Expanding the World of Marine Bacterial and Archaeal Clades

Abstract

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 "clades," at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.

Keywords: bacterial phylogeny; bacterial taxonomy; bacterioplankton; ecology; marine; rare taxa.

Figure 1

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Thaumarchaeota (A) and Euryarchaeota (B). The tree is displayed at order level (minimum 82% sequence identity). Colored branches and annotations in the light pink box next to the tree indicate different CTU classes. Annotations in the light blue box indicate alternate or currently used taxa names at different rank levels. Newly recognized clades are groups filled with solid color, whereas unfilled groups indicate known clades. Bootstrap support for topologies was calculated with 100 repetitions, and only values above 50% are shown on the branches. The numbers inside the groups indicate the number of sequences in that group. The outgroup sequences are indicated by an arrow. Bar = nucleotide changes per site.

Figure 2

Bubble plot showing the average relative abundances of newly recognized clades in different phyla across biomes. The scale for bubbles are indicated under the plot, and values were scaled from 0 to 1, with 0 representing the minimum average relative abundance, and 1 representing the maximum relative abundance.

Figure 3

Panel figure showing the average relative abundances of all new candidate orders across different water body types. The bars for each phylum are scaled according to the values within that phylum. To increase visibility of the bars, the relative abundance values are given separately in a table (Table S4). LP, low productivity; MP, mid productivity; HP, high productivity.

Figure 4

Spearman rank correlation coefficients between clade relative abundance and available physicochemical parameters. Only correlations that had a p-value of less than 0.05 are shown. Cells are colored with hues of red and blue to indicate the strength of positive or negative correlation coefficient, respectively.

Figure 5

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Acidobacteria. Other details of the figure are same as Figure 1.

Figure 6

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Actinobacteria and Firmicutes. Other details of the figure are same as Figure 1.

Figure 7

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Bacteroidetes, Chlorobi, and Fibrobacteres. Other details of the figure are same as Figure 1.

Figure 8

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Chloroflexi. Other details of the figure are same as Figure 1.

Figure 9

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured Deferribacteres/Caldithrix group. Other details of the figure are same as Figure 1. The groups Deferribacteres.Order10 and Deferribacteres.Order15 marked with an asterisk were previously associated with unidentified Halanaerobiales (Clostridia) and Gemmatimonadetes groups, but due to sequence identity values of above 75%, they were placed together with Deferribacteres/Caldithrix.

Figure 10

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Planctomycetes, Verrucomicrobia, and Lentisphaerae. Other details of the figure are same as Figure 1.

Figure 11

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Alphaproteobacteria. Other details of the figure are same as Figure 1. Alphaproteobacteria.Order1-10 marked with an asterisk was not included further analysis, as it was found to contain Nitratireductor indicus sequences in a more recent SILVA Ref dataset release.

Figure 12

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Beta- and Gammaproteobacteria. Other details of the figure are same as Figure 1.

Figure 13

Phylogenetic trees illustrating the relationships among SSU rRNA gene sequences belonging to uncultured marine Deltaproteobacteria. Other details of the figure are same as Figure 1.