Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte Chrysochromulina tobin

Abstract

The microalgal division Haptophyta uses a range of nutritional sourcing, including mixotrophy. The genome of a member of this taxon, Chrysochromulina tobin, suggests that interactions with its bacterial cohort are critical for C. tobin physiology. Here, we report the genomes of eight bacterial species in coculture with C. tobin.

GENOME ANNOUNCEMENT

Haptophytes encompass a large assemblage of microalgae that are abundant in both marine waters and freshwater environments, where they play an important role in global carbon sequestration (1, 2). The ecosystem dominance of these planktonic eukaryotes may be augmented by their mixotrophic ability to supplement photosynthesis with the acquisition of dissolved organic molecules, inorganic molecules, and particulate matter (including whole cells) from their surrounding medium (3).

Several haptophyte species have been observed to actively hunt bacteria using a specialized flagella-like appendage unique to haptophytes called the haptonema, suggesting that interaction of haptophytes with their eco-cohorts plays an important role in their physiology. This conclusion is further supported by recent sequencing of the genome of the haptophyte Chrysochromulina tobin. A notable observation is the putative dependence of C. tobin on its eco-cohorts for exogenous B₁₂ acquisition, given that the alga only encodes a B₁₂-dependent methionine synthase (4). To gain further insight into the metabolic interplay between C. tobin and its bacterial cohort, we carried out whole-genome sequencing of eight bacterial species of the nine identified bacteria present in coculture with this alga (Table 1).

TABLE 1 .

Genome features and GenBank accession numbers for eight bacterial species isolated in coculture with Chrysochromulina tobin

Organism	Accession no.	Genome size (bp)	Total no. of genes	No. of plasmids (plasmid accession no.)	Plasmid size (bp)	No. of plasmid-encoded genes	Fold coverage
Acidovorax sp. RAC01	CP016447	4,574,859	4,162	0	0		198
Sinorhizobium sp. RAC02	CP016450	6,626,583	6,327	1 (CP016451)			157
					258,555	566
Sphingobium sp. RAC03	CP016456	4,369,746	4,207	3 (CP016455, CP016454, CP016457)			242
					63,550	74
					49,737	52
					131,734	141
Blastomonas sp. RAC04	CP016460	4,403,499	4,178	4 (CP016461, CP016459, CP016458, CP016462)			298
					39,932	44
					42,134	52
					152,317	156
					186,489	189
Bosea sp. RAC05	CP016463	5.620,120	5,431	0	0		118
Agrobacterium sp. RAC06	CP016499	4,964,647	4,777	1 (CP016500)			329
					323,507	327
Hydrogenophaga sp. RAC07	CP016449	4,674,684	4,415	0	0		307
Methyloversatilis sp. RAC08	CP016448	3,937,190	3,610	0	0		305

Bacteria were isolated from a laboratory-maintained C. tobin P3 culture, grown in proprietary RAC5 medium (4). The bacteria were isolated using RAC5 medium supplemented with 0.2% yeast extract, 0.5% casamino acids, and 0.1% glycerol. For whole-genome sequencing, genomic DNA from each isolate was extracted using the Qiagen Puregene yeast/bacteria kit B. A Pacific Biosciences (5) single-molecule long-read library was constructed and sequenced for each bacterial isolate according to the manufacturer’s instructions. All genomes were assembled using HGAP version 2.2.0 (6) and were checked for misassemblies by mapping the data back to the consensus sequences using BridgeMapper version 2.3.0 (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Bridgemapper) and were corrected using Consed (7). Annotations of corrected assemblies were completed using an Ergatis workflow with minor manual curation (8). Bacterial taxonomic affinity was assessed by aligning PCR-recovered and genome-sequence-acquired 16S ribosomal DNA sequences using the SILVA Incremental Aligner (SINA) program (9). Six isolates are Alphaproteobacteria (Sinorhizobium sp. RAC02, Sphingobium sp. RAC03, Blastomonas sp. RAC04, Bosea sp. RAC05, Agrobacterium sp. RAC06, and Methyloversatilis sp. RAC08) and two isolates are Betaproteobacteria (Acidovorax sp. RAC01 and Hydrogenophaga sp. RAC07). Recovery of insufficient biomass precluded sequencing the genome of the final isolate, a Bacteroidetes sp. with >99% identity to Leadbetterella spp. Three of the eight bacterial isolates sequenced (Sinorhizobium sp. RAC02, Bosea sp. RAC05, and Agrobacterium sp. RAC08) encode the aerobic pathway for B₁₂ biosynthesis. It is unclear if these bacterial isolates produce B₁₂ in laboratory cultures of C. tobin since exogenous B₁₂ is provided in the algal culture medium. Further studies are needed to determine if these isolates play a role in providing B₁₂ to C. tobin under conditions where B₁₂ is limited.

Accession number(s).

The assembled and annotated genome sequences were deposited in GenBank under the accession numbers listed in Table 1.

Funding Statement

Funding for B.T.H. was provided by an Interdisciplinary Training Grant in Genomic Sciences (NHGRI T32-HG00035). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.