Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments

Abstract

Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.

The status of the species Hyphomonas rosenbergii Weiner et al. 2000. Request for an Opinion

“…It was later found that ATCC 43869 T did not conform to the description of the type strain of Hyphomonas rosenbergii. The resequenced 16S rRNA gene sequence of ATCC 43869 T (under GenBank accession number KF880383) shows only 92.84 % similarity to the original 16S rRNA gene sequence (Li et al, 2014). The 16S rRNA gene sequence of DSM 17769 T was identical with our result (KF880383) (http:// www.dsmz.de/catalogues/details/culture/DSM-17769.html).…”

Polyphasic approach using multilocus analyses supports the establishment of the new aerophytic cyanobacterial genus Pycnacronema (Coleofasciculaceae, Oscillatoriales)

“…, Li et al. , Glaeser and Kämpfer ). The 16S rRNA gene due to its conservation is useful for generic placement in cyanobacteria (Boyer et al.…”

Tideless estuaries in brackish seas as possible freshwater‐marine transition zones for bacteria: the case study of the Vistula river estuary

“…Sporichthyaceae are ubiquitous in freshwaters (Newton et al, 2011), and were abundant in oligosaline arctic lakes (Theroux et al, 2012) as well as in the Baltic Sea (Andersson et al, 2010;Piwosz et al, 2013), and so it is likely that more bacteria of this family tolerate salinity of up to 3-4 PSU, and, to a lesser extent 7-8 PSU. Similarly, typically marine members of the Hyphomonas genus (Li et al, 2014) appear to be able to tolerate mixing zone and freshwater conditions. Both marine (e.g.…”