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The ability to recover the oxygen reduction reaction of poisoned metal oxide surfaces, central to many energy related applications, is demonstrated by controlling relative surface acidity.

Knowledge of microbial gene functions comes from manipulating the DNA of individual strains in isolation from their natural communities. While this approach to microbial genetics has been foundational, its requirement for culturable microorganisms has left the majority of microbes and their interactions genetically unexplored. Here, we describe a generalizable strategy for editing the genomes of specific organisms within microbial communities. We identified genetically tractable bacteria within a community using Environmental Transformation Sequencing (ET-Seq), an approach in which non-targeted transposon integrations are mapped and quantified following community delivery. We next developed and used DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase (DART) systems formore » targeted DNA insertion into organisms identified as tractable by ET-Seq, enabling organism- and locus-specific genetic manipulation within the community context. To illustrate the utility of our approach, we selectively edited closely related strains, measured gene fitness, and enriched targeted members within soil and infant gut microbiota. These results establish a new paradigm for targeted community editing relevant to research and applications on medical, agricultural, and industrial microbiomes.« less

CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here that the inhibitor AcrVA4 uses a previously undescribed strategy to recognize the L. bacterium Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. The Ac. species Cas12a (AsCas12a) enzyme, widely used for genome editing applications, contains an ancestral helical bundle that blocks AcrVA4 binding and allows it to escape anti-CRISPR recognition. Using biochemical, microbiological, and human cellmore » editing experiments, we show that Cas12a orthologs can be rendered either sensitive or resistant to AcrVA4 through rational structural engineering informed by evolution. Together, these findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.« less

CRISPR-Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory "anti-CRISPR" (Acr) proteins, including six inhibitors (AcrIIA1-AcrIIA6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here that AcrIIA2 and its more potent homolog, AcrIIA2b, prevent Cas9 binding to DNA by occluding protein residues required for DNA binding. Cryo-EM-determined structures of AcrIIA2 or AcrIIA2b bound to S. pyogenes Cas9 reveal a mode of competitive inhibition of DNA binding that is distinct from other known Acrs. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arisemore » from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. Finally, these findings expand the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially, and conditionally.« less

Conversion and alloying electrode materials offer high specific capacity for emerging sodium- and potassium-ion batteries, but the larger volume changes compared to reaction with lithium are thought to limit cyclability. The reaction mechanisms of many materials with Na⁺ and K⁺ are unknown, however, and this knowledge is key for engineering mechanically resilient materials. Here, in situ transmission electron microscopy is used to uncover the nanoscale transformations during the reaction of FeS₂ electrode materials with Li⁺, Na⁺, and K⁺. Surprisingly, despite larger volume changes during the conversion reaction with Na⁺ and K⁺, the FeS₂ crystals only fracture during lithiation. Modeling ofmore » reaction-induced deformation shows that the shape of the two-phase reaction front influences stress evolution, and unique behavior during lithiation causes stress concentrations and fracture. The larger volume changes in Na- and K-ion battery materials may therefore be managed through understanding and control of reaction mechanisms, ultimately leading to better alkali-ion batteries.« less

Alloying anode materials offer high capacity for next-generation batteries, but the performance of these materials often decays rapidly with cycling because of volume changes and associated mechanical degradation or fracture. The direct measurement of crystallographic strain evolution in individual particles has not been reported, however, and this level of insight is critical for designing mechanically resilient materials. Here, we use operando X-ray diffraction to investigate strain evolution in individual germanium microparticles during electrochemical reaction with lithium. The diffraction peak was observed to shift in position and diminish in intensity during reaction because of the disappearance of the crystalline Ge phase.more » The compressive strain along the [111] direction was found to increase monotonically to a value of -0.21%. This finding is in agreement with a mechanical model that considers expansion and plastic deformation during reaction. As a result, this new insight into the mechanics of large-volume-change transformations in alloying anodes is important for improving the durability of high-capacity batteries.« less