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.
Highlights
Hyphomonas is a genus of budding, prosthecate bacteria that are primary colonizers of surfaces in the marine environment [1,2,3,4]
Further analysis indicated that genetic distance of the 16S rRNA gene ranged from 0 to 0.042 (Table 2)
Recent reports have demonstrated that the virtual DNA-DNA hybridization (DDH) values calculated by the GGDC web server can adequately mimic wet-lab DDH analysis [30,36,37]
Summary
Hyphomonas is a genus of budding, prosthecate bacteria that are primary colonizers of surfaces in the marine environment [1,2,3,4]. The genus Hyphomonas was first described by Pongratz [3,5] in the family Hyphomonadaceae of the order Caulobacterales. We have isolated many strains of Hyphomonas from various oceanic areas over the last eight years (unpublished). Most were isolated from the petroleum-degrading microbial community, indicating that Hyphomonas are likely involved in oil degradation. One Hyphomonas strain was isolated from a pyreneenriched consortium of Western Pacific sediment by our laboratory [6], and Zhang et al found others in oil reservoirs [7]. Hyphomonas has been reported in coastal regions such as Heita Bay [8], Milazzo Harbor [9] and the Thames Estuary [10]. Little is known about the biogeography of the genus Hyphomonas, or correlations between their genetic differentiation and geographical distribution
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