Diversity of anoxygenic phototrophic sulfur bacteria in the microbial mats of the Ebro Delta: a combined morphological and molecular approach

Abstract

The diversity of purple and green sulfur bacteria in the multilayered sediments of the Ebro Delta was investigated. Specific oligonucleotide primers for these groups were used for the selective amplification of 16S rRNA gene sequences. Subsequently, amplification products were separated by denaturing gradient gel electrophoresis and sequenced, which yielded a total of 32 sequences. Six of the sequences were related to different cultivated members of the green sulfur bacteria assemblage, whereas seven fell into the cluster of marine or halophilic Chromatiaceae. Six sequences were clustered with the family Ectothiorhodospiraceae, three of the six being closely related to chemotrophic bacteria grouped together with Halorhodospira genus, and the other three forming a group related to the genus Ectothiorhodospira. The last thirteen sequences constituted a cluster where no molecular isolate from microbial mats has so far been reported. Our results indicate that the natural diversity in the ecosystem studied has been significantly underestimated in the past and point out the presence of novel species not related to all known purple sulfur bacteria. Furthermore, the detection of green sulfur bacteria, after only an initial step of enrichment, suggests that -- with the appropriate methodology -- several genera, such as Prosthecochloris, could be established as regular members of marine microbial mats.

Comparison of cultivation‐dependent and molecular methods for studying the diversity of anoxygenic purple phototrophs in sediments of an eutrophic brackish lagoon

“…1). Both genera Allochromatium and Ectothiorhodospira are typical of eutrophic coastal lagoons (Imhoff, 2001; Martinez‐Alonso et al ., 2005). The majority of the isolates (approximately 61%) clustered with phototrophic purple non‐sulfur bacteria within the Alphaproteobacteria as shown in Fig.…”

Communities of purple sulfur bacteria in a Baltic Sea coastal lagoon analyzed by pufLM gene libraries and the impact of temperature and NaCl concentration in experimental enrichment cultures

“…This distinctive classification and the established phylogentic tree of purple sulfur bacterial pufLM genes (Tank et al ., ) allowed identification of the purple sulfur bacterial genera and species within habitat samples and mixed cultures and enabled the use of pufLM gene sequences for detailed analyses of PSB communities. The observed phylogenetic separation of pufLM nucleotide sequences of Gamma ‐ and Alphaproteobacteria is in contrast to a number of previous studies on the phylogeny of either pufL , pufM or pufLM gene fragments showing the anoxygenic phototrophic Gammaproteobacteria interspersed within anoxygenic phototrophic Alphaproteobacteria (Nagashima et al ., ; Martínez‐Alonso et al ., ; Cho et al ., ; Zeng & Jiao, ), but in line with our previous report on the phylogeny of pufLM genes in PSB (Tank et al ., ). It is considered that the largely increased number of pufLM reference sequences available in the public databases, the use of the almost entire pufLM fragment for phylogenetic calculations together with improved accuracy of the sequences and in alignment preparation have led to considerably more robust results.…”

“…The overall diversity of anoxygenic phototrophic purple bacteria found in the Baltic Sea lagoon was comparable to those found in other studies on communities of anoxygenic phototrophic purple bacteria using molecular techniques (Martínez‐Alonso et al ., ; Ranchou‐Peyruse et al ., ; Waidner & Kirchman, ). PSB were dominant in all pufLM clone libraries and represented approx.…”

Comparison of Different Denaturing Gradient Gel Electrophoresis Primer Sets for the Study of Marine Bacterioplankton Communities

“…Although it is used widely in different areas of research (5,7,8,10,14), there seems to be little testing or justification for the correct choice of primers for each type of microbial community.…”