RESEARCH ARTICLE INTERNATIONAL MICROBIOLOGY (2006) 9:259-266 www.im.microbios.org Boris Alexander Johannes F. Imhoff* Communities of green sulfur bacteria in marine and saline Leibniz Institute for Marine Sciences, University of Kiel, habitats analyzed by gene Germany sequences of 16S rRNA and Fenna-Matthews-Olson protein Summary. Communities of green sulfur bacteria were studied in selected marine and saline habitats on the basis of gene sequences of 16S rRNA and the Fenna- Matthews-Olson (FMO) protein. The availability of group-specific primers for both 16S rDNA and the fmoA gene, which is unique to green sulfur bacteria, has, for the first time, made it possible to analyze environmental communities of these bacteria by culture-independent methods using two independent genetic markers. Sequence results obtained with fmoA genes and with 16S rDNA were largely con- gruent to each other. All of the 16S rDNA and fmoA sequences from habitats of the Baltic Sea, the Mediterranean Sea, Sippewissett Salt Marsh (Massachusetts, USA), and Bad Water (Death Valley, California, USA) were found within salt-dependent phylogenetic lines of green sulfur bacteria established by pure culture studies. This strongly supports the existence of phylogenetic lineages of green sulfur bacteria specifically adapted to marine and saline environments and the exclusive occur- rence of these bacteria in marine and saline habitats. The great majority of clone Received 19 July 2006 sequences belonged to different clusters of the Prosthecochloris genus and proba- Accepted 7 November 2006 bly represent different species. Evidence for the occurrence of two new species of Prosthecochloris was also obtained. Different habitats were dominated by repre- *Corresponding author: J.F. Imhoff sentatives from the Prosthecochloris group and different clusters or species of this Leibniz-Institut für Meereswissenschaften an der genus were found either exclusively or as the clearly dominant green sulfur bac- Universität Kiel terium at different habitats. [Int Microbiol 2006; 9(4):259-266] Düsternbrooker Weg 20 D-24105 Kiel, Germany Tel. +49-4316004450. Fax +49-4316004452 Key words: Prosthecochloris · Chlorobiaceae · environmental diversity · Fenna- E-mail: [email protected] Matthews-Olson protein [27,34], as well as within the top millimeters of sediments with Introduction an oxic/anoxic boundary. A limited variety of green sulfur bac- teria have been isolated from marine habitats [11,33,34] and in Green sulfur bacteria are anoxygenic phototrophic bacteria, most cases were identified as belonging to Prosthecochloris obligate phototrophic and strictly anaerobic. Although widely aestuarii. This limited genetic variation of cultured green sulfur distributed, green sulfur bacteria are restricted to anoxic habitats bacteria known from marine habitats could be due to the selec- exposed to light; thus, they are found in brackish waters, marine tivity of their growth conditions and may represent only a frac- lagoons, hypersaline habitats, and freshwater pools [4,11,17, tion of the environmental communities. Therefore, a genetic 18,31,33]. Due to their adaptation to low light intensities and approach—one that was not biased by the limitations imposed high sulfide concentrations [2], these bacteria prevail in the by specific culture conditions—was used in the present study deeper anoxic layers of lagoons and lakes, in the Black Sea to analyze environmental communities of green sulfur bacteria. 260 INT. MICROBIOL. Vol. 9, 2006 ALEXANDER, IMHOFF One of the properties responsible for the specific low- sediment, including the thin pink layer of purple sulfur bacteria. The salini- light adaptation of green sulfur bacteria is the presence of ty approximated that of sea water, about 3.5%. The sample of Malo Jezero originated from a Winogradsky column set characteristic light-harvesting structures, the chlorosomes, up by Vlaho Cvii? in 1951 with mud and water from this lake; the column which are attached to the cytoplasmic membrane [6,29,30]. was reestablished in 1973 by JFI [7,13,14] and has been maintained since The Fenna-Matthews-Olson protein is part of this unique then in the author’s laboratory. At the time of sampling, the red water in the column had a salinity of ca. 3.8% [7]. Although these conditions are consid- photosynthetic apparatus in green sulfur bacteria. The water- ered to be quite close to those of the natural situation, the relative propor- soluble protein bacteriochlorophyll a (Bchl a) mediates ener- tions of individual strains of the community may have changed over time. gy transfer between the chlorosomes and the reaction center Nonetheless, the green sulfur bacteria identified from the column play a sig- in the cytoplasmic membrane. It is unique to green sulfur nificant role in Malo Jezero under appropriate environmental conditions. The sample from Bad Water (a hypersaline pool at the depth of Death Valley) bacteria and is not even present in Chloroflexus aurantiacus was taken from the top of the highly reduced and actively sulfate-reducing [3]. fmoA codes for the monomer of the FMO protein, which sediment. binds Bchl a and is associated in a trimeric structure [9]. Its Extraction of genomic DNA and PCR amplification. DNA unique occurrence in green sulfur bacteria makes fmoA an was extracted by using the CTAB method [35]: 1 g sediment was mixed with appropriate target for specifically analyzing environmental 2.7 ml DNA extraction buffer [100 mM Tris/HCl, pH 8.0; 100 mM EDTA, communities of these bacteria. pH 8.0; 1500 mM NaCl; 1% N-cetyl-N,N,N-trimethylammoniumbromide (CTAB)] and 20 μl proteinase K solution (10 mg/ml) and incubated for 30 Phylogenetic relationships of green sulfur bacteria have min at 37ºC. Three hundred μl of 20% SDS solution was added; the sample been investigated based on pure-culture studies that exam- was mixed and then incubated for 2 h at 65ºC with additional mixing every ined 16S rRNA [1,10,22,26] and fmoA [1] genes. These stud- 15–20 min. After centrifugation (10 min, 6000 ×g, 20ºC), the pellet was ies of pure culture isolates demonstrated different phyloge- washed twice with 0.9 ml DNA extraction buffer and 0.1 ml SDS solution, mixed thoroughly for 10 s, and centrifuged. The pellet was discarded, and netic lines for strains derived from marine and saline habitats the three solutions were combined and mixed with the same volume of chlo- and from freshwater habitats. However, evidence from envi- roform/isoamylalcohol (24:1). After a brief centrifugation, the aqueous ronmental studies for this distinction is so far lacking. Since phase was separated from the organic one, mixed with 0.6 vol% isopropanol, and centrifuged (20 min, 16,000 ×g, 20ºC). The supernatant was discarded; cultivation approaches generally are believed to detect only a the DNA pellet was washed with 500 μl ice-cold ethanol (70%), and cen- small fraction of the natural population, it would be interest- trifuged again (10 min, 16,000 ×g, 20ºC). The DNA contained in the pellet ing to instead prove this relationship by genetic analyses with was solved in 1 ml water and then purified with the QIAquick PCR Purification Kit (QIAgen, Hilden, Germany) according to the manufactur- environmental samples. In this study, several marine and one er’s instructions. hypersaline habitat were selected and the compositions of communities of green sulfur bacteria were analyzed using PCR amplifications. Reactions were carried out in a total volume of 25 specific primers for the 16S rRNA and FMO genes [1]. μl using ReadyToGo PCR beads (Amersham-Pharmacia, Freiburg), 10 pmol of each primer (10 pmol per ml), and DNA (10–100 ng). To decrease primer specificity, the annealing temperatures for PCR amplification of fragments from environmental samples were lower than those used for pure-culture studies. Optimum reproduction was achieved by individually adapting the PCR conditions to each environmental sample. Materials and methods Specific primers, well-established for all pure cultures of green sulfur bacteria (F-Start-fmo and R-889-fmo [1]), were used for amplification of Environmental samples. DNA was obtained from environmental fmoA gene sequences. After an initial denaturation step of 2 min at 94ºC, samples derived from different geographic locations on two continents and PCR was carried out in a Progene-Cycler (Thermo-Dux, Wertheim, from different habitats, including brackish and true marine coastal habitats Germany). The amplification of fmoA from environmental samples consist- as well as saline inland waters. These habitats were represented by sediments ed of the following cycles: 30 s denaturation at 94ºC, 30 s elongation at from the German Baltic Sea shore near Laboe, Stakendorf, and Stein (sam- 72ºC, and 40 s annealing. The number of cycles and the annealing tempera- ples Laboe-3, Stak-2 and Stein-1), by sediment and water samples from the ture varied depending on the sample (25–35 cycles, 40–45ºC). The final saline lake Malo Jezero, which is connected to the Adriatic Sea (Island of cycle consisted of 1 min at 42ºC and 5 min at 72ºC. A combination of primer Mljet, Croatia [7]; sample Cviic-2), by sediments from Great Sippewissett F-99-GSB, specifically designed for green sulfur bacteria [1], and the eubac- Salt Marsh (MA, USA; samples Sip-4 and SSM-3), and from the salt pool terial R-1388 primer (see below) were used to amplify 16S rRNA gene Bad Water (Death Valley, CA, USA; sample BW-4). sequences. PCR cycles were as described above but consisted of 25–30 The sediments from the Baltic Sea (salinity ca. 1.9 %) showed a pink cycles and an annealing temperature varying from 48–60ºC (depending on layer within the top 2 mm, but there were no signs indicating the develop- the sample). The amplification products were checked on agarose gels (1% ment of green sulfur bacteria. From previous studies in which agar dilution wt/vol, Biozym, Hess; Oldendorf, Germany) stained with ethidium bromide series with Pfennig’s medium were used to count viable numbers of green (0.5 mg/l).