CRISPR/Cas9 systems are a versatile tool for genome editing due to the highly efficient targeting of DNA sequences complementary to their RNA guide strands. However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. A better understanding of the CRISPR/Cas9 specificity is needed to minimize off-target cleavage in large mammalian genomes. Here we show that genomic sites could be cleaved by CRISPR/Cas9 systems when DNA sequences contain insertions (‘DNA bulge’) or deletions (‘RNA bulge’) compared to the RNA guide strand, and Cas9 nickases used for paired nicking can also tolerate bulges in one of the guide strands. Variants of single-guide RNAs (sgRNAs) for four endogenous loci were used as model systems, and their cleavage activities were quantified at different positions with 1- to 5-bp bulges. We further investigated 114 putative genomic off-target loci of 27 different sgRNAs and confirmed 15 off-target sites, each harboring a single-base bulge and one to three mismatches to the guide strand. Our results strongly indicate the need to perform comprehensive off-target analysis related to DNA and sgRNA bulges in addition to base mismatches, and suggest specific guidelines for reducing potential off-target cleavage.

SummaryBacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. DNA sequences from SAR11 are also abundant in oxygen minimum zones (OMZs) where oxygen falls below detection and anaerobic microbes play important roles in converting bioavailable nitrogen to N2 gas. Evidence for anaerobic metabolism in SAR11 has not yet been observed, and the question of how these bacteria contribute to OMZ biogeochemical cycling is unanswered. Here, we identify the metabolic basis for SAR11 activity in anoxic ocean waters. Genomic analysis of single cells from the world’s largest OMZ revealed diverse and previously uncharacterized SAR11 lineages that peak in abundance at anoxic depths, but are largely undetectable in oxygen-rich ocean regions. OMZ SAR11 contain adaptations to low oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalyzing the nitrite-producing first step of denitrification and constituted ~40% of all OMZ nar transcripts, with transcription peaking in the zone of maximum nitrate reduction rates. These results redefine the ecological niche of Earth’s most abundant organismal group and suggest an important contribution of SAR11 to nitrite production in OMZs, and thus to pathways of ocean nitrogen loss.

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 s of sequencing data, the classifier achieves significantly higher accuracy than base calling followed by sequence alignment. Our approach is also faster and requires an order of magnitude less memory than alignment-based approaches. SquiggleNet distinguished human from bacterial DNA with over 90% accuracy, generalized to unseen bacterial species in a human respiratory meta genome sample, and accurately classified sequences containing human long interspersed repeat elements.

Dedication: To Katrina Edwards 18 19 Originality-Significance Statement: This work provides insights into the metabolism and 20 adaptations of elusive Atribacteria (JS-1 clade) that are ubiquitous and abundant in methane-rich 21 ecosystems. We show that JS-1 (Genus 1) from methane hydrate stability zones contain 22 metabolisms and stress survival strategies similar to hyperthermophilic archaea. 23 35 were downstream from a novel helix-turn-helix transcriptional regulator, AtiR, which was not 36 present in Atribacteria from other sites. Overall, Atribacteria appear to be endowed with unique 37 strategies that may contribute to its dominance in methane-hydrate bearing sediments. Active 38 microbial transport of amino and carboxylic acids in the gas hydrate stability zone may influence 39 gas hydrate stability. 40 41 131 132 JS-1 Genus-1 partial genome. To gain insight into the function of JS-1 Atribacteria in the 133 GHSZ, we analyzed a 4-Mbp metagenome-assembled genome (MAG) from sample E10-H5 134 (Table S3). This MAG, hereafter designated "B2", was chosen for its relatively high 135 completeness (69%) and low contamination (2%). B2 lacked a 16S rRNA gene, but contained a 136 rpoB gene with 94% similarity to Atribacteria bacterium 34_128 from an oil reservoir (Hu et al., 137 2016). B2 had 35% GC content, similar to other Atribacteria (Carr et al., 2015). Phylogenetic 138 placement based on 69 concatenated single-copy genes confirmed that B2 belonged to JS1-Genus 139 195 heterodisulfide reductase (HdrA)-methyl viologen hydrogenase (MvhAGD) complex (Fig. 4). A 196 redox-sensing transcriptional repressor gene (hunR) immediately upstream of the hun operon 197 J