Benthic phototrophic community from Kiran soda lake,south-eastern Siberia

Phototrophic bacterial mats from Kiran soda lake (south-eastern Siberia) were studied using integrated approach including analysis of the ion composition of water, pigments composition, bacterial diversity and the vertical distribution of phototrophic microorganisms in the mats. Bacterial diversity was investigated using microscopic examination, 16S rRNA gene Illumina sequencing and culturing methods. The mats were formed as a result of decomposition of sedimented planktonic microorganisms, among which cyanobacteria of the genus Arthrospira predominated. Cyanobacteria were the largest part of phototrophs in the mats, but anoxygenic phototrophs were significant fraction. The prevailing species of the anoxygenic phototrophic bacteria are typical for soda lakes. The mats harbored aerobic anoxygenic phototrophic bacteria, purple sulfur and non-sulfur bacteria, as well as new filamentous phototrophic Chloroflexi. New strains of Thiocapsa sp. Kir-1, Ectothiorhodospira sp. Kir-2 and Kir-4, Thiorhodospira sp. Kir-3 and novel phototrophic Chloroflexi bacterium Kir15-3F were isolated and identified.

     

Rapid growth rates of aerobic anoxygenic phototrophs in the ocean

We analysed bacteriochlorophyll diel changes to assess growth rates of aerobic anoxygenic phototrophs in the euphotic zone across the Atlantic Ocean. The survey performed during Atlantic Meridional Transect cruise 16 has shown that bacteriochlorophyll in the North Atlantic Gyre cycles at rates of 0.91-1.08 day(-1) and in the South Atlantic at rates of 0.72-0.89 day(-1). In contrast, in the more productive equatorial region and North Atlantic it cycled at rates of up to 2.13 day(-1). These results suggest that bacteriochlorophyll-containing bacteria in the euphotic zone of the oligotrophic gyres grow at rates of about one division per day and in the more productive regions up to three divisions per day. This is in striking contrast with the relatively slow growth rates of the total bacterial community. Thus, aerobic anoxygenic phototrophs appear to be a very dynamic part of the marine microbial community and due to their rapid growth, they are likely to be larger sinks for dissolved organic matter than their abundance alone would predict.     

Diel changes in bacteriochlorophyll a concentration suggest rapid bacterioplankton cycling in the Baltic Sea

Aerobic anoxygenic phototrophs were recently found to constitute a significant portion of the marine microbial community. These bacteria use bacteriochlorophyll-containing reaction centers to perform photoheterotrophic metabolism. A new instrument for routine measurements of both chlorophyll a and bacteriochlorophyll a was used for monitoring anoxygenic phototrophs in the Baltic Sea in late summer 2003. Bacteriochlorophyll a concentration ranged from 8 to 50 ngl(-1), with an average bacteriochlorophyll/chlorophyll ratio of 4.2 x 10(-3). Moreover, diel trends in bacteriochlorophyll a signals were observed, with a distinct decline occurring during daylight hours. Based on laboratory measurements this phenomenon was ascribed to the complete inhibition of bacteriochlorophyll synthesis by light, which, in combination with a concurrent turnover of the cells, resulted in a pigment decline. Following this explanation, we postulate that bacteriochlorophyll a can serve as a natural 'pulse-and-chase' marker, allowing estimation of the mortality rates of anoxygenic phototrophs from the rates of pigment decline. Based on this assumption, we suggest that the Baltic photoheterotrophic community was characterized by high turnover rates, in a range of 0.7-2 d(-1).     

Distribution and growth of aerobic anoxygenic phototrophs in the Mediterranean Sea

The distribution of aerobic anoxygenic phototrophs (AAPs) was surveyed in various regions of the Mediterranean Sea in spring and summer. These phototrophic bacteria were present within the euphotic layer at all sampled stations. The AAP abundances increased with increasing trophic status ranging from 2.5 × 10(3) cells per ml in oligotrophic Eastern Mediterranean up to 90 × 10(3) cells per ml in the Bay of Villefranche. Aerobic anoxygenic phototrophs made up on average 1-4% of total prokaryotes in low nutrient areas, whereas in coastal and more productive stations these organisms represented 3-11% of total prokaryotes. Diel bacteriochlorophyll a decay measurements showed that AAP community in the Western Mediterranean grew rapidly, at rates from 1.13 to 1.42 day(-1). The lower AAP abundances registered in the most oligotrophic waters suggest that they are relatively poor competitors under nutrient limiting conditions. Instead, AAPs appear to be metabolically active organisms, which thrive better in more eutrophic environments providing the necessary substrates to maintain high growth rates.     

The structure of phototrophic communities of soda lakes of the southeastern Transbaikal region

The structure of benthic phototrophic communities of 24 soda lakes of the southeastern Transbaikal Region was studied. The physicochemical properties of the lakes were determined. The results of the cell count of anoxygenic phototrophic bacteria (APB) belonging to various groups are presented. The influence of salinity on the structure of APB communities was investigated. The APB reaction to environmental conditions was determined. Massive development of phototrophic microorganisms in the form of mats and films was observed in the majority of the investigated lakes. The APB communities were characterized by a wide diversity of species and evenness of species composition. Purple sulfur bacteria of the families Ectothiorhodospiraceae and Chromatiaceae were predominant. Purple nonsulfur bacteria of the family Rhodobacteraceae, green filamentous bacteria Oscillochloris sp., and heliobacteria were also detected. According to preliminary data, no less than 15 species of APB occur in the studied lakes. Among them, three novel genera and four species have already been described. Identification of other isolates is still in progress. The lakes make an almost continuous series of fresh, brackish, and saline water bodies, varying in their degree of mineralization. It was demonstrated that the structure of APB communities was unaffected by salinity ranging from 5 to 40 g/l. At salt concentrations of lower than 5 g/l, the level of water mineralization became a limiting factor. Experiments with the isolated cultures showed that the APB were obligately dependent on the presence of carbonate ions in the medium. They were haloalkalitolerant or haloalkaliphilic. Thus, they are well adapted to the conditions of soda lakes with a high mineralization. It was demonstrated that soda lakes of the southeastern Transbaikal Region represent a special type of habitat which harbors a peculiar autochthonous microflora and differs from both highly mineralized soda lakes and shallow saline water bodies of the sea origin.     

Abundant presence of the gamma-like Proteobacterial pufM gene in oxic seawater

Known anoxygenic photosynthetic bacteria (APB) affiliated to Gammaproteobacteria usually use anaerobic metabolism and are restricted to oxygen-free habitats. Here, we report abundant (average of 34.5%) presence of diverse APB related to gamma-like Proteobacteria in oxic oceanic surface water as indicated by the pufM gene, that encodes the M subunit of the light reaction centre complex. Thus, our sequences were most likely derived from aerobic anoxygenic phototrophs (AAnP). Two genetically distinct genotypes were revealed: one was from the oligotrophic North Pacific Ocean Gyre and the other, was from the trophic East China Sea and Bering Sea. The discovery of abundant presence of novel gamma-like Proteobacterial pufM gene in the oxic seawater extends the functional ecotypes of AAnP.     

Distribution of aerobic anoxygenic phototrophs in temperate freshwater systems

The presence of aerobic anoxygenic phototrophs (AAPs) was recently reported from various marine environments; however, there is little information regarding their distribution in fresh waters. We surveyed a number of freshwater systems in central Europe, by infra-red fluorometry, infra-red epifluorescence microscopy, fluorescence emission spectroscopy and pigment analyses. AAPs were found to be abundant in several oligotrophic and mesotrophic lakes (50–400 ng of bacteriochlorophyll a l⁻¹, 10–80% of bacterial biomass), while in more eutrophized water bodies they represented a negligible part of the total microbial community (< 1%). The observed freshwater AAPs were morphologically diverse and different from previously observed marine species. Under temperate European climatic conditions, AAP populations undergo strong seasonal changes in terms of both abundance and species composition, with the maximum biomass in summer and the minimum in winter. In the mountain lakes Čertovo and Plešné, AAPs contributed more than one half of total bacterial biomass during their summer maximum. These results show that photoheterotrophic bacteria represent an important part of the microbial community in many freshwater systems.     

The structure of phototrophic communities of soda lakes of the southeastern Transbaikal Region

The structure of benthic phototrophic communities of 24 soda lakes of the southeastern Transbaikal Region was studied. The physicochemical properties of the lakes were determined. The results of enumeration of anoxygenic phototrophic bacteria (APB) belonging to various groups are presented. The influence of salinity on the structure of APB communities was investigated. The APB reaction to environmental conditions was determined. Massive development of phototrophic microorganisms in the form of mats and films was observed in the majority of the investigated lakes. The APB communities were characterized by a wide diversity and evenness of species composition. Purple sulfur bacteria of the families Ectothiorhodospiraceae and Chromatiaceae were predominant. Purple nonsulfur bacteria of the family Rhodobacteraceae, green filamentous bacteria Oscillochloris sp., and heliobacteria were also detected. According to preliminary data, no less than 15 species of APB occur in the studied lakes. Among them, three novel genera and four species have already been described. Identification of other isolates is still in progress. The lakes make an almost continuous series of fresh, brackish, and saline water bodies, varying in their degree of mineralization. It was demonstrated that the structure of APB communities was unaffected by changes in salinity from 5 to 40 g/l. At salt concentrations of lower than 5 g/l, the level of water mineralization became a limiting factor. Experiments with the isolated cultures showed that the APB were obligately dependent on the presence of carbonate ions in the medium. They were haloalkalitolerant or haloalkaliphilic. Thus, they are well adapted to the conditions of soda lakes with a low of moderate mineralization. It was demonstrated that soda lakes of the southeastern Transbaikal Region represent a special type of habitat which harbors a peculiar autochthonous microflora and differs from both highly mineralized soda lakes and shallow saline water bodies of the sea origin.     

<Emphasis Type="Italic">Chromocurvus halotolerans</Emphasis> gen. nov., sp. nov., a gammaproteobacterial obligately aerobic anoxygenic phototroph,isolated from a Canadian hypersaline spring

A strain EG19^T of aerobic bacteria able to form pleomorphic cells was isolated from a brine spring runoff stream in the west central region of the province of Manitoba, Canada. The pale pinkish purple strain contained bacteriochlorophyll a incorporated into light-harvesting I and reaction center complexes. Its inability to grow under anaerobic illuminated conditions prompted designation as a member of the functional group known as aerobic anoxygenic phototrophic bacteria. Phylogenetic analysis of the 16S rRNA gene sequence revealed that it belonged to the Gammaproteobacteria, forming a distinct branch of phototrophs distantly related to most described aerobic anoxygenic phototrophs, quite marginally related (95.6%) both to the only other described gammaproteobacterial aerobic phototroph, Congregibacter litoralis, and also to nonphototrophs in the genus Haliea (95.1–96.1%). Physiological tests demonstrated tolerance profiles to salinity (0–18% NaCl), pH (7–12), and temperature (7–40°C) consistent with survival in a shallow hypersaline stream on the exposed, vegetation-depleted salt playa of its native East German Creek. Phylogenetic data and phenotypic properties such as pigment composition, morphology, and physiology support the proposal of the novel genus and species Chromocurvus halotolerans gen. nov., sp. nov., with EG19^T (=DSM 23344^T, =VKM B-2659^T) as the type strain.     

Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains,East Antarctica

This study investigated the culturable aerobic phototrophic bacteria present in soil samples collected in the proximity of the Belgian Princess Elisabeth Station in the Sør Rondane Mountains, East Antarctica. Until recently, only oxygenic phototrophic bacteria (Cyanobacteria) were well known from Antarctic soils. However, more recent non-cultivation-based studies have demonstrated the presence of anoxygenic phototrophs and, particularly, aerobic anoxygenic phototrophic bacteria in these areas. Approximately 1000 isolates obtained after prolonged incubation under different growth conditions were studied and characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Representative strains were identified by sequence analysis of 16S rRNA genes. More than half of the isolates grouped among known aerobic anoxygenic phototrophic taxa, particularly with Sphingomonadaceae, Methylobacterium and Brevundimonas. In addition, a total of 330 isolates were tested for the presence of key phototrophy genes. While rhodopsin genes were not detected, multiple isolates possessed key genes of the bacteriochlorophyll synthesis pathway. The majority of these potential aerobic anoxygenic phototrophic strains grouped with Alphaproteobacteria (Sphingomonas, Methylobacterium, Brevundimonas and Polymorphobacter).     

Anoxygenic phototrophic bacteria from microbial communities of Goryachinsk thermal spring (Baikal Area,Russia)

Species composition of anoxygenic phototrophic bacteria in microbial mats of the Goryachinsk thermal spring was investigated along the temperature gradient. The spring belonging to nitrogenous alkaline hydrotherms is located at the shore of Lake Baikal 188 km north-east from Ulan-Ude. The water is of the sulfate-sodium type, contains trace amounts of sulfide, and salinity does not exceed 0.64 g/L, pH 9.5. The temperature at the outlet of the spring may reach 54°C. The cultures of filamentous anoxygenic phototrophic bacteria, nonsulfur and sulfur purple bacteria, and aerobic anoxygenic phototrophic bacteria were identified using the pufLM molecular marker. The fmoA marker was used for identification of green sulfur bacteria. Filamentous cyanobacteria predominated in the mats, with anoxygenic phototrophs comprising a minor component of the phototrophic communities. Thermophilic bacteria Chloroflexus aurantiacus were detected in the samples from both the thermophilic and mesophilic mats. Cultures of nonsulfur purple bacteria similar to Blastochloris sulfoviridis and Rhodomicrobium vannielii were isolated from the mats developed at high (50.6–49.4°C) and low temperatures (45–20°C). Purple sulfur bacteria Allochromatium sp. and Thiocapsa sp., as well as green sulfur bacteria Chlorobium sp., were revealed in low-temperature mats. Truly thermophilic purple and green sulfur bacteria were not found in the spring. Anoxygenic phototrophic bacteria found in the spring were typical of the sulfur communities, for which the sulfur cycle is mandatory. The presence of aerobic bacteriochlorophyll a-containing bacteria identified as Agrobacterium (Rhizobium) tumifaciens in the mesophilic (20°C) mat is of interest.     

Comparative study of metabolism of the purple photosynthetic bacteria grown in the light and in the dark under anaerobic and aerobic conditions

For three species of anoxygenic phototrophic alphaproteobacteria differing in their reaction to oxygen and light, physiological characteristics (capacity for acetate assimilation, activity of the tricarboxylic acid (TCA) cycle enzymes, respiration, and the properties of the oxidase systems) were studied. Nonsulfur purple bacteria Rhodobacter sphaeroides, Rhodobaca bogoriensis, and aerobic anoxygenic phototrophic bacteria Roseinatronobacter thiooxidans were the subjects of investigation. All of these organisms were able to grow under aerobic conditions in the dark using the respiratory system with cytochrome aa ₃ as the terminal oxidase. They differed, however, in their capacity for growth in the light, bacteriochlorophyll synthesis, and regulation of activity of the TCA cycle enzymes. Oxygen suppressed bacteriochlorophyll synthesis by Rha. sphaeroides and Rbc. bogoriensis both in the dark and in the light. Bacteriochlorophyll synthesis in Rna. thiooxidans occurred only in the dark and was suppressed by light. The results on acetate assimilation by the studied strains reflected the degree of their adaptation to aerobic growth in the dark. Acetate assimilation by light-grown Rha. sphaeroides was significantly higher than by the dark-grown ones. Unlike Rha. sphaeroides, acetate assimilation by Rbc. bogoriensis in the light under anaerobic and aerobic conditions was much less dependent on the growth conditions. Aerobic acetate assimilation by all studied bacteria was promoted by light. In Rha. sphaeroides, activity of the TCA cycle enzymes increased significantly in the cells grown aerobically in the dark. In Rbc. bogoriensis, activity of most of the TCA cycle enzymes under aerobic conditions either decreased or remained unchanged. Our results confirm the origin of modern chemoorganotrophs from anoxygenic phototrophic bacteria. The evolution from anoxygenic photoorganotrophs to aerobic chemoorganotrophs included several stages: nonsulfur purple bacteria → nonsulfur purple bacteria similar to Rbc. bogoriensis → aerobic anoxygenic phototrophs → chemoorganotrophs.     

Potential activity of methane and ammonia oxidation by methanotropic communities from soda lakes of the southern Transbaikal

Radioisotopic measurements of the methane consumption by mud samples taken from nine Southern Transbaikal soda lakes (pH 9.5-10.6) showed an intense oxidation of methane in the muds of lakes Khuzhirta, Bumalai Nur, Gorbunka, and Suduntuiskii Torom, with the maximum oxidation rate in the mud of lakes Khuzhirta (33.2 nmol/(ml day)). The incorporation rate of the radioactive label from 14CH4 into 14CO2 was higher than into acid-stable metabolites. Optimum pH values for methane oxidation in water samples were 7-8, whereas mud samples exhibited two peaks of methane oxidation activity (at pH 8.15-9.4 and 5.8-7.0). The majority of samples could oxidize ammonium to nitrites; the oxidation was inhibited by methane. The PCR amplification analysis of samples revealed the presence of genes encoding soluble and particulate methane monooxygenase and methanol dehydrogenase. Three alkaliphilic methanotrophic bacteria of morphotype I were isolated from mud samples in pure cultures, one of which, B5, was able to oxidize ammonium to nitrites at pH 7-11. The data obtained suggest that methanotrophs are widely spread in the soda lakes of Southern Transbaikal, where they actively oxidize methane and ammonium.     

Microbial communities of the stratified soda Lake Doroninskoe (Transbaikal region)

The physicochemical properties, species composition, and vertical distribution of microorganisms in the water column, shoreline microbial mat, and small shoreline mud volcanoes of the stratified soda Lake Doroninskoe were investigated in September 2007. The lake is located in the Transbaikal region, in the permafrost zone (51°25′N; 112°28′E). The maximal depth of the contemporary lake is about 6 m, the pH value of the water is 9.72, and the water mineralization in the near-bottom horizon is 32.3 g l⁻¹. In summer, the surface oxygen-containing horizon of the water column becomes demineralized to 26.5 g l⁻¹; at a depth of 3.5–4.0 m, an abrupt transition occurs to the aerobic zone containing hydrosulfide (up to 12.56 g l⁻¹). Hydrosulfide was also detected in trace quantities in the upper water horizons. The density stratification of the water column usually ensures stable anaerobic conditions until the freezing period (November and December). The primary production of oxygenic phototrophs reached 176–230 μg l⁻¹. High rates of dark CO₂ assimilation (61–240 μg l⁻¹) were detected in the chemocline. Within this zone, an alkaliphilic species of sulfur-oxidizing bacteria of the genus Thioalkalivibrio was detected (10⁴ cells ml⁻¹). Lithoheterotrophic bacteria Halomonas spp., as well as bacteriochlorophyll a-containing aerobic anoxygenic phototrophic bacteria (AAP) Roseinatronobacter sp. capable of thiosulfate oxidation, were isolated from samples collected from the aerobic zone (0–3 m). The water transparency in September was extremely low; therefore, no visible clusters of anoxygenic phototrophic bacteria (APBs) were detected at the boundary of the hydrosulfide layer. However, purple sulfur bacteria which, according to the results of the 16S rRNA gene analysis, belong to the species Thioalkalicoccus limnaeus, Ectothiorhodospira variabilis, “Ect. magna,” and Ect. shaposhnikovii, were isolated from samples of deep silt sediments. Ect. variabilis and Ect. shaposhnikovii were the major APB species in the shoreline algo-bacterial mat. The halotolerant bacterium Ect. shaposhnikovii, purple nonsulfur bacteria of the genus Rhodobacter, and AAP of Roseococcus sp. were isolated from the samples collected from mud volcanoes. All these species are alkaliphiles, moderate halophiles, or halotolerant microorganisms.     

Temporal Changes and Altitudinal Distribution of Aerobic Anoxygenic Phototrophs in Mountain Lakes

Aerobic anoxygenic phototrophs (AAPs) are bacteriochlorophyll a-containing microorganisms that use organic substrates for growth but can supplement their energy requirements with light. They have been reported from various marine and limnic environments; however, their ecology remains largely unknown. Here infrared epifluorescence microscopy was used to monitor temporal changes in AAPs in the alpine lake Gossenköllesee, located in the Tyrolean Alps, Austria. AAP abundance was low (10³ cells ml⁻¹) until mid-July and reached a maximum of ∼1.3 × 10⁵ cells ml⁻¹ (29% of all prokaryotes) in mid-September. We compared the studied lake with other mountain lakes located across an altitudinal gradient (913 to 2,799 m above sea level). The concentration of dissolved organic carbon and water transparency seem to be the main factors influencing AAP abundance during the seasonal cycle as well as across the altitudinal gradient. While the AAP populations inhabiting the alpine lakes were composed of intensely pigmented large rods (5 to 12 μm), the lakes below the tree line were inhabited by a variety of smaller morphotypes. Analysis of pufM diversity revealed that AAPs in Gossenköllesee were almost exclusively Sphingomonadales species, which indicates that AAP communities inhabiting alpine lakes are relatively homogeneous compared to those in low-altitude lakes.     

Novel halophilic aerobic anoxygenic phototrophs from a Canadian hypersaline spring system

The first enumeration of cultivable obligately aerobic phototrophic bacteria from a terrestrial saline spring was accomplished in the East German Creek system (salinity approximately 6%), near Lake Winnipegosis, Manitoba, Canada. Occurring at densities up to 3.3 x 10(7) CFU/ml of sample, aerobic phototrophs comprised 15-36% of the total cultivable bacterial population in the diatom- and chlorophyte-dominated aerobic microbial mats. Many of the representative strains isolated for phenotypic characterization and phylogenetic analysis possessed <96% 16S rDNA sequence overlap with published species, including an obligately aerobic phototrophic gammaproteobacterium displaying only 92.9% 16S rDNA sequence similarity to Congregibacter litoralis. The springs yielded the most highly halotolerant aerobic anoxygenic phototroph yet recorded, strain EG11, which grew with 26% NaCl.     

Comparison of <Emphasis Type="Italic">Chloroflexus aurantiacus</Emphasis> strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically

Chloroflexus aurantiacus J-10-fl is a thermophilic green bacterium, a filamentous anoxygenic phototroph, and the model organism of the phylum Chloroflexi. We applied high-throughput, liquid chromatography–mass spectrometry in a global quantitative proteomics investigation of C. aurantiacus cells grown under oxic (chemoorganoheterotrophically) and anoxic (photoorganoheterotrophically) redox states. Our global analysis identified 13,524 high-confidence peptides that matched to 1,286 annotated proteins, 242 of which were either uniquely identified or significantly increased in abundance under photoheterotrophic culture condition. Fifty-four of the 242 proteins are previously characterized photosynthesis-related proteins, including chlorosome proteins, proteins involved in the bacteriochlorophyll biosynthesis, 3-hydroxypropionate (3-OHP) CO₂ fixation pathway, and components of electron transport chains. The remaining 188 proteins have not previously been reported. Of these, five proteins were found to be encoded by genes from a novel operon and observed only in photoheterotrophically grown cells. These proteins candidates may prove useful in further deciphering the phototrophic physiology of C. aurantiacus and other filamentous anoxygenic phototrophs.