Novel lineages of Prochlorococcus and Synechococcus in the global oceans

Abstract

Picocyanobacteria represented by Prochlorococcus and Synechococcus have an important role in oceanic carbon fixation and nutrient cycling. In this study, we compared the community composition of picocyanobacteria from diverse marine ecosystems ranging from estuary to open oceans, tropical to polar oceans and surface to deep water, based on the sequences of 16S-23S rRNA internal transcribed spacer (ITS). A total of 1339 ITS sequences recovered from 20 samples unveiled diverse and several previously unknown clades of Prochlorococcus and Synechococcus. Six high-light (HL)-adapted Prochlorococcus clades were identified, among which clade HLVI had not been described previously. Prochlorococcus clades HLIII, HLIV and HLV, detected in the Equatorial Pacific samples, could be related to the HNLC clades recently found in the high-nutrient, low-chlorophyll (HNLC), iron-depleted tropical oceans. At least four novel Synechococcus clades (out of six clades in total) in subcluster 5.3 were found in subtropical open oceans and the South China Sea. A niche partitioning with depth was observed in the Synechococcus subcluster 5.3. Members of Synechococcus subcluster 5.2 were dominant in the high-latitude waters (northern Bering Sea and Chukchi Sea), suggesting a possible cold-adaptation of some marine Synechococcus in this subcluster. A distinct shift of the picocyanobacterial community was observed from the Bering Sea to the Chukchi Sea, which reflected the change of water temperature. Our study demonstrates that oceanic systems contain a large pool of diverse picocyanobacteria, and further suggest that new genotypes or ecotypes of picocyanobacteria will continue to emerge, as microbial consortia are explored with advanced sequencing technology.

Effects of low temperature on tropical and temperate isolates of marine Synechococcus

“…Their growth physiology is consistent with the environmental distribution of these clades reported in the previous studies (Zwirglmaier et al, 2007(Zwirglmaier et al, , 2008Ahlgren and Rocap, 2012;Huang et al, 2012;Sohm et al, 2016). Growth rates were marginally lower at low temperature in strains of clade I (CC9311) and IV (BL107, CC9902), which are dominant in temperate regions.…”

“…Clades I and IV are predominant in oceanic latitudes above 30°N and below 30°S. Clades II and III are found mostly within tropical and sub-tropical oceanic latitudes (Zwirglmaier et al, 2007(Zwirglmaier et al, , 2008Scanlan et al, 2009;Mella-Flores et al, 2011;Post et al, 2011;Ahlgren and Rocap, 2012;Mazard et al, 2012;Huang et al, 2012;Sohm et al, 2016). In relation to temperature, clades I and IV occur at higher abundances at 10 -20°C whereas clades II and III occur in the range of 20-28°C (Zwirglmaier et al, 2008) suggesting that temperature, among other environmental factors, may have a key role in their partitioning.…”

“…The largest, sub-cluster 5.1, is the dominant cluster in the marine environment (Urbach et al, 1998;Herdman et al, 2001;Fuller et al, 2003;Dufresne et al, 2008;Ahlgren and Rocap, 2012). Oceanic surveys indicate that these clades exhibit broad distribution from the equator to the polar regions having colonized habitats defined by a broad range of light, temperature and nutrient regimes (Fuller et al, 2003;Ahlgren and Rocap, 2006;Penno et al, 2006;Paerl et al, 2008;Zwirglmaier et al, 2008;Scanlan et al, 2009;Post et al, 2011;Huang et al, 2012;Mazard et al, 2012). The genomic complements of strains from different clades provide insights to preferential habitat niches .…”

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

“…For clarity and conformity with existing nomenclature, we refer to these clades as HL III and HL IV following Huang et al (2012).…”

“…Analyses of environmental DNA sequences have recently revealed new clades of HL-adapted Prochlorococcus that currently lack cultured representatives (Rusch et al, 2010;West et al, 2011;Huang et al, 2012). More specifically, Rusch et al (2010) identified two groups through phylogenetic analysis of several 'core' functional genes, that is, those common to all sequenced Prochlorococcus genomes, from the Global Ocean Survey (GOS) metagenomic data set, whereas West et al (2011) recovered novel 16S rRNA sequences in a separate sampling expedition.…”