Biochemistry

Summary Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture‐independent approaches to characterization. Biocathode MCL ( Marinobacter , Chromatiaceae , Labrenzia ) is a microbial community proposed to couple CO 2 fixation to extracellular electron transfer and O 2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system ( BES ) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES , we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady‐state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units ( OTU s) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTU s were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing ‘ Ca . Tenderia electrophaga’ was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.

Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we describe the genome of an uncultured symbiotic bacterium that makes such a cytotoxic metabolite. This symbiont is losing genes that do not endow a selective advantage in a hospitable host environment. Secondary metabolism genes, however, are repeated multiple times in the genome, directly demonstrating their selective advantage. This finding shows the strength of selective forces in symbiotic relationships and suggests that uncultured bacteria in such relationships should be targeted for drug discovery efforts.

Nitrospira -like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

Summary A novel candidate species of the liberibacter genus, ‘ Candidatus Liberibacter brunswickensis’ ( CL br), was identified in the Australian eggplant psyllid, Acizzia solanicola . This is the first discovery of a species belonging to the liberibacter genus in Australia and the first report of a liberibacter species in the psyllid genus Acizzia . This new candidate liberibacter species has not been associated with plant disease, unlike other psyllid‐vectored species in the genus including ‘ Candidatus Liberibacter asiaticus ’ ( CL as), ‘ Candidatus Liberibacter africanus’ ( CL af) and ‘ Ca . Liberibacter solanacearum’ ( CL so). This study describes novel generic liberibacter genus primers, used to screen Australian psyllids for the presence of microflora that may confound diagnosis of exotic pathogens. CL br forms a unique clade in the liberibacter genus based on phylogenetic analysis of the 16S ribosomal ribonucleic acid ( rRNA ) region and multilocus sequence analysis ( MLSA ) of seven highly conserved genes, dnaG , gyrB , mutS , nusG , rplA , rpoB and tufB . The MLSA mapping approach described in this article was able to discriminate between two ‘ Ca . Liberibacter’ species within a metagenomic data set and represents a novel approach to detecting and differentiating unculturable species of liberibacter. Further, CL br can confound the Li et al . (2006) quantitative PCR ( qPCR ) diagnostic tests for CL as and CL af.