Molecular Biology

ABSTRACT “ Candidatus Synechococcus spongiarum” represents the widespread cyanobacterial symbionts found in marine sponges with relatively high genomic variability and likely important ecological roles. We present here the draft genome sequence of “ Candidatus Synechococcus spongiarum” m9, which was assembled from a metagenome of Theonella swinhoei sampled in the South China Sea.

ABSTRACT We describe the draft genome sequence of “ Candidatus Methylomonas sp. LWB” isolated from Movile Cave microbial mat samples. The genome contains both the soluble and particular methane monooxygenase; however, one of the putative particulate methane monooxygenase gene clusters is ordered pmoABC rather than in the canonical gene arrangement of pmoCAB .

ABSTRACT The anaerobic ammonium-oxidizing (anammox) bacterium “ Candidatus Brocadia sp. 40” demonstrated the fastest growth rate compared to others in this taxon. Here, we report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565 gene-coding regions, 41 tRNAs, and a single rrn operon.

ABSTRACT “ Candidatus Erwinia dacicola” is a Gammaproteobacterium that forms a symbiotic association with the agricultural pest Bactrocera oleae . Here, we present a 2.1-Mb draft hybrid genome assembly for “ Ca. Erwinia dacicola” generated from single-cell and metagenomic data.

ABSTRACT Iron- and manganese-depositing bacteria occur in many soils and all water systems, and their biogenic depositions of ochre in technical systems may cause severe clogging problems and monetary losses. “ Candidatus Viadribacter manganicus” is a small coccoid, iron- and manganese-depositing bacterium isolated from the Lower Oder Valley National Park, Germany.

Abstract Dactylopius species, known as cochineal insects, are the source of the carminic acid dye used worldwide. The presence of two Wolbachia strains in Dactylopius coccus from Mexico was revealed by PCR amplification of wsp and sequencing of 16S rRNA genes. A metagenome analysis recovered the genome sequences of Candidatus Wolbachia bourtzisii wDacA (supergroup A) and Candidatus Wolbachia pipientis wDacB (supergroup B). Genome read coverage, as well as 16S rRNA clone sequencing, revealed that wDacB was more abundant than wDacA. The strains shared similar predicted metabolic capabilities that are common to Wolbachia, including riboflavin, ubiquinone, and heme biosynthesis, but lacked other vitamin and cofactor biosynthesis as well as glycolysis, the oxidative pentose phosphate pathway, and sugar uptake systems. A complete tricarboxylic acid cycle and gluconeogenesis were predicted as well as limited amino acid biosynthesis. Uptake and catabolism of proline were evidenced in Dactylopius Wolbachia strains. Both strains possessed WO-like phage regions and type I and type IV secretion systems. Several efflux systems found suggested the existence of metal toxicity within their host. Besides already described putative virulence factors like ankyrin domain proteins, VlrC homologs, and patatin-like proteins, putative novel virulence factors related to those found in intracellular pathogens like Legionella and Mycobacterium are highlighted for the first time in Wolbachia. Candidate genes identified in other Wolbachia that are likely involved in cytoplasmic incompatibility were found in wDacB but not in wDacA.

“ Ca . Pelagibacter ubique” is a key driver of marine biogeochemistry cycles and a model for understanding how minimal genomes evolved in free-living anucleate organisms. This study explores the unusual sulfur acquisition strategy that has evolved in these cells, which lack assimilatory sulfate reduction and instead rely on reduced sulfur compounds found in oxic marine environments to meet their cellular quotas. Our findings demonstrate that the sulfur acquisition systems are constitutively expressed but the enzymatic steps leading to the essential sulfur-containing amino acid methionine are regulated by a unique array of riboswitches and genes, many of which are encoded in a rapidly evolving genome region. These findings support mounting evidence that streamlined cells have evolved regulatory mechanisms that minimize transcriptional switching and, unexpectedly, localize essential sulfur acquisition genes in a genome region normally associated with adaption to environmental variation.