Deborah O. Jung

Remarkable Diversity of Phototrophic Purple Bacteria in a Permanently Frozen Antarctic Lake

ABSTRACT Although anoxygenic photosynthesis is thought to play an important role in the primary productivity of permanently frozen lakes in the Antarctic dry valleys, the bacterial communities responsible for this metabolism remain uncharacterized. Here we report the composition and activity of phototrophic purple bacteria in Lake Fryxell, Antarctica, as determined by analysis of a photosynthesis-specific gene, pufM. The results revealed an extensive diversity and highly stratified distribution of purple nonsulfur bacteria in Lake Fryxell and showed which phylotypes produced pufM transcripts in situ. Enrichment cultures for purple bacteria yielded two morphotypes, each with a pufM signature identical to signatures detected by environmental screening. The isolates also contained gas vesicles, buoyancy structures previously unknown in purple nonsulfur bacteria, that may be necessary for these organisms to position themselves at specific depths within the nearly freezing water column.

Diversity and distribution of sulfate-reducing bacteria in permanently frozen Lake Fryxell, McMurdo Dry Valleys, Antarctica

ABSTRACT The permanently frozen freshwater Lake Fryxell, located in the Dry Valleys of Antarctica, exhibits an ideal geochemistry for microbial sulfate reduction. To investigate the population of sulfate-reducing bacteria in Lake Fryxell, both 16S rRNA gene and metabolic primer sets targeting the dsrA gene for the dissimilatory sulfite reductase alpha subunit were employed to analyze environmental DNA obtained from the water column and sediments of Lake Fryxell. In addition, enrichment cultures of sulfate-reducing bacteria established at 4°C from Lake Fryxell water were also screened using the dsrA primer set. The sequence information obtained showed that a diverse group of sulfate-reducing prokaryotes of the domain Bacteria inhabit Lake Fryxell. With one exception, the enrichment culture sequences were not represented within the environmental sequences. Sequence data were compared with the geochemical profile of Lake Fryxell to identify possible connections between the diversity of sulfate-reducing bacteria and limnological conditions. Several clone groups were highly localized with respect to lake depth and, therefore, experienced specific physiochemical conditions. However, all sulfate-reducing bacteria inhabiting Lake Fryxell must function under the constantly cold conditions characteristic of this extreme environment.

Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15–18 °C with a growth temperature range of 0–25 °C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.

The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus.

Despite the fact that heliobacteria are the only phototrophic representatives of the bacterial phylum Firmicutes, genomic analyses of these organisms have yet to be reported. Here we describe the complete sequence and analysis of the genome of Heliobacterium modesticaldum, a thermophilic species belonging to this unique group of phototrophs. The genome is a single 3.1-Mb circular chromosome containing 3,138 open reading frames. As suspected from physiological studies of heliobacteria that have failed to show photoautotrophic growth, genes encoding enzymes for known autotrophic pathways in other phototrophic organisms, including ribulose bisphosphate carboxylase (Calvin cycle), citrate lyase (reverse citric acid cycle), and malyl coenzyme A lyase (3-hydroxypropionate pathway), are not present in the H. modesticaldum genome. Thus, heliobacteria appear to be the only known anaerobic anoxygenic phototrophs that are not capable of autotrophy. Although for some cellular activities, such as nitrogen fixation, there is a full complement of genes in H. modesticaldum, other processes, including carbon metabolism and endosporulation, are more genetically streamlined than they are in most other low-G+C gram-positive bacteria. Moreover, several genes encoding photosynthetic functions in phototrophic purple bacteria are not present in the heliobacteria. In contrast to the nutritional flexibility of many anoxygenic phototrophs, the complete genome sequence of H. modesticaldum reveals an organism with a notable degree of metabolic specialization and genomic reduction.

An Overview of Purple Bacteria: Systematics, Physiology, and Habitats

Anoxygenic phototrophic purple bacteria are a major group of photosynthetic microorganisms widely distributed in nature, primarily in aquatic habitats. Nearly 50 genera of these organisms are known and some have become prime model systems for the experimental dissection of photosynthesis. Purple sulfur bacteria differ from purple nonsulfur bacteria on both metabolic and phylogenetic grounds, but species of the two major groups often coexist in illuminated anoxic habitats in nature. Purple sulfur bacteria are strong photoautotrophs and capable of limited photoheterotrophy, but they are poorly equipped for metabolism and growth in the dark. By contrast, purple nonsulfur bacteria, nature’s preeminent photoheterotrophs, are capable of photoautotrophy, and possess diverse capacities for dark metabolism and growth. Several purple bacteria inhabit extreme environments, including extremes of temperature, pH, and salinity. Collectively, purple bacteria are important phototrophs because they (1) consume a toxic substance, H2S, and contribute organic matter to anoxic environments by their autotrophic capacities; (2) consume organic compounds, primarily non-fermentable organic compounds, in their roles as photoheterotrophs; and (3) offer scientists in the photosynthesis community a smorgasbord of molecular diversity for the study of photosynthesis.

Cold-active chemoorganotrophic bacteria from permanently ice-covered Lake Hoare, McMurdo Dry Valleys, Antarctica.

ABSTRACT Eight strains of chemoorganotrophic bacteria were isolated from the water column of Lake Hoare, McMurdo Dry Valleys, Antarctica, using cold enrichment temperatures. The isolates were Alpha-, Beta-, and Gammaproteobacteria and Actinobacteria spp. All isolates grew at 0°C, and all but one grew at subzero temperatures characteristic of the water column of Lake Hoare. Growth temperature optima varied among isolates, but the majority showed optima near 15°C, indicative of cold-active phenotypes. One isolate was truly psychrophilic, growing optimally around 10°C and not above 20°C. Half of the isolates grew at 2% salt while the other half did not, and all but one isolate grew at 2 atm of O2. Our isolates are the first prokaryotes from the water column of Lake Hoare to be characterized phylogenetically and physiologically and show that cold-active species of at least two major phyla of Bacteria inhabit Lake Hoare.

Novel carotenoid glucoside esters from alkaliphilic heliobacteria

Pigments of three species of alkaliphilic heliobacteria of the genus Heliorestis, H. daurensis, H. baculata and an undescribed species Heliorestis strain HH, were identified using spectroscopic methods. In these species, bacteriochlorophyll g esterified with farnesol was present, as for other heliobacteria. The carotenoids consisted of 4,4′-diaponeurosporene, also found in other heliobacteria, plus the novel pigments OH-diaponeurosporene glucoside esters (C16:0 and C16:1). In addition, trace amounts of biosynthetic intermediates, OH-diaponeurosporene and OH-diaponeurosporene glucoside, were found. Trace amounts of a carotenoid with 20 carbon atoms, 8,8′-diapo-ζ-carotene, were also found in these species as well as in the non-alkaliphilic heliobacteria. The non-alkaliphilic species Heliophilum fasciatum also contained trace amounts of the two OH-diaponeurosporene glucoside esters. The results are used to predict the pathway of carotenoid biosynthesis in heliobacteria.

Accumulation of unusual carotenoids in the spheroidene pathway, demethylspheroidene and demethylspheroidenone, in an alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis

Carotenoids extracted from cells of a novel alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis strain LBB1 included unusual carotenoids in the spheroidene pathway; demethylspheroidene, demethylspheroidenone, neurosporene and spheroidenone. Spheroidene was present in only small amounts, and the demethyl-carotenoids demethylspheroidene and demethylspheroidenone predominated in phototrophic cultures. Furthermore, the keto-carotenoids spheroidenone and demethylspheroidenone constituted nearly half of the total carotenoids, even in strict anaerobic phototrophic cultures. Spheroidenone was, however, the sole carotenoid in aerobic cultures. Phototrophic cultures of Rbc. bogoriensis were yellow in colour and quite distinct from the brown-red colour of cultures of Rhodobacter species. The carotenogenesis pathways of Rhodobaca and Rhodobacter species are compared with special reference to two key enzymes of the spheroidene pathway, CrtA and CrtF, whose activities are thought to be responsible for the unusual carotenoid composition of Rhodobaca. This bacterium also contained bacteriochlorophyll ap and ubiquinone-10.

Evidence for limited species diversity of bacteriochlorophyll b-containing purple nonsulfur anoxygenic phototrophs in freshwater habitats

Thirteen new isolates of bacteriochlorophyll b-containing purple nonsulfur bacteria were isolated from four freshwater habitats using specific enrichment methods including the use of long wavelength filters and extincting dilution of the inoculum. The new isolates were compared with the type strain of Blastochloris viridis, strain DSM 133(T), as regards pigments, morphology, carbon nutrition, and phylogeny. All new isolates were budding bacteria, and phototrophic mass cultures were green, brown, or brown-green in color. The pattern of carbon sources photocatabolized were similar in all strains; however, sugars, both mono- and disaccharides, were widely used by the new isolates while they did not support growth of strain DSM 133(T). Phylogenetic analysis showed all new strains to cluster tightly with the type strain with the exception of one brown-colored strain and a mildly thermophilic strain. The results suggest that in contrast to purple nonsulfur bacteria containing bacteriochlorophyll a, those containing bacteriochlorophyll b may not be morphologically or phylogenetically diverse, and group into a tight phylogenetic clade distinct from all other anoxygenic phototrophs.

Heliorestis convoluta sp. nov., a coiled, alkaliphilic heliobacterium from the Wadi El Natroun, Egypt

A morphologically distinct heliobacterium, strain HH, was isolated from Lake El Hamra, a soda lake in the Wadi El Natroun region of northwest Egypt. Strain HH consisted of ring-shaped cells that remained attached after cell division to yield coils of various lengths. Strain HH showed several of the physiological properties of known heliobacteria and grouped in the Heliorestis clade by virtue of its phylogeny and alkaliphily. The closest relative of strain HH was the filamentous alkaliphilic heliobacterium Heliorestis daurensis. However, genomic DNA:DNA hybridization results clearly indicated that strain HH was a distinct species of Heliorestis. Based on its unique phenotypic and genetic properties we describe strain HH here as a new species of the genus Heliorestis, H. convoluta sp. nov.