Suzanne D. Golding

Bio: Suzanne D. Golding is an academic researcher from University of Queensland. The author has contributed to research in topics: Coal & Coal mining. The author has an hindex of 42, co-authored 220 publications receiving 5537 citations. Previous affiliations of Suzanne D. Golding include University of Melbourne & Cooperative Research Centre.

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

Abstract: Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl–coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.

Continental-scale magmatic carbon-dioxide seepage recorded by Dawsonite in the Bowen-Gunnedah-Sydney Basin System, eastern Australia

Abstract: Dawsonite, NaAlCO3(OH)2, is widespread as a cement, replacement, and cavity filling in Permo-Triassic sedimentary rocks of the Bowen-Gunnedah-Sydney basin system, eastern Australia. The origin of dawsonite in these rocks was studied by petrographic and stable isotope analysis. Dawsonite d13C (PDB) values range from -4.0 to +4.1% and are remarkably consistent throughout the Bowen-Gunnedah-Sydney basin system. These values indicate either a marine carbonate or magmatic source for carbon in the dawsonite. A magmatic carbon source is considered more likely on the basis that (1) evidence of and the cause for widespread marine carbonate dissolution in the sedimentary successions are not apparen , (2) dawsonite is widespread in both marine and nonmarine facies, (3) the region has been the site of major igneous activity, (4) other dawsonite deposits of similar carbon isotopic composition are linked to igneous activity, and (5) magmatic CO2 accumulations are known in parts of the Bowen-Gunnedah. Sydney basin system. The timing of igneous activity in the Bowen Basin constrains the timing of dawsonite formation in the Bowen-Gunnedah-Sydney basin system to the Tertiary, consistent with textural relationships, which indicate that dawsonite formed late during the burial history of the Permo-Triassic sequences. The distribution and interpreted origin of dawsonite implies magmatic CO2 seepage in the Bowen-Gunnedah-Sydney basin system on a continental scale.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Porphyry Copper Systems

Abstract: Porphyry Cu systems host some of the most widely distributed mineralization types at convergent plate boundaries, including porphyry deposits centered on intrusions; skarn, carbonate-replacement, and sediment-hosted Au deposits in increasingly peripheral locations; and superjacent high- and intermediate-sulfidation epithermal deposits. The systems commonly define linear belts, some many hundreds of kilometers long, as well as occurring less commonly in apparent isolation. The systems are closely related to underlying composite plutons, at paleodepths of 5 to 15 km, which represent the supply chambers for the magmas and fluids that formed the vertically elongate (>3 km) stocks or dike swarms and associated mineralization. The plutons may erupt volcanic rocks, but generally prior to initiation of the systems. Commonly, several discrete stocks are emplaced in and above the pluton roof zones, resulting in either clusters or structurally controlled alignments of porphyry Cu systems. The rheology and composition of the host rocks may strongly influence the size, grade, and type of mineralization generated in porphyry Cu systems. Individual systems have life spans of ~100,000 to several million years, whereas deposit clusters or alignments as well as entire belts may remain active for 10 m.y. or longer. The alteration and mineralization in porphyry Cu systems, occupying many cubic kilometers of rock, are zoned outward from the stocks or dike swarms, which typically comprise several generations of intermediate to felsic porphyry intrusions. Porphyry Cu ± Au ± Mo deposits are centered on the intrusions, whereas carbonate wall rocks commonly host proximal Cu-Au skarns, less common distal Zn-Pb and/or Au skarns, and, beyond the skarn front, carbonate-replacement Cu and/or Zn-Pb-Ag ± Au deposits, and/or sediment-hosted (distal-disseminated) Au deposits. Peripheral mineralization is less conspicuous in noncarbonate wall rocks but may include base metal- or Au-bearing veins and mantos. High-sulfidation epithermal deposits may occur in lithocaps above porphyry Cu deposits, where massive sulfide lodes tend to develop in deeper feeder structures and Au ± Ag-rich, disseminated deposits within the uppermost 500 m or so. Less commonly, intermediate-sulfidation epithermal mineralization, chiefly veins, may develop on the peripheries of the lithocaps. The alteration-mineralization in the porphyry Cu deposits is zoned upward from barren, early sodic-calcic through potentially ore-grade potassic, chlorite-sericite, and sericitic, to advanced argillic, the last of these constituting the lithocaps, which may attain >1 km in thickness if unaffected by significant erosion. Low sulfidation-state chalcopyrite ± bornite assemblages are characteristic of potassic zones, whereas higher sulfidation-state sulfides are generated progressively upward in concert with temperature decline and the concomitant greater degrees of hydrolytic alteration, culminating in pyrite ± enargite ± covellite in the shallow parts of the litho-caps. The porphyry Cu mineralization occurs in a distinctive sequence of quartz-bearing veinlets as well as in disseminated form in the altered rock between them. Magmatic-hydrothermal breccias may form during porphyry intrusion, with some of them containing high-grade mineralization because of their intrinsic permeability. In contrast, most phreatomagmatic breccias, constituting maar-diatreme systems, are poorly mineralized at both the porphyry Cu and lithocap levels, mainly because many of them formed late in the evolution of systems. Porphyry Cu systems are initiated by injection of oxidized magma saturated with S- and metal-rich, aqueous fluids from cupolas on the tops of the subjacent parental plutons. The sequence of alteration-mineralization events charted above is principally a consequence of progressive rock and fluid cooling, from >700° to <250°C, caused by solidification of the underlying parental plutons and downward propagation of the lithostatic-hydrostatic transition. Once the plutonic magmas stagnate, the high-temperature, generally two-phase hyper-saline liquid and vapor responsible for the potassic alteration and contained mineralization at depth and early overlying advanced argillic alteration, respectively, gives way, at <350°C, to a single-phase, low- to moderate-salinity liquid that causes the sericite-chlorite and sericitic alteration and associated mineralization. This same liquid also causes mineralization of the peripheral parts of systems, including the overlying lithocaps. The progressive thermal decline of the systems combined with synmineral paleosurface degradation results in the characteristic overprinting (telescoping) and partial to total reconstitution of older by younger alteration-mineralization types. Meteoric water is not required for formation of this alteration-mineralization sequence although its late ingress is commonplace. Many features of porphyry Cu systems at all scales need to be taken into account during planning and execution of base and precious metal exploration programs in magmatic arc settings. At the regional and district scales, the occurrence of many deposits in belts, within which clusters and alignments are prominent, is a powerful exploration concept once one or more systems are known. At the deposit scale, particularly in the porphyry Cu environment, early-formed features commonly, but by no means always, give rise to the best ore-bodies. Late-stage alteration overprints may cause partial depletion or complete removal of Cu and Au, but metal concentration may also result. Recognition of single ore deposit types, whether economic or not, in porphyry Cu systems may be directly employed in combination with alteration and metal zoning concepts to search for other related deposit types, although not all those permitted by the model are likely to be present in most systems. Erosion level is a cogent control on the deposit types that may be preserved and, by the same token, on those that may be anticipated at depth. The most distal deposit types at all levels of the systems tend to be visually the most subtle, which may result in their being missed due to overshadowing by more prominent alteration-mineralization.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Abstract: Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.