Molecular Biology

ABSTRACT “ Candidatus Phycosocius bacilliformis” is an alphaproteobacterial ectosymbiont of the hydrocarbon-producing green alga Botryococcus braunii . We sequenced the whole genome of “ Ca. P. bacilliformis” BOTRYCO-2, isolated from a two-membered culture with B. braunii . The genome contains approximately 3.3 Mb, with an average G+C content of 56.91% and 3,125 predicted protein-coding genes.

Citrus production throughout the world is being severely threatened by Huanglongbing (HLB), which is a disease associated with the bacteria ‘Candidatus Liberibacter asiaticus’ (CLas), africanus, and americanus. This Resource Announcement provides amplicon-based next generation sequencing (NGS) datasets of the bacterial and fungal rRNA internal transcribed spacer (ITS) region from CLas-infected citrus budwood, leaves, and roots from five orchards located in different geographical regions in Florida (USA). To our knowledge, this is the first amplicon-based NGS study (i) that describes the fungal taxa associated with citrus and (ii) that provides comparative analyses of the bacterial and fungal taxa associated with budwood, leaves, and roots from the same citrus trees. This report also provides the sample metadata linked to these sequence datasets including HLB severity rating, tissue type, citrus rootstock, citrus scion, geographical region, and year trees were planted. When analyzed with other similar datasets, we anticipate that researchers will be able to obtain a greater understanding of the factors that shape the citrus microbiome as well as identify individual microorganisms or consortia of microorganisms that play a role in HLB suppression or exacerbation.

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.

ABSTRACT The high-quality draft genome of “ Candidatus Methanoperedens sp.” strain BLZ2, a nitrate-reducing archaeon anaerobically oxidizing methane, is presented. The genome was obtained from an enrichment culture and measures 3.74 Mb. It harbors two nitrate reductase gene clusters, an ammonium-forming nitrite reductase, and the complete reverse methanogenesis pathway. Methane that escapes to the atmosphere acts as a potent greenhouse gas. Global methane emissions are mitigated by methanotrophs, which oxidize methane to CO 2 . “ Candidatus Methanoperedens spp.” are unique methanotrophic archaea that can perform nitrate-dependent anaerobic oxidation of methane. A high-quality draft genome sequence of only 85 contigs from this archaeon is presented here.

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.