Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data

Abstract

Background: The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome.

Results: Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment.

Conclusions: Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.

Keywords: Comparative genomics; Metagenomics; Microbial ecology.

Figure 1

Maximum likelihood tree generated using PHYML (bootstrap 1,000) of DNA primase (DnaG) identified in the four phylogenetic bins and other members of the class Flavobacteriaceae (489 amino acids). Only bootstrap values greater than 50% are shown.

Figure 2

Gene synteny map of a ~21 kbp homologous region identified using the progressiveMauve aligner. Annotations were generated using the RAST service. Arrows indicate putative CDS and the direction indicates strand orientation. CDS are color coded to indicate genes common between phylogenetic bins (green = identified in all four bins; black = only present in corresponding bin; purple = identified in FlavI and FlavG; grey = identified in FlavH, FlavI, and FlavG; orange = identified in FlavA, FlavH, and FlavI; blue = identified in FlavA and FlavH).

Figure 3

Gene synteny map of a ~64 kbp homologous region identified using the progressiveMauve aligner. Annotations were generated using the RAST service. Arrows indicate putative CDS; the direction of which indicates strand orientation. CDS are color coded to indicate genes common between phylogenetic bins (green = identified in all four bins; black = only present in corresponding bin; purple = identified in FlavI and FlavG; yellow = identified in FlavA, FlavG, and FlavH. Red asterisks denote putative CDS with identified glycoside hydrolase domains.

Figure 4

Diversity of the underlying reads for putative CDS annotated as phospho-N-acetylmuramoyl-pentapeptide transferase. Each variant has a final protein sequence (grey bars). Below are the nucleotide sequences used to reconstruct the protein. The nucleotide sequences are color coded based on season and sampling location (yellow colors = summer; blue colors = winter; gold = GOM13; yellow = GOM12; blue-green = GOM04; blue = GOM06). Unique sequence reads were aligned to the assembled nucleotide sequence using CLUSTAL W. The colors represent SNP locations in relation to the assembled nucleotide sequence (green = A; blue = C; black = G; red = T). The three protein variants were aligned to each other using CLUSTAL W. Colors along the length of the protein represent amino acid changes.

Figure 5

dN/dS ratio plotted against dS. dN/dS and dS values were calculated by comparing the identified proteins and nucleotide sequences for each variant pair using the PAL2NAL software and the codeml program within PAML. (A) All variants and corresponding dS and dN/dS values. (B) Enlargement of the indicated section of (A). (C) Enlargement of the indicated section of (B).