Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

Standards in Genomic Sciences, May 2018

“Thiodictyon syntrophicum” sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.

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Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

Luedin et al. Standards in Genomic Sciences Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain T Cad16 , a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno Samuel M. Luedin 0 1 2 Joël F. Pothier 4 Francesco Danza 0 1 Nicola Storelli 0 1 Niels-Ulrik Frigaard 3 Matthias Wittwer 2 Mauro Tonolla 0 1 0 University of Applied Sciences of Southern Switzerland (SUPSI), Department of Environment , Constructions and Design (DACD) , Laboratory of Applied Microbiology (LMA) , Via Mirasole 22A, 6500 Bellinzona , Switzerland 1 University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology Unit , 1211 Geneva , Switzerland 2 Federal Office for Civil Protection, Spiez Laboratory, Biology Division , Spiez , Switzerland 3 University of Copenhagen, Department of Biology , Helsingør , Denmark 4 Zurich University of Applied Sciences (ZHAW), Institute of Natural Resource Sciences, Environmental Genomics and System Biology Research Group , Wädenswil , Switzerland “Thiodictyon syntrophicum” sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno. Phototrophic sulfur bacteria; Chromatiaceae; Sulfur cycling; Meromictic lake; CRISPR; Okenone Introduction PSB belonging to the family of Chromatiaceae are generally found at the interface of aerobic and sulfidic-anaerobic zones that are exposed to sunlight such as stagnant, hypertrophic water bodies, littoral zones and bacterial mats [ 1 ]. The genus Thiodictyon was first described by Winogradsky in 1888 [ 2 ] and comprises two type strains, Thiodictyon elegans strain DSM 232T and Thiodictyon bacillosum strain DSM 234T. “Thiodictyon syntrophicum” sp. nov. strain Cad16T is the proposed type strain of the species “Thiodictyon syntrophicum” [ 3 ] within the family of Chromatiaceae of the genus Thiodictyon [ 4 ]. Cultures of strain Cad16T were isolated from the chemocline of the alpine meromictic Lake Cadagno (Ticino, Switzerland). This lake is characterized by high influx of sulfate, magnesium and calcium in the euxinic monimolimnion which favors the formation of a steep chemocline at 10 to 14 m depth [ 5, 6 ]. Within this zone a dense population (up to 107 cells per ml in summer) of mainly anaerobic phototrophic sulfur bacteria belonging to the PSB genera Chromatium, Lamprocystis, Thiodictyon, Thiocystis, and the GSB Chlorobium [7] is responsible for up to 40% of the total CO2 fixation measured in Lake Cadagno [ 8 ]. Strain Cad16T has been shown to be highly active in CO2 fixation both in situ and in vitro [ 9 ]. Furthermore, aggregation of strain Cad16T with SRBof the genus Desulfocapsa has been described [ 3 ]. In this publication we describe the first complete genome of strain Cad16T providing details especially on CO2 fixation, sulfur metabolism and on CRISPRs. The sequencing of strain Cad16T is part of a larger sequencing project that includes the key species of the microbial community from the anoxic layers of Lake Cadagno. Organism information Classification and features Strain Cad16T is Gram-negative, the cells are oval-sphere shaped and 1.4–2.4 μm in diameter, non-motile, vacuolated and contain BChl a. Isolate Cad16T can grow as single cells, as well as in cell aggregates with up to 100 cells contained in EPS layer (Fig. 1). It was isolated from the chemocline of Lake Cadagno in a depth of 10–14 m where it grows in a non-obligate mutualistic association with sulfur-reducing bacteria of the genus Desulfocapsa [ 10 ]. Based upon morphology and partial 16S rRNA sequence analysis, the strain Cad16T was classified as a member of the genus Thiodictyon within the family Chromatiaceae before [ 10 ]. Figure 2 shows the phylogenetic placement of strain Cad16T (complete 16S rRNA sequence) in a 16S rRNA based maximum likelihood phylogenetic tree. The closest relatives of isolate Cad16T are T. bacillosum DSM 234T and T. elegans DSM 232T with 99% sequence identity (partial 16S rRNA sequences). A comparison of the strain Cad16T core genome with other wh (...truncated)


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Samuel M. Luedin, Joël F. Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla. Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno, Standards in Genomic Sciences, 2018, pp. 14, Volume 13, Issue 1, DOI: 10.1186/s40793-018-0317-z