Publications

4839

ABSTRACT The Sulfolobales archaea have been found inhabiting acidic hot springs all over the world. Here, we report the 1.798-Mbp draft genome sequence of the thermoacidophilic Sulfolobales archaeon AZ1, reconstructed from the metagenome of a Mexican hot spring. Sequence-based comparisons revealed that the Sulfolobales archaeon AZ1 represents a novel candidate genus.

ABSTRACT The draft genome sequence of “ Candidatus Liberibacter asiaticus” strain A4, isolated from a mandarin citrus in Guangdong, People's Republic of China, is reported. The A4 strain has a genome size of 1,208,625 bp, G+C content of 36.4%, 1,107 predicted open reading frames, and 53 RNA genes.

ABSTRACT Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. “ Candidatus Methylomirabilis oxyfera” is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase reaction. Previous genome analysis has suggested that, like the verrucomicrobial methanotrophs, “ Ca. Methylomirabilis oxyfera” encodes and transcribes genes for the Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. Here we provide multiple independent lines of evidence for autotrophic carbon dioxide fixation by “ Ca. Methylomirabilis oxyfera” via the CBB cycle. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme of the CBB cycle, in cell extracts from an “ Ca. Methylomirabilis oxyfera” enrichment culture was shown to account for up to 10% of the total methane oxidation activity. Labeling studies with whole cells in batch incubations supplied with either 13 CH 4 or [ 13 C]bicarbonate revealed that “ Ca. Methylomirabilis oxyfera” biomass and lipids became significantly more enriched in 13 C after incubation with 13 C-labeled bicarbonate (and unlabeled methane) than after incubation with 13 C-labeled methane (and unlabeled bicarbonate), providing evidence for autotrophic carbon dioxide fixation. Besides this experimental approach, detailed genomic and transcriptomic analysis demonstrated an operational CBB cycle in “ Ca. Methylomirabilis oxyfera.” Altogether, these results show that the CBB cycle is active and plays a major role in carbon assimilation by “ Ca. Methylomirabilis oxyfera” bacteria. Our results suggest that autotrophy might be more widespread among methanotrophs than was previously assumed and implies that a methanotrophic community in the environment is not necessarily revealed by 13 C-depleted lipids.

So far, anaerobic sulfate-dependent acetate oxidation at high pH has only been demonstrated for a low-salt-tolerant syntrophic association of a clostridium ‘CandidatusContubernalis alkalaceticum’ and its hydrogenotrophic sulfate-reducing partnerDesulfonatronum cooperativum. Anaerobic enrichments at pH 10 inoculated with sediments from hypersaline soda lakes of the Kulunda Steppe (Altai, Russia) demonstrated the possibility of sulfate-dependent acetate oxidation at much higher salt concentrations (up to 3.5 M total Na+). The most salt-tolerant purified cultures contained two major components apparently working in syntrophy. The primary acetate-fermenting component was identified as a member of the orderClostridialesforming, together with ‘Ca.Contubernalis alkalaceticum’, an independent branch within the familySyntrophomonadaceae. A provisional name, ‘Ca.Syntrophonatronum acetioxidans’, is suggested for the novel haloalkaliphilic clostridium. Two phylotypes of extremely haloalkaliphilic sulfate-reducing bacteria of the genusDesulfonatronospirawere identified as sulfate-reducing partners in the acetate-oxidizing cultures under extreme salinity. The dominant phylotype differed from the two species ofDesulfonatronospiradescribed so far, whilst a minor component belonged toDesulfonatronumthiodismutans. The results proved that, contrary to previous beliefs, sulfate-dependent acetate oxidation is possible, albeit very slowly, in nearly saturated soda brines.