Geobiology of the late Paleoproterozoic Duck Creek Formation, Western Australia

The ca. 1.8 Ga Duck Creek Formation, Western Australia, preserves 1000 m of carbonates and minor iron formation that accumulated along a late Paleoproterozoic ocean margin. Two upward-deepening stratigraphic packages are preserved, each characterized by peritidal precipitates at the base and iron formation and carbonate turbidites in its upper part. Consistent with recent studies of Neoarchean basins, carbon isotope ratios of Duck Creek carbonates show no evidence for a strong isotopic depth gradient, but carbonate minerals in iron formations can be markedly depleted in C-13. In contrast, oxygen isotopes covary strongly with depth; delta O-18 values as positive as 2%. VPDB in peritidal facies systematically decline to values of 6 to 16% in basinal rocks, reflecting, we posit, the timing of diagenetic closure. The Duck Creek Formation contains microfossils similar to those of the Gunflint Formation, Canada; they are restricted to early diagenetic cherts developed in basinal facies, strengthening the hypothesis that such fossils capture communities driven by iron metabolism. Indeed, X-ray diffraction data indicate that the Duck Creek basin was ferruginous throughout its history. The persistence of ferruginous waters and iron formation deposition in Western Australia for at least several tens of millions of years after the transition to sulfidic conditions in Laurentia suggests that the late Paleoproterozoic expansion of sulfidic subsurface waters was globally asynchronous

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat: a paired nanoSIMS and CARD-FISH approach

The metabolic activities of microbial mats have likely regulated biogeochemical cycling over most of Earth's history. However, the relationship between metabolic activity and the establishment of isotopic geochemical gradients in these mats remains poorly constrained. Here we present a parallel microgeochemical and microbiological study of micron-scale sulfur cycling within hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. Dissolved sulfide within the mats was captured on silver discs and analyzed for its abundance and δ^(34)S isotopic composition using high-resolution secondary ion mass spectrometry (nanoSIMS). These results were compared to sulfide and oxygen microelectrode profiles. Two-dimensional microgeochemical mapping revealed well-defined laminations in sulfide concentration (on scales from 1 to 200 μm), trending toward increased sulfide concentrations at depth. Sulfide δ^(34)S decreased from ~+10‰ to −20‰ in the uppermost 3 mm and oscillated repeatedly between −10‰ and −30‰ down to a depth of 8 mm. These variations are attributed to spatially variable bacterial sulfate reduction within the mat. A parallel examination of the spatial distribution of known sulfate-reducing bacteria within the family Desulfobacteraceae was conducted using catalyzed reporter deposition fluorescence in situ hybridization. Significant concentrations of Desulfobacteraceae were observed in both oxic and anoxic zones of the mat and occurred in several distinct layers, in large aggregates and heterogeneously dispersed as single cells throughout. The spatial distribution of these microorganisms is consistent with the variation in sulfide concentration and isotopic composition we observed. The parallel application of the methodologies developed here can shed light on micron-scale sulfur cycling within microbially dominated sedimentary environments

The ties that bind: Dynamics of syntrophic associations in marine methane seeps

The deep-sea methane seep environment supports active and diverse microbial assemblages supported by the anaerobic oxidation of methane (AOM). Unknown to science less than a decade ago, the microorganisms and the molecular mechanisms underlying this enigmatic and globally important biogeochemical process have been the subject of intensive study worldwide. The identification, activity, distribution, and partial metabolic pathway reconstruction of methanotrophic archaea and co-associated sulfate reducing bacteria has been characterized. However fundamental questions still remain regarding the necessity of a physically coupled syntrophic association between sulfate reducing bacteria and methane oxidizing archaea, the underlying biochemistry enabling sulfate-coupled methane oxidation, and the extent of the diversity of microbial assemblages involved in AOM. Using microanalytical stable isotope analyses of whole cells in tandem with genomics enabled molecular methods, we examined the variation in metabolic activity between individual aggregations of microorganisms recovered from methane seep sediments. Significant differences in activity were observed between archaeal-bacterial associations and mono-specific aggregations of putative methanotrophic archaea and sulfate-reducing populations, supporting enhanced metabolism in multi-species aggregates. Application of a new SSU rRNA targeted method for capturing and concentrating specific uncultured microbial populations from methane seep sediments has uncovered novel partnerships and additional insights into the metabolic potential of the methanotrophic archaea and co-associated bacteria

Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat

We present a parallel microgeochemical and microbiological study of μm-scale sulfur cycling within hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. Diel variations (day/night) in sulfur cycling were investigated in field incubations as well as in mats grown under controlled conditions in the laboratory at NASA Ames Research Center. Sulfur cycling in the laboratory mats was examined under a variety of different sulfate concentrations to evaluate the role this had on sulfide concentration and isotopic composition. Sulfate levels in the overlying water column were: 80 mM SO_4 (natural level at Guerrero Negro); 1 mM SO_4; and 200 uM SO_4. Dissolved sulfide within the mat was captured on silver discs and analyzed for its abundance and δ^(34)S isotopic composition using high resolution secondary ion mass spectrometry (SIMS) on a Cameca 7F Geo