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Alkanes are major constituents of crude oil and are released to the marine environment by natural seepage and from anthropogenic sources. Due to their chemical inertness, their removal from anoxic marine sediments is primarily controlled by the activity of anaerobic alkane-degrading microorganisms. To facilitate comprehensive cultivation-independent surveys of the diversity and distribution of anaerobic alkane degraders, we designed novel PCR primers that cover all known diversity of the 1-methylalkyl succinate synthase gene (masD/assA), which catalyzes the initial activation of alkanes. We studied masD/assA gene diversity in pristine and seepage-impacted Danish coastal sediments, as well as in sediments and alkane-degrading enrichment cultures from the Middle Valley (MV) hydrothermal vent system in the Pacific Northwest. MasD/assA genes were ubiquitously present, and the primers captured the diversity of both known and previously undiscovered masD/assA gene diversity. Seepage sediments were dominated by a single masD/assA gene cluster, which is presumably indicative of a substrate-adapted community, while pristine sediments harbored a diverse range of masD/assA phylotypes including those present in seepage sediments. This rare biosphere of anaerobic alkane degraders will likely increase in abundance in the event of seepage or accidental oil spillage. Nanomolar concentrations of short-chain alkanes (SCA) were detected in pristine and seepage sediments. Interestingly, anaerobic alkane degraders closely related to strain BuS5, the only SCA degrader in pure culture, were found in mesophilic MV enrichments, but not in cold sediments from Danish waters. We propose that the new masD/assA gene lineages in these sediments represent novel phylotypes that are either fueled by naturally occurring low levels of SCA or that metabolize medium- to long-chain alkanes. Our study highlights that masD/assA genes are a relevant diagnostic marker to identify seepage and microseepage, e.g., during prospecting for oil and gas, and may act as an indicator of anthropogenic oil spills in marine sediments. [ABSTRACT FROM AUTHOR]

The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

Constraining the mechanisms that control organic matter (OM) reactivity and, thus, degradation, preservation and burial in marine sediments across spatial and temporal scales is key to understanding carbon cycling in the past, present, and future. However, we still lack a quantitative understanding of what controls OM reactivity in marine sediments and, as a result, how to constrain it in global models. To fill this gap, we quantify apparent OM reactivity (i.e., model-derived estimates) by extracting reactive continuum model parameters (a and v) from observed benthic organic carbon and sulfate dynamics across 14 contrasting depositional settings distributed over five distinct benthic provinces. Our analysis shows that the large-scale range in apparent OM reactivity is largely driven by the wide variability in parameter a (10-3 < a < 107) with a high frequency of values in the range 100 < a < 104 years. In contrast, inversely determined v-values fall within a narrow range (0.1 < v < 0.2). Results also show that the variability in parameter a and, thus, in apparent OM reactivity is a function of the whole depositional environment, rather than the traditionally proposed, single environmental controls (e.g., water depth, sedimentation rate, OM fluxes). Thus, we caution against the simplifying use of a single environmental predictor for apparent OM reactivity beyond a specific local environmental context. In addition, diagenetic model results also indicate that, while OM fluxes exert a dominant control on depth-integrated OM degradation rates across most depositional environments, apparent OM reactivity becomes a dominant control in depositional environments that receive exceptionally reactive OM. Model results also show that apparent OM reactivity largely controls the relative significance of OM degradation pathways, and thus the redox zonation of the sediment, as well as depth of the sulfate-methane transition zone and rates of anaerobic oxidation of methane. Consequently, apparent OM reactivity also determines uptake and consumption of benthic terminal electron acceptors and nutrient recycling fluxes across a wide range of different depositional environments. In summary, our large-scale assessment not only further support the notion of apparent OM reactivity as a dynamic ecosystem property and highlights its crucial role for benthic biogeochemical cycling and exchange, but it also provides the first quantitative constraint on the most plausible range of reactivity parameters a and v. It thus represents an important advance for model parameterization as it largely alleviates the difficulty of determining OM reactivity in such models by constraining it to only one variable, i.e. the parameter a. [ABSTRACT FROM AUTHOR]

Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0- 2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfaterich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous. [ABSTRACT FROM AUTHOR]