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Open Access Publications from the University of California

Earth and Planetary Science - Open Access Policy Deposits

This series is automatically populated with publications deposited by UC Berkeley Department of Earth and Planetary Science researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Cover page of 3D architecture and complex behavior along the simple central San Andreas fault.

3D architecture and complex behavior along the simple central San Andreas fault.


The central San Andreas Fault (CSAF) exhibits a simple linear large-scale fault geometry, yet seismic and aseismic deformation features vary in a complex way along the fault. Here we investigate fault zone behaviors using geodetic observation, seismicity and microearthquake focal mechanisms. We employ an improved focal-mechanism characterization method using relative earthquake radiation patterns on 75,164 Ml ≥ 1 earthquakes along a 2-km-wide, 190-km-long segment of the CSAF, from 1984 to 2015. The data reveal the 3D fine-scale structure and interseismic kinematics of the CSAF. Our findings indicate that the first-order spatial variations in interseismic fault creep rate, creep direction, and the fault zone stress field can be explained by a simple fault coupling model. The inferred 3D mechanical properties of a mechanically weak and poorly coupled fault zone provide a unified understanding of the complex fine-scale kinematics, indicating distributed slip deficits facilitating small-to-moderate earthquakes, localized stress heterogeneities, and complex multi-scale ruptures along the fault. Through this detailed mapping, we aim to relate the fine-scale fault architecture to potential future faulting behavior along the CSAF.

Cover page of Superconductivity in Dilute Hydrides of Ammonia under Pressure

Superconductivity in Dilute Hydrides of Ammonia under Pressure


The past decade has witnessed great progress in predicting and synthesizing polyhydrides that exhibit superconductivity under pressure. Dopants allow these compounds to become metals at pressures lower than those required to metallize elemental hydrogen. Here, we show that by combining the fundamental planetary building blocks of molecular hydrogen and ammonia, conventional superconducting compounds can be formed at high pressure. Through extensive theoretical calculations, we predict metallic metastable structures with NHn (n = 10, 11, 24) stoichiometries that are based on NH4+ superalkali cations and complex hydrogenic lattices. The hydrogen atoms in the molecular cation contribute to the superconducting mechanism, and the estimated superconducting critical temperatures, Tc's, are comparable to the highest values computed for the alkali metal polyhydrides. The largest calculated (isotropic Eliashberg) Tc is ∼180 K for Pnma-NH10 at 300 GPa. Our results suggest that other molecular cations can be mixed with hydrogen under pressure, yielding superconducting compounds.

Cover page of Stressful crystal histories recorded around melt inclusions in volcanic quartz

Stressful crystal histories recorded around melt inclusions in volcanic quartz


Magma ascent and eruption are driven by a set of internally and externally generated stresses that act upon the magma. We present microstructural maps around melt inclusions in quartz crystals from six large rhyolitic eruptions using synchrotron Laue X-ray microdiffraction to quantify elastic residual strain and stress. We measure plastic strain using average diffraction peak width and lattice misorientation, highlighting dislocations and subgrain boundaries. Quartz crystals across studied magma systems preserve similar and relatively small magnitudes of elastic residual stress (mean 53–135 MPa, median 46–116 MPa) in comparison to the strength of quartz (~ 10 GPa). However, the distribution of strain in the lattice around inclusions varies between samples. We hypothesize that dislocation and twin systems may be established during compaction of crystal-rich magma, which affects the magnitude and distribution of preserved elastic strains. Given the lack of stress-free haloes around faceted inclusions, we conclude that most residual strain and stress was imparted after inclusion faceting. Fragmentation may be one of the final strain events that superimposes stresses of ~ 100 MPa across all studied crystals. Overall, volcanic quartz crystals preserve complex, overprinted deformation textures indicating that quartz crystals have prolonged deformation histories throughout storage, fragmentation, and eruption.

Cover page of COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes

COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes


Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

Cover page of Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes.

Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes.


BACKGROUND: Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS: Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS: Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.

Chronostratigraphy of Miocene strata in the Berkeley Hills (California Coast Ranges, USA) and the arrival of the San Andreas transform boundary


Miocene strata of the Claremont, Orinda, and Moraga formations of the Berkeley Hills (California Coast Ranges, USA) record sedimentation and volcanism during the passage of the Mendocino triple junction and early evolution of the San Andreas fault system. Detrital zircon laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) age spectra indicate a change in sedimentary prove nance between the marine Claremont formation (Monterey Group) and the terrestrial Orinda and Moraga Formations associated with uplift of Franciscan Complex lithologies. A sandstone from the Claremont formation produced a detrital zircon chemical abrasion–isotope dilution–thermal ionization mass spec trometry (CA-ID-TIMS) maximum depositional age of 13.298 ± 0.046 Ma, indicating younger Claremont deposition than previously interpreted. A trachydacite tuff clast within the uppermost Orinda Formation yielded a CA-ID-TIMS U-Pb zircon date of 10.094 ± 0.018 Ma, and a dacitic tuff within the Moraga Formation produced a CA-ID-TIMS U-Pb zircon date of 9.974 ± 0.014 Ma. These results indicate rapid progression from subsidence in which deep-water siliceous sediments of the Claremont formation were deposited to uplift that was followed by subsidence during deposition of terrestrial sediments of the Orinda Forma tion and subsequent eruption of the Moraga Formation volcanics. We associate the Orinda tuff clast and Moraga volcanics with slab-gap volcanism that followed the passage of the Mendocino triple junction. Given the necessary time lag between triple junction passage and the removal of the slab that led to this volcanism, subsidence associated with ca. 13 Ma Claremont sedimentation and subsequent Orinda to Moraga deposition can be attributed to basin formation along the newly arrived transform boundary.

Tracking Rodinia Into the Neoproterozoic: New Paleomagnetic Constraints From the Jacobsville Formation


The paleogeography of Laurentia throughout the Neoproterozoic is critical for reconstructing global paleogeography due to its central position in the supercontinent Rodinia. We develop a new paleomagnetic pole from red siltstones and fine-grained sandstones of the early Neoproterozoic Jacobsville Formation which is now constrained to be ca. 990 Ma in age. High-resolution thermal demagnetization experiments resolve detrital remanent magnetizations held by hematite. These directions were reoriented within siltstone intraclasts and pass intraformational conglomerate tests—giving confidence that the magnetization is detrital and primary. An inclination-corrected mean paleomagnetic pole position for the Jacobsville Formation indicates that Laurentia's motion slowed down significantly following the onset of the Grenvillian orogeny. Prior rapid plate motion associated with closure of the Unimos Ocean between 1,110 and 1,090 Ma transitioned to slow drift of Laurentia across the equator in the late Mesoproterozoic to early Neoproterozoic. We interpret the distinct position of this well-dated pole from those in the Grenville orogen that have been assigned a similar age to indicate that the ages of the poles associated with the Grenville Loop likely need to be revised to be younger due to prolonged exhumation.

Cover page of The Northbrae rhyolite of Berkeley (California, USA) constrains motion of the proto-Hayward Fault

The Northbrae rhyolite of Berkeley (California, USA) constrains motion of the proto-Hayward Fault


Right-lateral transform motion associated with the Pacific-North American plate boundary in the modern-day San Francisco Bay Area occurs across a series of sub-parallel fault zones. Much of this motion is accommodated east of the San Andreas Fault by the faults of the East Bay fault system. A major tool for reconstructing the spatial and temporal history of fault motion is the correlation of offset Neogene volcanic rocks. These Neogene volcanics within the California Coast Ranges formed in association with the slab gap that grew as the Mendocino Triple Junction migrated northward. Some of the volcanic centres have been variably offset by subsequent strike-slip faulting. A felsic volcanic unit exposed in Berkeley, CA, known as the Northbrae rhyolite has variably been interpreted to be one of these Neogene volcanic units or to be a Mesozoic volcanic unit associated with the Coast Range ophiolite. A new U-Pb zircon date of 11.10 (Formula presented.) 0.09 Ma confirms the Neogene volcanic interpretation. This date is indistinguishable from previously published Ar/Ar dates from the Burdell Mountain volcanics of the North Bay region as well as a new U-Pb zircon date of 11.07 (Formula presented.) 0.10 Ma. In addition to the indistinguishable ages, similarities in bulk lithology, zircon crystallization/dissolution textures, and zircon trace element geochemistry are consistent with these rhyolites being associated with the same volcanic centre. This correlation implies that 40 (Formula presented.) 5 km of right-lateral offset occurred to the west of the modern-day position of the Hayward-Rodgers Creek fault zone. This offset represents (Formula presented.) 20% of the total offset along the East Bay fault system. A proto-Hayward Fault with a different geometry than that of the present-day played a significant role in the evolution of the fault system. This result highlights the dynamic spatiotemporal variability of strike-slip faults along transform margins.

Cover page of Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism



Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.


Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.


Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.