Publications

4887

Abstract The candidate archaeal phylum ‘Aigarchaeota’ contains microorganisms from terrestrial and subsurface geothermal ecosystems. The phylogeny and metabolic potential of Aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. Here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of Aigarchaeota in an oxic, hot spring filamentous ‘streamer’ community. Fluorescence in situ hybridization showed that these newly discovered Aigarchaeota are filamentous, which is consistent with the presence and transcription of an actin-encoding gene. Aigarchaeota filaments are intricately associated with other community members, which include both bacteria (for example, filamentous Thermocrinis spp.) and archaea. Metabolic reconstruction of genomic and metatranscriptomic data suggests that this aigarchaeon is an aerobic, chemoorganoheterotroph with autotrophic potential. A heme copper oxidase complex was identified in the environmental genome assembly and highly transcribed in situ. Potential electron donors include acetate, fatty acids, amino acids, sugars and aromatic compounds, which may originate from extracellular polymeric substances produced by other microorganisms shown to exist in close proximity and/or autochthonous dissolved organic carbon (OC). Transcripts related to genes specific to each of these potential electron donors were identified, indicating that this aigarchaeon likely utilizes several OC substrates. Characterized members of this lineage cannot synthesize heme, and other cofactors and vitamins de novo, which suggests auxotrophy. We propose the name Candidatus ‘Calditenuis aerorheumensis’ for this aigarchaeon, which describes its filamentous morphology and its primary electron acceptor, oxygen.

Summary The bacterial tree contains many deep‐rooting clades without any cultured representatives. One such clade is ‘ E ndomicrobia’, a class‐level lineage in the phylum E lusimicrobia represented so far only by intracellular symbionts of termite gut flagellates. Here, we report the isolation and characterization of the first free‐living member of this clade from sterile‐filtered gut homogenate of defaunated (starch‐fed) R eticulitermes santonensis . Strain R sa215 is a strictly anaerobic ultramicrobacterium that grows exclusively on glucose, which is fermented to lactate, acetate, hydrogen and CO 2 . Ultrastructural analysis revealed a G ram‐negative cell envelope and a peculiar cell cycle. The genome contains a single set of nif genes that encode homologues of G roup IV nitrogenases, which were so far considered to have functions other than nitrogen fixation. We documented nitrogenase activity and diazotrophic growth by measuring acetylene reduction activity and 15 N 2 incorporation into cell mass, and demonstrated that transcription of nifH and nitrogenase activity occur only in the absence of ammonium. Based on the ancestral relationship to ‘ C andidatus   E ndomicrobium trichonymphae’ and other obligate endosymbionts, we propose the name ‘ E ndomicrobium proavitum ’ gen. nov., sp. nov. for the first isolate of this lineage and the name ‘ E ndomicrobia ’ class. nov. for the entire clade.

ABSTRACT The draft genome sequence of “ Candidatus Liberibacter asiaticus” strain SGCA5 from an orange citrus tree in San Gabriel, California, is reported here. SGCA5 has a genome size of 1,201,445 bp, a G+C content of 36.4%, 1,152 predicted open reading frames (ORFs), and 42 RNA genes.

ABSTRACT The genome of “ Candidatus Profftella armatura” strain YCPA from Diaphorina citri in Guangdong, China, was sequenced. The strain has a chromosome of 457,565 bp, 24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNAs, and a plasmid, pYCPA54, of 5,458 bp with 23.9% G+C content and 5 ORFs.

ABSTRACT Here we present the draft genome of a distantly related member within the phylum Bacteriodetes , “ Candidatus Bacteroides periocalifornicus .” The draft genome sequence was assembled with metagenomic data from a patient with periodontitis. The closest relative has less than 68% average nucleic identity, supporting a novel family within Bacteriodetes .

ABSTRACT The draft genome sequence of “ Candidatus Liberibacter asiaticus” strain YCPsy from an Asian citrus psyllid ( Diaphorina citri ) in Guangdong, China, is reported here. The YCPsy strain has a genome size of 1,233,647 bp, 36.5% G+C content, 1,171 open reading frames (ORFs), and 53 RNAs.

ABSTRACT The draft genome sequence of “ Candidatus Liberibacter solanacearum” strain RSTM from a potato psyllid ( Bactericera cockerelli ) in California is reported here. The RSTM strain has a genome size of 1,286,787 bp, a G+C content of 35.1%, 1,211 predicted open reading frames (ORFs), and 43 RNA genes.