Colorless sulfur bacteria Thioploca from different sites in Lake Baikal

Zemskaya, Т. I.; Chernitsyna, S. M.; Dul’tseva, N. M.; Sergeeva, V. N.; Pogodaeva, T. V.; Намсараев, Б. Б.

doi:10.1134/s0026261709010159

Cited by 12 publications

(12 citation statements)

References 13 publications

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“…Large T. ingrica (i.e. diameter 4.2 μm: Kojima et al , 2003 and 7.4 μm: Zemskaya et al , 2009) affiliate with the small Hjarbæk fjord sequence.…”

Section: Discussioncontrasting

confidence: 54%

“…It was first found in the Neva river, Russia (Wislouch, 1912), and later in scattered populations in European freshwater habitats (Koppe, 1922; Kolkwitz, 1955; Maier & Preissner, 1979) and in Lake Erie (Maier & Murray, 1965). More recently, populations in Lake Biwa and Lake Ogawara, Japan (Nishino et al , 1998; Kojima et al , 2007), Lake Ontario, North America (Dermott & Legner, 2002), and Lake Baikal, Russia (Zemskaya et al , 2001, 2009), have been reported.…”

Section: Introductionmentioning

confidence: 99%

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Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments

Høgslund

Nielsen

2010

FEMS Microbiology Ecology

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The distribution of Thioploca populations was investigated in Danish fjords, brackish lakes and coastal waters. Thioploca was found in three geographically distinct populations, where biomasses reached 33.8 AE 14.3 g wet weight m À2 (mean AE SD). Mats or lawns were not formed at the sediment surfaces and Thioploca biomasses peaked 4-7 cm into the sediment and extended down to 18 cm depth. Morphology and 16S rRNA gene sequences classified all populations as Thioploca ingrica. A sequence divergence of 1.7-2.2% indicated that T. ingrica comprise at least two genotypes. Physiological analysis showed that T. ingrica accumulate nitrate in concentrations of approximately 3 mM and that bicarbonate and acetate are used as a carbon source. The presence of oxygen promoted carbon incorporation, but T. ingrica could survive up to 3 months without an external supply of nitrate or oxygen. Thioploca ingrica populations were exclusively found close to river outlets in a bioturbated sediment with separate sulphidic spots and worm burrow walls containing nitrate and oxygen. It is hypothesized that the subsurface T. ingrica have a special advantage in this heterogeneous environment using their sheath surrounding the bacterial trichomes when navigating between electron donor and acceptor.

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“…Large T. ingrica (i.e. diameter 4.2 μm: Kojima et al , 2003 and 7.4 μm: Zemskaya et al , 2009) affiliate with the small Hjarbæk fjord sequence.…”

Section: Discussioncontrasting

confidence: 54%

Section: Introductionmentioning

confidence: 99%

Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments

Høgslund

Nielsen

2010

FEMS Microbiology Ecology

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“…Morphologically, T. ingrica was defined as a Thioploca species having a trichome 2.0-4.5 mm in diameter (Wislouch, 1912;Maier, 1984). Organisms that fit this description have been found in freshwater and brackish sediments of various localities, and the placement of these organisms in the same species has been generally supported by their 16S rRNA gene sequences (Maier and Murray, 1965;Nishino et al, 1998;Zemskaya et al, 2001Zemskaya et al, , 2009Dermott and Legner, 2002;Kojima et al, 2003Kojima et al, , 2006Høgslund et al, 2010;Nemoto et al, 2011Nemoto et al, , 2012Salman et al, 2011). Nitrate accumulation by T. ingrica was reported in previous studies, although the intracellular concentrations were much lower than in relatives with large vacuoles (Zemskaya et al, 2001;Kojima et al, 2007;Høgslund et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

et al. 2014

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Large sulfur-oxidizing bacteria, which accumulate a high concentration of nitrate, are important constituents of aquatic sediment ecosystems. No representative of this group has been isolated in pure culture, and only fragmented draft genome sequences are available for these microorganisms. In this study, we successfully reconstituted the genome of Thioploca ingrica from metagenomic sequences, thereby generating the first complete genome sequence from this group. The Thioploca samples for the metagenomic analysis were obtained from a freshwater lake in Japan. A PCR-free paired-end library was constructed from the DNA extracted from the samples and was sequenced on the Illumina MiSeq platform. By closing gaps within and between the scaffolds, we obtained a circular chromosome and a plasmid-like element. The reconstituted chromosome was 4.8 Mbp in length with a 41.2% GC content. A sulfur oxidation pathway identical to that suggested for the closest relatives of Thioploca was deduced from the reconstituted genome. A full set of genes required for respiratory nitrate reduction to dinitrogen gas was also identified. We further performed a proteomic analysis of the Thioploca sample and detected many enzymes/proteins involved in sulfur oxidation, nitrate respiration and inorganic carbon fixation as major components of the protein extracts from the sample, suggesting that these metabolic activities are strongly associated with the physiology of T. ingrica in lake sediment.

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“…The phylogenetic diversity within Thioploca of Lake Tonle Sap was consistently shown in the analyses of 16S rRNA, 23S rRNA, and the ITS region. In other habitats, only a single 16S rRNA gene sequence of Thioploca has been reported from each lake (Kojima et al 2003, 2006, Zemskaya et al 2009, Nemoto et al 2011, although the coexistence of different sequences was reported in a brackish fjord (Høgslund et al 2010, Salman et al 2011. In the present study, DNA was extracted from a clump of tangled filaments obtained by sieving bulk sediment.…”

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confidence: 73%

Filamentous sulfur-oxidizing bacteria of the genus Thioploca from Lake Tonle Sap in Cambodia

Nemoto¹,

Kojima²,

Ohtaka³

et al. 2012

Aquat. Microb. Ecol.

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Members of the genus Thioploca are uncultured filamentous sulfur-oxidizing bacteria that live in freshwater/brackish sediments and have the ability to store nitrate in high concentrations in their cells. Their close relatives that inhabit marine sediments, such as Thiomargarita and 'Candidatus Marithioploca', are thought to greatly influence cycles of sulfur, nitrogen, and phosphorus. To date, the genus Thioploca has been reported only from temperate and subarctic areas. Our demonstration of Thioploca in Lake Tonle Sap, Cambodia, is the first report of this genus in a tropical lake. The filaments obtained from Lake Tonle Sap were morphologically similar to those of other lakes. Phylogenetic analysis based on genes for 16S rRNA, 23S rRNA, and the 16S-23S rRNA internal transcribed spacer (ITS) region revealed that 3 distinct lineages coexist in this lake. These results indicate that the geographical distribution and phylogenetic diversity of the genus Thioploca is greater than previously thought.KEY WORDS: Sulfur-oxidizing bacteria · Freshwater lake · Sediment · Phylogeny Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 66: [295][296][297][298][299][300] 2012 (Lauter born 1907). Subsequently, populations were reported from Lake Erie and Lake Ontario in North America (Maier & Murray 1965, Dermott & Legner 2002, Lake Baikal in Siberia (Zemskaya et al. 2001), and Lake Biwa, Lake Ogawara, and Lake Okotanpe in Japan (Nishino et al. 1998, Kojima et al. 2006, Nemoto et al. 2011. These lakes are located in areas of mid-range to high latitudes in the northern hemisphere. The 16S rRNA gene sequences of Thioploca in these lakes are very closely related, even though they are separated geographically.In the present study, we report the occurrence of the genus Thioploca in Lake Tonle Sap (Cambodia), which is located in a tropical monsoon climatic zone, and show results of phylogenetic analyses. MATERIALS AND METHODS Samples were obtained in May 2005, from the south basin of Lake Tonle Sap. This lake is characterized by a dramatic seasonal change of water level, and the samples were obtained in the season of shallow water depth. The sampling site, Site S3 (12°33' 57'' N, 104°22' 10'' E; 0.4 m deep), corresponds to the site of a previous study (Ohtaka et al. 2010). At the sampling time, the pH and specific conductivity of surface water were 8.0 and 155 µS cm −1 respectively (Ohtaka et al. 2010). The lake water was characterized by very low transparency (0.02 m). The sediment samples, taken using an Ekman-Birge grab sampler, were passed through a mesh with a pore size of 0.25 mm. The retained filamentous materials were immediately fixed in 100% ethanol.Before microscopic observation, the filamentous samples were soaked in distilled water for 30 min to replace the ethanol with water. The shapes of the filaments were observed, and the diameters of 200 trichomes were measured under an optical microscope (Axioplan 2, Zeiss).Thioploca filaments (sheaths with trichomes) were c...

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Colorless sulfur bacteria Thioploca from different sites in Lake Baikal

Cited by 12 publications

References 13 publications

Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments

Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

Filamentous sulfur-oxidizing bacteria of the genus Thioploca from Lake Tonle Sap in Cambodia

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