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).     

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

Phototrophic anoxygenic purple bacteria play a key role in many aquatic ecosystems by oxidizing sulfur compounds and low-molecular-weight organic compounds using light as energy source. In this study, molecular methods based upon pufM gene (photosynthetic unit forming gene) were compared with culture-dependent methods to investigate anoxygenic purple phototrophic communities in sediments of an eutrophic brackish lagoon. Thirteen strains, belonging to eight different genera of purple phototrophic bacteria were isolated with a large dominance of the metabolically versatile purple non-sulfur bacteria (eight strains), some purple sulfur bacteria (three strains) and two strains belonging to the Roseobacter clade (aerobic phototrophs). The pufM genes amplified from the isolated strains were not detected by the molecular methods [terminal-restriction fragment length polymorphism (T-RFLP)] applied on in situ communities. An environmental clone library of the pufM gene was thus constructed from sediment samples. The results showed that most of the clones probably corresponded to aerobic phototrophic bacteria. Our results demonstrate that the culture-dependent techniques remain the best experimental approach for determining the diversity of phototrophic purple non-sulfur bacteria whereas the molecular approach clearly illustrated the abundance of organisms related to the Roseobacter clade in these eutrophic sediments.     

Characterization of new phototrophic heliobacteria and their habitats

Specific enrichment culture methods were used to isolate new phototrophic heliobacteria (anoxygenic phototrophic bacteria containing bacteriochlorophyll g) from various natural samples. A survey of terrestrial and aquatic habitats yielded heliobacteria only from soils, in particular rice soils, and from certain hot springs. Thirteen nonthermophilic and 7 thermophilic (capable of growth above 50) strains of heliobacteria were isolated from such habitats and characterized as to their basic cellular and nutritional properties. Phylogenetic studies of four strains showed them to be related to known species of heliobacteria. It is concluded that, unlike phototrophic purple and green bacteria, heliobacteria are primarily (if not exclusively) terrestrial, except for hot spring species. This suggests that the ecology of heliobacteria is fundamentally different from that of other anoxyphototrophs.     

Aerobic Phototrophic Bacteria: New Evidence for the Diversity,Ecological Importance and Applied Potential of this Previously Overlooked Group

The aerobic phototrophic bacteria are a recently discovered group capable of producing a photosynthetic apparatus similar to that of purple phototrophic bacteria. However, this apparatus, in contrast to that of their anaerobic counterparts, is functional in terms of photoinduced electron transport only under aerobic conditions. Although these bacteria have been widely studied, little is yet known about their ecological importance, and why they differ from other anoxygenic phototrophs with respect to oxygen requirements. In recent years a large number of new genera and species have been described from a wide variety of habitats, and evidence has been presented to support their important ecological role. This minireview focuses on recent discoveries regarding taxonomy, ecology and physiology, as well as the latest advances in the understanding of their photosynthetic apparatus and its genetic regulation.This revised version was published online in October 2005 with corrections to the Cover Date.     

Anoxygenic phototrophic bacteria of the Kislo-Sladkoe stratified lake (White Sea,Kandalaksha Bay)

The community of anoxygenic phototrophic bacteria (APB) in the water column of the Kislo-Sladkoe stratified lake recently isolated from the sea (White Sea, Kandalaksha Bay) was investigated in September 2010. The water of the sulfide-rich zone was greenish-brown due to intense development of green sulfur bacteria (GSB). Nine APB strains were isolated from the water samples: three belonging to GSB, five, to purple sulfur bacteria (PSB), and one, to purple nonsulfur bacteria (PNB). GSB predominated in the phototrophic community of the chemocline. Unexpectedly, two morphologically different green-colored GSB strains were found to be phylogenetically identical and related to the brown-colored Chlorobium phaeovibrioides (99% similarity according to the 16S rRNA gene sequencing). Homology to the closest green-colored species (Chlorobium luteolum) was 98%. Two morphologically and physiologically similar PSB strains (TcrPS10 and AmPS10) had rounded cells containing okenone and gas vesicles. According to the 16S rRNA gene sequencing, these strains were most closely related (99%) to two different Thiocapsa species: Tca. marina (containing okenonee and no gas vesicles) and Tca. rosea (containing spirilloxanthin and gas vesicles). The remaining isolates of purple bacteria were similar to the already described APB species.     

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.

     

Anoxygenic phototrophic bacterial community of Lake Shira (Khakassia)

The anoxygenic phototrophic bacterial community of the brackish meromictic Lake Shira (Khakassia) was investigated in August 2001, July 2002, and February-March 2003. In all the periods of investigation, the prevailing microorganisms were purple sulfur bacteria similar to Lamprocystis purpurea in morphology and pigment composition. Their highest number (3 x 10(5) cells/ml) was recorded in July 2002 at the depth of 15 m. According to 16S rRNA gene analysis, the strain of purple sulfur bacteria isolated in 2001 and designated ShAm01 exhibited 98.6% similarity to the type strain of Thiocapsa roseopersicina and 94.4-97.1% similarity to the type strains of Tca. pendens, Tca. litoralis, and Tea. rosea. The minor microorganisms of the anoxygenic phototrophic bacterial community within the period of investigation were nonsulfur purple bacteria phylogenetically close to Rhodovulum strictum (98.3% similarity, strain ShRb01), Ahrensia kielensis (of 93.9% similarity, strain ShRb02), Rhodomicrobium vannieli (of 99.7% similarity, strain ShRmc01), and green sulfur bacteria, phylogenetically close to Chlorobium limicola (of 98.7% similarity, strain ShCl03).     

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.     

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.     

Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria

The phylogeny, abundance, and biogeography of the NOR5/OM60 clade was investigated. This clade includes “Congregibacter litoralis” strain KT71, the first cultured representative of marine aerobic anoxygenic phototrophic Gammaproteobacteria. More than 500 16S rRNA sequences affiliated with this clade were retrieved from public databases. By comparative sequence analysis, 13 subclades could be identified, some of which are currently restricted to discrete habitat types. Almost all sequences in the largest subclade NOR5-1 and related subclade NOR5-4 originated from marine surface water samples. Overall, most of the NOR5/OM60 sequences were retrieved from marine coastal settings, whereas there were fewer from open-ocean surface waters, deep-sea sediment, freshwater, saline lakes and soil.     

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.     

Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae,isolated from a terrestrial hot spring

A bacteriochlorophyll-containing bacterium, designated as strain N10^T, was isolated from a terrestrial hot spring in Nagano Prefecture, Japan. Gram-stain-negative, oxidase- and catalase-positive and ovoid to rod-shaped cells showed the features of aerobic anoxygenic phototrophic bacteria, i.e., strain N10^T synthesised bacteriochlorophylls under aerobic conditions and could not grow anaerobically even under illumination. Genome analysis found genes for bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes and type-2 photosynthetic reaction centre in the chromosome. Phylogenetic analyses based on the 16S rRNA gene sequence and 92 core proteins revealed that strain N10^T was located in a distinct lineage near the type species of the genera Tabrizicola and Xinfangfangia and some species in the genus Rhodobacter (e.g., Rhodobacter blasticus). Strain N10^T shared?<?97.1% 16S rRNA gene sequence identity with those species in the family Rhodobacteraceae. The digital DNA–DNA hybridisation, average nucleotide identity and average amino acid identity values with the relatives, Tabrizicola aquatica RCRI19^T (an aerobic anoxygenic phototrophic bacterium), Xinfangfangia soli ZQBW^T and R. blasticus ATCC 33485^T were 19.9–20.7%, 78.2–79.1% and 69.1–70.1%, respectively. Based on the phenotypic features, major fatty acid and polar lipid compositions, genome sequence and phylogenetic position, a novel genus and species are proposed for strain N10^T, to be named Neotabrizicola shimadae (=?JCM 34381^T?=?DSM 112087T). Strain N10^T which is phylogenetically located among aerobic anoxygenic phototrophic bacteria (Tabrizicola), bacteriochlorophyll-deficient bacteria (Xinfangfangia) and anaerobic anoxygenic phototrophic bacteria (Rhodobacter) has great potential to promote studies on the evolution of photosynthesis in Rhodobacteraceae.

     

小花老鼠簕可培养细菌多样性及其生物学活性研究

小花老鼠簕(Acanthus ebracteatus)是一种生长在红树生态系统的珍稀真红树植物,具有较高的药用价值。为研究小花老鼠簕内生及根际可培养细菌多样性,挖掘其潜在新物种及具有特殊生物学活性的菌株,该文利用7种不同培养基,通过传统稀释涂布法对小花老鼠簕各植物组织及根际土壤可培养细菌进行分离,基于16S rRNA基因序列解析其内生及根际细菌群落结构和多样性特征,应用植物病原菌平板对峙实验和平铺捕食活性测试分析其可培养细菌的抗菌活性。结果表明：(1)基于16S rRNA基因序列分析,发现从小花老鼠簕的根、茎、叶、花及根际土壤中分离得到144株可培养细菌,这些细菌隶属于18目26科37属66种,芽孢杆菌属(Bacillus)和链霉菌属(Streptomyces)为优势菌属,分别占细菌种数的15.1%和13.6%;(2)拮抗多种植物病原菌试验结果显示,获得29株具有拮抗植物病原菌活性的细菌,10株具有广谱抑菌活性,其中链霉菌属菌株拮抗作用最强且菌株Y129为潜在新物种。(3)捕食活性测试结果显示,有5株细菌对金黄色葡萄球菌(Staphylococcus aureus)、耐甲氧西林金黄色葡...     

Polyphasic classification of 0.2 microm filterable bacteria from the western Mediterranean Sea

The 0.2 microm filtration of sea water samples from the Mediterranean Sea (Bay of Calvi, Corsica), collected from 10 m and 35 m depth led to the isolation of several gram-negative bacterial strains able to grow on full-strength media as well as on diluted media. The analysis of the 16S rRNA gene sequences and estimation of the phylogenetic relationships of these facultative oligotrophic bacteria indicated that they grouped into two phylogenetic branches. The strains RE10F/2, RE10F/5 (10 m depth samples) and RE35/F12 (35 m depth samples) were assigned to the gamma-subclass, while RE35F/1 (35m depth sample) was assigned to the alpha-4-subclass of the Proteobacteria. The strains RE10/F2 and RE10/F5 were most closely related to species and strains of the Pseudoalteromonas group, whereas the strain RE35F/12 placed adjacent to the family Vibrionaceae. The phylogenetic analysis of strain RE35F/1 revealed that this bacterium clusters with marine strains and species of the aerobic anoxygenic phototrophic bacteria Erythrobacter as well as Erythromicrobium and more distantly to Sphingomonas spp. Supplementary to those genotypic classifications the chemotaxonomic signatures including the major respiratory lipoquinone systems, the cellular fatty acid compositions as well as the polyamine contents of the bacteria were investigated. The isolated organisms displayed differences in their physiological and biochemical properties to already described strains belonging to the same genera or families, as revealed by the comparative 16S rRNA analysis. Despite the fact that these bacteria were isolated from a 0.2 microm filtrate, the cultured organisms which were all rod-shaped, displayed width dimensions ranging from 0.4 up to 0.7 microm, indicating that these bacteria were starvation forms at the time of isolation and not ultramicrobacteria as defined by Torella and Morita (1981) or by Schut et al. (1993). Because our isolated strains represent potentially new taxa, this first investigation on 0.2 pm filterable bacteria from the Western Mediterranean Sea supports the hypothesis that this bacterial fraction contributes to the diversity of marine bacteria.     

A comparative analysis of extreme thermophilic bacteria belonging to the genus Thermus

Several extreme thermophilic Gram negative bacteria found in a thermally polluted river in Belgium have been compared with Thermus strains isolated from widely distant geographical areas. This analysis has become possible after the design of a new culture medium (162).All strains examined (including the isolate successively denominated Flavobacterium thermophilum and Thermus thermophilus) were found to be morphologically identical with strain YT-1 of Thermus aquaticus. The cells are immotile, rod-like, strictly aerobic, catalase and oxidase positive. They produce amylase, hydrolyze gelatin and are confirmed to be highly sensitive towards penicillin.The nutritional pattern of all strains has been analysed extensively, by testing a broad spectrum of possible substrates.The strains display a uniform response to the microbiological tests applied and most probably belong to the same species: Thermus aquaticus.Abbreviations GC guanosine cytosine - ATCC American Type Culture Collection - DSM Deutsche Sammlung von Mikroorganismen     

Anoxygenic phototrophic bacteria of the high-altitude meromictic Lake Gek-Gel,Azerbaijan

The anoxygenic phototrophic bacterial community of the high-altitude meromictic Lake Gek-Gel (Azerbaijan) was investigated in September 2003. The highest concentration of bacteriochlorophyll e (48 μg/l) was detected at a depth of 30 m; the peak of bacteriochlorophyll a (4.5 μg/l) occurred at 29 m. Phylogenetic analysis revealed that brown-colored green sulfur bacteria Chlorobium phaeobacteroides predominated in the lake. Nonsulfur purple bacteria phylogenetically close to Blastochloris sulfoviridis were found in insignificant amounts; these organisms have not been previously reported in Lake Gek-Gel.