To understand the impact of particle size on phase stability and phase transformation during growth of nanocrystalline aggregates we conducted experiments using titania (TiO2) samples consisting of nanocrystalline anatase (46.7 wt %, 5.1 nm) and brookite (53.3 wt %, 8.1 nm). Reactions were studied isochronally at reaction times of 2 h in the temperature range 598−1023 K and isothermally at 723, 853, and 973 K by X-ray diffraction (XRD). A numerical deconvolution method was developed to separate overlapping XRD peaks, and an analytical method for determining phase contents of anatase, brookite, and rutile from XRD data was established. Results show that, in contrast to previous studies, anatase in our samples transforms to brookite and/or rutile before brookite transforms to rutile. Thermodynamic and kinetic analyses further support this conclusion. For general titania samples, the transformation sequence among anatase and brookite depends on the initial particle sizes of anatase and brookite, since particle sizes determine the thermodynamic phase stability at ultrafine sizes. These results highlight extremely important size-dependent behavior that may be expected in other nanocrystalline systems where multiple polymorphs are possible.

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Crystal growth during hydrothermal coarsening of mercaptoethanol-capped nanocrystalline ZnS occurs via a two-stage process. In the first stage, the primary particle quickly doubles in volume. The initial growth rate can be fitted by an asymptotic curve that cannot be explained by any existing power-law dependence kinetic model developed for more coarsely crystalline material. High-resolution transmission electron microscope (HRTEM) data indicate that crystal growth within spherical nanoparticle aggregates occurs via crystallographically specific oriented attachment, despite the presence of surface-bound organic ligands. The size stabilizes for a period of time that depends on the coarsening temperature. In the second stage, following the dispersal of nanoparticles, an abrupt transition from asymptotic to cubic parabola growth kinetics occurs. The crystal growth data can be fitted by a standard Ostwald ripening volume diffusion model consistent with growth controlled by the volume diffusion of ions in solution. However, HRTEM data indicate that oriented attachment-based growth occurs in the early part of the second stage, followed by a significant reduction in aggregate surface topography, probably via surface diffusion as well as volume diffusion. We propose a new kinetic model based on oriented attachment-based growth to explain the asymptotic growth in the first stage of coarsening. The presence of surface-bound organic ligands may control the aggregation state of the nanoparticles and may permit an almost exclusive crystallographically specific oriented attachment-based growth to dominate in the first stage.

Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.Phages-viruses that infect bacteria-are considered distinct from cellular life owing to their inability to carry out most biological processes required for reproduction. They are agents of ecosystem change because they prey on specific bacterial populations, mediate lateral gene transfer, alter host metabolism and redistribute bacterially derived compounds through cell lysis 2-4 . They spread antibiotic resistance 5 and disperse pathogenicity factors that cause disease in humans and animals 6,7 . Most knowledge about phages is based on laboratorystudied examples, the vast majority of which have genomes that are a few tens of kb in length. Widely used isolation-based methods select against large phage particles, and they can be excluded from phage concentrates obtained by passage through 100-nm or 200-nm filters 1 . In 2017, only 93 isolated phages with genomes that were more than 200 kb in length were published 1 . Sequencing of whole-community DNA can uncover phage-derived fragments; however, large genomes can still escape detection owing to fragmentation 8 . A new clade of human-and animal-associated megaphages was recently described on the basis of genomes that were manually curated to completion from metagenomic datasets 9 . This finding prompted us to carry out a more-comprehensive analysis of microbial communities to evaluate the prevalence, diversity and ecosystem distribution of phages with large genomes. Previously, phages with genomes of more than 200 kb have been referred to as 'jumbophages' 1 or, in the case of phages with genomes of more than 500 kb, as megaphages 9 . As the set reconstructed here span both size ranges we refer to them simply as 'huge phage...

Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation ‘Melainabacteria’. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut.DOI: http://dx.doi.org/10.7554/eLife.01102.001

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Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane oxidizing archaea. Five of these MAGs represent under-sampled (e.g., Verstraetearchaeota, Methanonatronarchaeia, ANME-1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation significantly expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘ Ca . Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

CRISPR-Cas systems are found widely in prokaryotes, where they provide adaptive immunity against virus infection and plasmid transformation. We describe a minimal functional CRISPR-Cas system, comprising a single ~70-kilodalton protein, CasΦ, and a CRISPR array, encoded exclusively in the genomes of huge bacteriophages. CasΦ uses a single active site for both CRISPR RNA (crRNA) processing and crRNA-guided DNA cutting to target foreign nucleic acids. This hypercompact system is active in vitro and in human and plant cells with expanded target recognition capabilities relative to other CRISPR-Cas proteins. Useful for genome editing and DNA detection but with a molecular weight half that of Cas9 and Cas12a genome-editing enzymes, CasΦ offers advantages for cellular delivery that expand the genome editing toolbox.