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3000 m below the surface in the Pacific, a new species of hydrothermal bacterium

An unknown bacterium was found in hydrothermal sediments in the eastern Pacific and reveals its identity through the exploration of its morphological, genetic and physiological characteristics. The new strain is indeed a new species, named Kosmotoga pacifica.

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Be they aquatic or terrestrial, natural or man-made, surface or underground, hot or very hot environments are a habitat for a rich yet still poorly known microbial diversity. Since the mid-eighties, over forty species have been isolated within Thermotogae, one of the divisions of Bacteria living in moderate to very high temperatures. Deep-sea environments associated with hydrothermal vents (particularly along mid-oceanic ridges) host micro-organisms whose growth requires the absence of oxygen and high temperatures. Many species of bacteria were described there, but their diversity is far from being known, and each sample can contain new ones. This work deals with the status of a bacterial strain sampled in the east Pacific compared to the already described species.

During a research survey, samples of hydrothermal sediments were collected at 2891 m on the east Pacific Rise. They were immediately transferred into sterile plastic bags and stored at 4°C. In the laboratory, an unknown bacterial strain was observed in the sediments and temporarily named SLHLJ1. It was inoculated on culture media and its identity was defined through analyses based on the comparison of its characteristics with those of already described strains, in terms of morphology (shape, size,…) but mainly of genetics (DAN or RNa gene sequences), physiology (limit and optimum growth conditions), metabolism (molecules used or not) and biochemistry (nature of synthesized molecules).

 After three days of incubation at 55°C, dense populations appeared; the cells were purified and transferred on a culture medium. Cells were short rods (about 1 µm long ) or oval-shaped cells depending on growth conditions. They were surrounded by the typical sheath of Thermotogae (the "toga" which gave them their name) and appeared singly or occasionally in chains of 3–4 cells within the sheath.

LHaridon 2014 Fig2b.jpg
Transmission electron microscopy observation of a dividing SLHLJ1 cell surrounded by its toga (the scale is given by the black bar: 0.5 µm)

The relatedness of SLHLJ1 and known species was studied from the nucleotide sequences within a RNA bacterial ribosome gene called 16S rRNA. The RNA was first sequenced (about 1,500 pairs of bases), then the arrangement of its nucleotides was compared to that of known species. SLHLJ1 shares 98 % 16S rRNA gene sequence similarity with the closest species among Thermotogae, Kosmotoga arenicorallina; it is more distantly related to the other species of the genus, K. olearia et K. shengliensis (about 92 % similarity). However, other techniques based on DNA hybridization showed that the relatedness with K. arenicorallina is low (16 %), far below the threshold value of 70 % above which it is considered the individuals belong to the same species. SLHLJ1 therefore represents a novel species, closely related to but still distinct from K. arenicorallina.

 While the genetic data unquestionably support the delineation of a novel species, they are not sufficient to determine if it also belongs to the genus Kosmotoga or if it needs to create a new genus. Among Bacteria, the concepts of species and genus are complex as no clear-cut definition of genus is available in terms of genetic difference (which measures the evolutionary divergence between two groups of species) and this divergence does not always lead to different physiological and biochemical properties. This situation is particularly true within Thermotogales, which form a relatively homogeneous group of microorganisms where genus delineations have been essentially proposed on the basis of genetics. The SLHLJ1 strain should have very different physiological and biochemical properties from the existing genera to justify the creation of a novel genus.

LHaridon 2014 Fig1.jpg

Simplified phylogenetic tree based on the 16S rRNA gene, showing the position of strain SLHLJ1 within the order Thermotogales.

The culture of SLHLJ1 in various conditions showed that its growth is possible only at given ranges of temperature (33 to 78°C, with an optimum at 70°C), pH (5.5 to 8.5) and salinity (5 to 60 g/l). In optimal growth conditions, the doubling time of the population is 95 minutes. A list of substances used or ignored by cell metabolism was established, and

their sensitivity to a number of antibiotics was determined. Based on these results, SLHLJ1 was compaed with the genetically closest species (K. arenicorallina), the other two within the same genus (K. olearia and K. shengliensis) and one from the related genus Mesotoga. In spite of the observed differences, the new strain shares numerous morphological, physiological, biochemical and metabolic features with members of the genus Kosmotoga; for instance, the molecules used or ignored by SLHLJ1 and K. arenicorallina are the same. The differences with the already described species are greater for the Mesotoga species than with the three Kosmotoga species: the doubling time is 1.48 hour for SLHLJ1, 1.75 to 2.9 hours for Kosmotoga and 16.5 hours for Mesotoga, and the optimal growth temperature is 70°C, 60 to 65°C and 37°C respectively. Kosmotoga species live in hotter environments and grows more rapidly than Mesotoga. It is in view of these distinctive features that the authors propose to place the new species within the genus Kosmotoga. As a reminder of the place of its discovery, they named it Kosmotoga pacifica.

 

The paper

L’Haridon S., Jiang L., Alain K., Chalopin M., Rouxel O., Beauverger M., Xu H., Shao Z., Jebbar M., 2014. Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment. Extremophiles 18 : 81–88.

See the first page

 

The authors

This work was done in collaboration by researchers of the Laboratoire de Microbiologie des Environnements Extrêmes (LMEE) of IUEM and of the Key Laboratory of Marine Biogenetic Resources of Xiamen (China)

 

The journal

Extremophiles is a recent scientific journal (founded in 1997) of the international publisher Springer. Its interests are on the biology, structure, function and applications of microbial life at the limit conditions of survival: high or low temperature, pressure, acidity, alkalinity, salinity, or desiccation; or in the presence of organic solvents, heavy metals, normally toxic substances, or radiations.

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