Metagenome-Assembled Genome Sequence of Rhodobacteraceae Bacterium Strain Clear-D3, Assembled from a Dolichospermum Consortium from Clear Lake, California

Here, we report the metagenome-assembled genome sequence of a Rhodobacteraceae bacterium strain, Clear-D3, that was reconstructed from a cyanobacterial enrichment from a eutrophic lake. The draft genome sequence shows evidence of an anoxygenic photoautotrophic lifestyle. Other potential capabilities include aerobic heterotrophy, flagellar motility, chemotaxis, and utilization of complex C-P compounds.

C yanobacterial harmful algal blooms (cyanoHABs) pose an environmental threat to freshwater bodies globally. Dolichospermum is a common genus of cyanoHABforming cyanobacteria. The frequency of Dolichospermum blooms has increased in recent years, prompting a need to investigate and understand the biological underpinnings of bloom formation (1). We generated enrichments from Dolichospermum aggregates to investigate microbial interactions supporting these common harmful algal bloom (HAB) communities. Metagenomic sequencing and assembly yielded a novel Rhodobacteraceae metagenome-assembled genome (MAG) that will help downstream efforts to understand Dolichospermum symbioses.
We collected Dolichospermum aggregates from surface water using a bucket tow in Clear Lake, CA (lat 38.973166, long 122.72809), in August 2019. Colonies were hand separated, enriched for a total of 7 months in 50% BG-11 0 medium (50% BG-11 0 medium contains 1 part BG-11 0 medium and 1 part sterile Milli-Q water), and incubated at 25°C at 100 mmol Q/m 2 /s on a 12:12-h light/dark cycle, with NaNO 3 excluded to promote the growth of diazotrophic taxa and their symbionts. Additional medium was added to the enrichments every 2 weeks to maintain growth. Prior to sequencing, we identified the core strain of the aggregates morphologically as a Dolichospermum sp.
The genome assembly pipeline yielded a 4,519,349-bp MAG we designated Clear-D3, which was taxonomically placed within the provisional genus TH137 in the family Rhodobacteraceae. Clear-D3 included 93 contigs (N 50 value, 168,577 bp) with a GC content of 65.25% and 4,396 coding sequences. The average coverage of the contigs was 41.28Â. CheckM v1.0.18 (12) predicted the genome as 98.44% complete with 1.73% contamination. Strain Clear-D3 has predicted complete central carbon metabolism (glycolysis, the tricarboxylic acid cycle, and NADH-quinone oxidoreductase), showing its potential for a heterotrophic lifestyle. However, it also has genes for the Calvin-Benson-Bassham cycle, anoxygenic type II reaction centers, and sulfite dehydrogenase (quinone), suggesting the potential for photolithoautotrophy. Furthermore, this MAG shows potential in both transporting (phnCED) and utilizing (C-P lyase tetradimer complex phnJGHI) phosphonate compounds.
Data availability. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JACVZW000000000. The version described in this paper is version JACVZW010000000. The BioProject number is PRJNA657201, and the reads are available at the SRA under accession number SRX8961729.

ACKNOWLEDGMENTS
This work was funded by the University of Southern California and was part of the laboratory component of BISC419, Environmental Microbiology.
We thank Elaina Graham, Ben Tully, and John F. Heidelberg for assistance with the data analysis.
C.C., K.M.F., E.A.W., and J.C.T. wrote the paper, and K.M.F. and E.A.W. are the sources of the cultures.