Publications

4512

AbstractGenome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been found in the uncultured bacterial WPS-2 clade that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a completely new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the nameCandidatusPalusbacterota for the phylum-level aerobic WPS-2 clade which contains phototrophic lineages, from the Latin for “bog bacteria”, distinguishing it from the anaerobic, non-phototrophic sister phylumCandidatusEremiobacterota for “desert bacteria”, typically found in dry environments.

The draft genome sequence of the green filamentous anoxygenic phototrophic (FAP) bacterium “ Candidatus Viridilinea halotolerans” strain Chok-6, isolated from a cold saline sulfide-rich spring near Lake Chokrak, is presented. The genome sequence is annotated for elucidation of the taxonomic position of Chok-6 and to extend the public genome database.

The draft genome sequence of “ Candidatus Liberibacter asiaticus” strain YNJS7C, isolated from a navel orange tree in Yunnan Province, China, is presented here. The YNJS7C strain has a genome size of 1,258,986 bp, with a G+C content of 36.6%, 1,174 predicted open reading frames, and 53 RNA genes.

The genome of “ Candidatus Sulcia muelleri” strain KPTW1 from Kolla paulula , a vector of Xylella fastidiosa that causes Pierce’s disease (PD) of grapevine in Taiwan, was sequenced. The strain has a genome size of 253,942 bp, GC content of 22.7%, 237 predicted protein-coding genes, and 34 RNA genes.

Summary The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN‐A) is one of the most abundant and widespread nitrogen (N 2 )‐fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase ( nifH ) gene sequences, including the four most commonly detected sublineages UCYN‐A1, UCYN‐A2, UCYN‐A3 and UCYN‐A4. However, very little is known about UCYN‐A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD‐FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN‐A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN‐A3 sublineage. We designed new CARD‐FISH probes that allowed us to distinguish and observe UCYN‐A2 in a coastal location (SIO Pier; San Diego) and UCYN‐A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN‐A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN‐A3 symbiosis in open ocean waters suggesting that the different UCYN‐A sublineages are distributed along different size fractions of the plankton defined by the cell‐size ranges of their prymnesiophyte hosts.