Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis

Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.

Ectothiorhodospira lacustris sp. nov., a New Purple Sulfur Bacterium from Low-Mineralized Soda Lakes That Contains a Unique Pathway for Nitric Oxide Reduction

Several strains of a Gram-negative, anaerobic photoautotrophic, motile, rod-shaped bacterium, designated as B14B, A-7R, and A-7Y were isolated from biofilms of low-mineralized soda lakes in central Mongolia and Russia (southeast Siberia). They had lamellar stacks as photosynthetic structures and bacteriochlorophyll a as the major photosynthetic pigment. The strains were found to grow at 25-35 °C, pH 7.5-10.2 (optimum, pH 9.0), and with 0-8% (w/v) NaCl (optimum, 0%). In the presence of sulfide and bicarbonate, acetate, butyrate, yeast extract, lactate, malate, pyruvate, succinate, and fumarate promoted growth. The DNA G + C content was 62.9-63.0 mol%. While the 16S rRNA gene sequences confirmed that the new strains belonged to the genus Ectothiorhodospira of the Ectothiorhodospiraceae, comparison of the genome nucleotide sequences of strains B14B, A-7R, and A-7Y revealed that the new isolates were remote from all described Ectothiorhodospira species both in dDDH (19.7-38.8%) and in ANI (75.0-89.4%). The new strains are also genetically differentiated by the presence of a nitric oxide reduction pathway that is lacking from all other Ectiothiorhodospiraceae. We propose to assign the isolates to the new species, Ectothiorhodospira lacustris sp. nov., with the type strain B14B^T (=DSM 116064^T = KCTC 25542^T = UQM 41491^T).

Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov

The Ectothiorhodospiraceae family represents purple sulfur bacteria of the Gammaproteobacteria found primarily in alkaline soda lakes of moderate to extremely high salinity. The main microscopically visible characteristic separating them from the Chromatiaceae is the excretion of the intermediate elemental sulfur formed during oxidation of sulfide prior to complete oxidation to sulfate rather than storing it in the periplasm. We present a comparative study of 38 genomes of all species of phototrophic Ectothiorhodospiraceae. We also include a comparison with those chemotrophic bacteria that have been assigned to the family previously and critically reevaluate this assignment. The data demonstrate the separation of Halorhodospira species in a major phylogenetic branch distant from other Ectothiorhodospiraceae and support their separation into a new family, for which the name Halorhodospiraceae fam. nov. is proposed. In addition, the green-colored, bacteriochlorophyll-containing species Halorhodospira halochloris and Halorhodospira abdelmalekii were transferred to the new genus Halochlorospira gen. nov. of this family. The data also enable classification of several so far unclassified isolates and support the separation of Ectothiorhodospira shaposhnikovii and Ect. vacuolata as well as Ect. mobilis and Ect. marismortui as distinct species.

Metabolites Produced by Alkaliphiles with Potential Biotechnological Applications

Alkaliphiles are a diverse group of relatively less known microorganisms living in alkaline environments. To thrive in alkaline environments, alkaliphiles require special adaptations. This adaptation may have evolved metabolites which can be useful for biotechnological processes or other applications. In fact, certain metabolites are found unique to alkaliphiles or are effectively produced by alkaliphiles. This probably aroused the interest in metabolites of alkaliphiles. During recent years, many alkaliphilic microbes have been isolated, especially in countries having alkaline environments, like soda lakes. Even if the number of such isolated alkaliphiles is large, their metabolites have not yet been extensively analyzed and exploited. This is expected to come in the years ahead. So far, the focus of interests in metabolites from alkaliphiles falls into categories such as organic acids, ingredients for foodstuffs and cosmetics, antibiotics, and substances which modify properties of other materials used in industry. This chapter deals with biotechnologically important metabolites of alkaliphiles including compatible solutes, biosurfactants, siderophores, carotenoids, exopolysaccharides, and antimicrobial agents. It also covers the promising potential of alkaliphiles as sources of bioplastic raw materials. Moreover, an overview of the patent literature related to alkaliphiles is highlighted. Graphical Abstract.

Enhancement of COD, ammonia, phosphate and sulfide simultaneous removal by the anaerobic photosynthetic bacterium of Ectothiorhodospira magna in batch and sequencing batch culture

An anaerobic photosynthetic bacterium, with chemical oxygen demand (COD), ammonia nitrogen (NH₃-N), total phosphorus (TP) and sulfide (S^2-) simultaneous removal ability, strain SU6, was isolated and identified as belonging to Ectothiorhodospira magna. Its removal efficiencies were simultaneously evaluated in batch culture and influenced in sequencing batch culture. The maximum COD, NH₃-N, TP and S^2- removal rates of 93.04%, 86.70%, 37.55% and 99.99% were obtained in batch culture with an initial pH 8.0 at 35 °C after 72 h. The simultaneous removal efficiency was enhanced in sequencing batch culture, and 789.27 mg/L COD, 68.91 mg/L NH₃-N, 70.20 mg/L S^2- and 5.26 mg/L TP were removed by the end of the last cycle within 24 h. This was the first time of reporting contaminants' simultaneous removal by a pure-cultured photosynthetic bacterium. The experimental results demonstrate that E. magna can efficiently serve as a good candidate in anaerobic wastewater contaminants' simultaneous removal, and maybe as another model anaerobic photosynthetic microorganism for water purification investigations.

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.

Aquichromatium aeriopus gen. nov., sp. nov., A Non-phototrophic Aerobic Chemoheterotrophic Bacterium, and Proposal of Aquichromatiaceae fam. nov. in the Order Chromatiales

A gram-staining negative, non-motile, aerobic chemoheterotrophic, ovoid or short rod-shaped bacterium, designated as J89^T, was isolated from a seawater sample collected from the coast of Yellow Sea in Qingdao, China. The strain grew at salinities of 1.0-6.0% (w/v) NaCl (optimum, 3.0%). Growth occurred at pH 6.0-9.0 (optimum, pH 7.0) and at 10-35 °C (optimum, 25-30 °C). The genomic DNA G+C content was determined to be 59.3 mol%. Q-8 was detected as the respiratory quinone. The major fatty acids (>10%) were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), and C_16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids, and an unidentified polar lipid. Comparison of the 16S rRNA gene sequence indicated that the strain was most closely related (<91%) to members of the order Chromatiales in the class Gammaproteobacteria. Phylogenetic analyses showed that this strain represented a distinct phylogenetic lineage in the order Chromatiales and could not be assigned to any of the defined families in the order. On the basis of low sequence similarities and differential characteristics of strain J89^T from the genera of neighboring families, the strain is proposed to be a representative of a novel genus Aquichromatium gen. nov. A new family Aquichromatiaceae with the type genus Aquichromatium is proposed. Strain J89^T (=MCCC 1K03281T=CMRC C2017206T) is the type strain of the type species Aquichromatium aeriopus sp. nov.

Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov

A novel Gram-stain-negative, rods or bent rods, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated XK5T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Optimal growth occurred at 28-35 °C (range 8-42 °C) and pH 7.0-8.0 (range pH 6.0-9.0) with 1-3 % (w/v) NaCl (range 0.5-8 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain XK5T was 92.1 % similar to the type strain of Thioalkalivibrio thiocyanodenitrificans, 91.9 % to the type strain of Thioalkalivibrio sulfidiphilus and 91.8 % to the type strain of Thioalkalivibrio denitrificans; similarity to other species was less than 91 %. The isolate and closely related environmental clones formed a novel family level clade in the order Chromatiales. The polar lipid profile of the novel isolate consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown phospholipids, aminolipids and lipids. Major cellular fatty acids were iso-C17 : 1ω9c and iso-C15 : 0 and the main respiratory lipoquinone was Q-8. The DNA G+C content of strain XK5T was 59.3 mol%. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain XK5T represents a novel species of a new genus within a novel family of the order Chromatiales, for which the name Woeseia oceani gen. nov., sp. nov. is proposed. The type strain of Woeseia oceani is XK5T ( = ATCC BAA-2615T = CICC 10905T). In addition, a novel family name, Woeseiaceae fam. nov., is proposed to accommodate the genus Woeseia.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.