Evidence for a persistent microbial seed bank throughout the global ocean

Abstract

Do bacterial taxa demonstrate clear endemism, like macroorganisms, or can one site's bacterial community recapture the total phylogenetic diversity of the world's oceans? Here we compare a deep bacterial community characterization from one site in the English Channel (L4-DeepSeq) with 356 datasets from the International Census of Marine Microbes (ICoMM) taken from around the globe (ranging from marine pelagic and sediment samples to sponge-associated environments). At the L4-DeepSeq site, increasing sequencing depth uncovers greater phylogenetic overlap with the global ICoMM data. This site contained 31.7-66.2% of operational taxonomic units identified in a given ICoMM biome. Extrapolation of this overlap suggests that 1.93 × 10(11) sequences from the L4 site would capture all ICoMM bacterial phylogenetic diversity. Current technology trends suggest this limit may be attainable within 3 y. These results strongly suggest the marine biosphere maintains a previously undetected, persistent microbial seed bank.

Fig. 1.

L4-DeepSeq rarefaction depth vs. percent phylogenetic gain of the pooled ICoMM data relative to the L4 site. Rarefaction depth is plotted on a log scale (base 10). Rarefaction was replicated 10 times at each depth. Error bars represent the SD. The arrow indicates the sequencing depth when phylogenetic overlap is complete (when overlap = 100%, depth = 1.93E11).

Fig. 2.

(A) Percent OTU overlap across marine biomes (relative to the L4-DeepSeq sample). (B) Phylogenetic gain across marine biomes. For both A and B, individual biomes were rarefied to 15,790 sequences and compared with the full L4-DeepSeq sample (∼10 million reads). The dashed lines represent the average across all biomes.

Fig. 3.

Biome-specific community clustering and phylogenetic differences between biomes and the L4-DeepSeq sample. The network in the center of the figure was constructed in Cytoscape, using the BioLayout format (edge-weighted, force-directed). To reduce the complexity of the network, only OTUs that appear more than 500 times in the OTU table were included. Nodes and edge colors represent biome type (see Figs. S4 and S5). OTUs are represented as invisible points at the fringes of the plot (i.e., at the termini of the edges). Each OTU is connected to the samples in which it appears via an edge (colored according to the biome to which the sample belongs). The white-colored node at the center of the network represents the L4-DeepSeq sample. All edges connected to the L4-DeepSeq sample also are colored white to allow visualization of overlap with other biomes. The phylogenetic tree in the upper left corner of the plot shows taxa that are unique to particular environments (i.e., that are not present in the L4-DeepSeq sample; the wedge area is proportional to abundance). Smaller trees highlight individual biomes (only taxa contributed from that biome are shown in color, and the remaining branches of the tree are shown in white). The larger tree serves as the key for the smaller identical trees, displaying the names of each lineage. A high-resolution version of this figure is available in Fig. S3 (see Figs. S4 and S5 for keys).