Sulfolobus acidocaldariusis an aerobic thermoacidophilic crenarchaeon which grows optimally at 80°C and pH 2 in terrestrial solfataric springs. Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted protein-encoding genes. Many of the smaller genes were identified for the first time on the basis of comparison of threeSulfolobusgenome sequences. Of the protein-coding genes, 305 are exclusive toS. acidocaldariusand 866 are specific to theSulfolobusgenus. Moreover, 82 genes for untranslated RNAs were identified and annotated. Owing to the probable absence of active autonomous and nonautonomous mobile elements, the genome stability and organization ofS. acidocaldariusdiffer radically from those ofSulfolobus solfataricusandSulfolobus tokodaii. TheS. acidocaldariusgenome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange inS. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of otherSulfolobusspecies. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly identified protein-coding genes forSulfolobus, are incorporated into a publicSulfolobusdatabase which can be accessed athttp://dac.molbio.ku.dk/dbs/Sulfolobus.

The obligate intracellular bacterium Wolbachia pipientis infects around 20% of all insect species. It is maternally inherited and induces reproductive alterations of insect populations by male killing, feminization, parthenogenesis, or cytoplasmic incompatibility. Here, we present the 1,445,873-bp genome of W. pipientis strain w Ri that induces very strong cytoplasmic incompatibility in its natural host Drosophila simulans . A comparison with the previously sequenced genome of W. pipientis strain w Mel from Drosophila melanogaster identified 35 breakpoints associated with mobile elements and repeated sequences that are stable in Drosophila lines transinfected with w Ri. Additionally, 450 genes with orthologs in w Ri and w Mel were sequenced from the W. pipientis strain w Uni, responsible for the induction of parthenogenesis in the parasitoid wasp Muscidifurax uniraptor . The comparison of these A-group Wolbachia strains uncovered the most highly recombining intracellular bacterial genomes known to date. This was manifested in a 500-fold variation in sequence divergences at synonymous sites, with different genes and gene segments supporting different strain relationships. The substitution-frequency profile resembled that of Neisseria meningitidis , which is characterized by rampant intraspecies recombination, rather than that of Rickettsia , where genes mostly diverge by nucleotide substitutions. The data further revealed diversification of ankyrin repeat genes by short tandem duplications and provided examples of horizontal gene transfer across A- and B-group strains that infect D. simulans . These results suggest that the transmission dynamics of Wolbachia and the opportunity for coinfections have created a freely recombining intracellular bacterial community with mosaic genomes.

Chromosome replication origins were mapped in vivo in the two hyperthermophilic archaea, Sulfolobus acidocaldarius and Sulfolobus solfataricus , by using microarray-based marker frequency analysis. Bidirectional replication was found to be initiated in near synchrony from three separate sites in both organisms. Two of the three replication origins in each species were located in the vicinity of a cdc6 / orc1 replication initiation gene, whereas no known replication-associated gene could be identified near the third origin in either organism. In contrast to initiation, replication termination occurred asynchronously, such that certain replication forks continued to progress for >40 min after the others had terminated. In each species, all replication forks advanced at similar DNA polymerization rates; this was found to be an order of magnitude below that displayed by Escherichia coli and thus closer to eukaryotic elongation rates. In S. acidocaldarius , a region containing short regularly spaced repeats was found to hybridize aberrantly, as compared to the rest of the chromosome, raising the possibility of a centromere-like function.

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini-CRISPR array and a donor DNA containing a non-target sequence. Transformation of a pGE plasmid would yield two alternative fates to transformed cells: wild-type cells are to be targeted for chromosomal DNA degradation, leading to cell death, whereas those carrying the mutant gene would survive the cell killing and selectively retained as transformants. Using this strategy, different types of mutation were generated, including deletion, insertion and point mutations. We envision this method is readily applicable to different bacteria and archaea that carry an active CRISPR-Cas system of DNA interference provided the protospacer adjacent motif (PAM) of an uncharacterized PAM-dependent CRISPR-Cas system can be predicted by bioinformatic analysis.

It has been widely recognised that the threats to human health from global environmental changes (GECs) are increasing in the Anthropocene epoch, and urgent actions are required to tackle these pressing challenges. A scoping review was conducted to provide an overview of the nine planetary boundaries and the threats to population health posed by human activities that are exceeding these boundaries in the Anthropocene. The research progress and key knowledge gaps were identified in this emerging field. Over the past three decades, there has been a great deal of research progress on health risks from climate change, land-use change and urbanisation, biodiversity loss and other GECs. However, several significant challenges remain, including the misperception of the relationship between human and nature; assessment of the compounding risks of GECs; strategies to reduce and prevent the potential health impacts of GECs; and uncertainties in fulfilling the commitments to the Paris Agreement. Confronting these challenges will require rigorous scientific research that is well-coordinated across different disciplines and various sectors. It is imperative for the international community to work together to develop informed policies to avert crises and ensure a safe and sustainable planet for the present and future generations.