Methanobacterium thermoautotrophicum ⌬H, isolated in 1971 from sewage sludge in Urbana, Ill. (72), is a lithoautotrophic, thermophilic archaeon that grows at temperatures ranging from 40 to 70°C and optimally at 65°C. M. thermoautotrophicum conserves energy by using H 2 to reduce CO 2 to CH 4 and synthesizes all of its cellular components from these same gaseous substrates plus N 2 or NH 4 ϩ and inorganic salts, but despite this impressive biosynthetic capacity, M. thermoautotrophicum ⌬H and related strains have very small genomes (ϳ1.7 Ϯ 0.2 Mb [57,58]). M. thermoautotrophicum ⌬H, Marburg, and Winter are the foci of many methanogenesis, archaeal physiology, and molecular biology investigations, and M. thermoautotrophicum ⌬H was chosen as a representative of this group for genome sequencing. These thermophilic methanogens have mesophilic and hyperthermophilic relatives, Methanobacterium formicicum and Methanothermus fervidus, respectively, so that comparisons can be made of homologous

Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans.

Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix, with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, shedding light on the origin of the nucleosome.

Inhabitants of a cryoconite hole formed in the Canada Glacier in the McMurdo Dry Valley region of Antarctica have been isolated and identified by small subunit (16S/18S) rDNA amplification, cloning, and sequencing. The sequences obtained revealed the presence of members of eight bacterial lineages (Acidobacterium, Actinobacteria, Cyanobacteria, Cytophagales, Gemmimonas, Planctomycetes, Proteobacteria, and Verrucomicrobia) and metazoan (nematode, tardigrade, and rotifer), truffle (Choiromyces), ciliate (Spathidium), and green algal (Pleurastrium) Eukarya. Bacterial recovery was approximately 20-fold higher at 4 degrees C and 15 degrees C than at 22 degrees C, and obligately psychrophilic bacteria were identified and isolated. Several of the rDNA molecules amplified from isolates and directly from cryoconite DNA preparations had sequences similar to rDNA molecules of species present in adjacent lake ice and microbial mat environments. This cryoconite hole community was therefore most likely seeded by particulates from these local environments. Cryoconite holes may serve as biological refuges that, on glacial melting, can repopulate the local environments.

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SummaryArchaea contain a variety of sequence-independent DNA binding proteins consistent with the evolution of several different, sometimes overlapping and exchangeable solutions to the problem of genome compaction. Some of these proteins undergo residuespecific post-translational lysine acetylation or methylation, hinting at analogues of the histone modifications that regulate eukaryotic chromatin structure and transcription. Archaeal transcription initiation most closely resembles the eukaryotic RNA polymerase II (RNAPII) system, but Archaea do not appear to have homologues of the multisubunit complexes that remodel eukaryotic chromatin and activate RNAPII initiation. In contrast, they have sequence-specific regulators that repress and perhaps activate archaeal transcription by mechanisms superficially similar to the bacterial paradigm of regulating promoter binding by RNAP. Repressors compete with archaeal TATAbox binding protein (TBP) and TFB for the TATA-box and TFB-recognition elements (BRE) of the archaeal promoter, or with archaeal RNAP for the site of transcription initiation. Transcript-specific regulation by repressors binding to sites of transcript initiation is consistent with such sites having very little sequence conservation. However, most Archaea have only one TBP and/or TFB that presumably must therefore bind to similar TATA-box and BRE sequences upstream of most genes. Repressors that function by competing with TBP and/or TFB binding must therefore also make additional contacts with transcript-specific regulatory sites adjacent or remote from the TATA-box/ BRE region. The fate of the archaeal TBP and TFB following transcription initiation remains to be determined. Based on functional homology with their eukaryotic RNAPII-system counterparts, archaeal TBP and possibly also TFB should remain bound to the TATA-box/BRE region after transcription initiation. However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation.

Lake Vostok, the largest subglacial lake in Antarctica, is separated from the surface by approximately 4 km of glacial ice. It has been isolated from direct surface input for at least 420 000 years, and the possibility of a novel environment and ecosystem therefore exists. Lake Vostok water has not been sampled, but an ice core has been recovered that extends into the ice accreted below glacial ice by freezing of Lake Vostok water. Here, we report the recovery of bacterial isolates belonging to the Brachybacteria, Methylobacterium, Paenibacillus and Sphingomonas lineages from a sample of melt water from this accretion ice that originated 3593 m below the surface. We have also amplified small-subunit ribosomal RNA-encoding DNA molecules (16S rDNAs) directly from this melt water that originated from alpha- and beta-proteobacteria, low- and high-G+C Gram-positive bacteria and a member of the Cytophaga/Flavobacterium/Bacteroides lineage.