbes, regarded as modulators and regulators of gene expression and also known to play their regulatory role in the environmentally significant process. It has been estimated that less than 1% of the microbes in nature are culturable in the laboratory, hindering our understanding of their physiology, and living strategies. However, recent big advancing of DNA sequencing and omics-related data analysis makes the understanding of the genetics, metabolic potentials, even ecological roles of uncultivated microbes possible. In this study, we used a metagenome and metatranscriptome based integrated approach to identifying small RNAs in the microbiome of Guaymas Basin sediments. Hundreds of environmental sRNAs comprising of 228 groups were identified based on their homology, 82% of which displayed high similarity with previously known small RNAs in Rfam database, whereas, “18%” are putative novel sRNA motifs. A putative cis-acting sRNA potentially binding to methyl coenzyme M reductase, a key enzyme in methanogenesis or anaerobic oxidation of methane (AOM), was discovered in the genome of ANaerobic MEthane oxidizing archaea group 1 (ANME-1), which were the dominate microbe in the sample. These sRNAs were actively expressed in local Guaymas Basin hydrothermal environment, suggesting important roles of sRNAs in regulating microbial activity in natural environments.

Measurement report: Photochemical production and loss rates of formaldehyde and ozone across Europe

Various atmospheric sources and sinks regulate the abundance of tropospheric formaldehyde (HCHO), which is an important trace gas impacting the HOx (≡ HO2 + OH) budget and the concentration of ozone (O3). In this study, we present the formation and destruction terms of ambient HCHO and O3 calculated from in situ observations of various atmospheric trace gases measured at three different sites across Europe during summertime. These include a coastal site in Cyprus, in the scope of the Cyprus Photochemistry Experiment (CYPHEX) in 2014, a mountain site in southern Germany, as part of the Hohenpeißenberg Photochemistry Experiment (HOPE) in 2012, and a forested site in Finland, where measurements were performed during the Hyytiälä United Measurements of Photochemistry and Particles (HUMPPA) campaign in 2010. We show that, at all three sites, formaldehyde production from the OH oxidation of methane (CH4), acetaldehyde (CH3CHO), isoprene (C5H8) and methanol (CH3OH) can almost completely balance the observed loss via photolysis, OH oxidation and dry deposition. Ozone chemistry is clearly controlled by nitrogen oxides (NOx ≡ NO + NO2) that include O3 production from NO2 photolysis and O3 loss via the reaction with NO. Finally, we use the HCHO budget calculations to determine whether net ozone production is limited by the availability of VOCs (volatile organic compounds; VOC-limited regime) or NOx (NOx-limited regime). At the mountain site in Germany, O3 production is VOC limited, whereas it is NOx limited at the coastal site in Cyprus. The forested site in Finland is in the transition regime.

KINETIC ISOTOPIC EFFECT: STATIC RAYLEIGH EQUATION AND BASIC DYNAMIC ISOTOPE EQUATION FOR THE SUBSTRATE IN THE DESCRIPTION OF NITRITE-DEPENDENT ANAEROBIC OXIDATION OF METHANE

The article analyzes the results of modeling the dynamics of nitrite-dependent methane oxidation (N-DAMO) by Methylomirabilis oxyfera microorganisms using the standard isotope dynamic equations. Without specifying a specific function of the rate of the process, the traditional static Rayleigh equation is derived from the basic dynamic isotope equation. Thus, the equation of the 1st order in terms of the substrate is only a special case in the derivation of the Rayleigh equation. It was shown that the dominant fractionation of carbon isotopes occurs in the process of the microbiological reaction of anaerobic oxidation of methane by nitrite, and not in the physical process of mass transfer of dissolved methane into the gas phase. In contrast to the static Rayleigh equation, the dynamic description of the process of fractionation of stable isotopes is important when describing the parallel transformations of the substrate.