Distinct life cycle stages of an ectosymbiotic DPANN archaeon.

DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell-cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic cells are intimately linked with the host through an elaborate attachment organelle. Our data suggest that free cells may actively seek a new host, while the ectobiotic state is adapted to mediate intricate interaction with the host.

Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'.

Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales). Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate- and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life-limiting extremes.

'Candidatus Oscillochloris kuznetsovii' a novel mesophilic filamentous anoxygenic phototrophic Chloroflexales bacterium from Arctic coastal environments.

Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named 'Candidatus Oscillochloris kuznetsovii'. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf.

Cryo-Electron Tomography Reveals the Complex Ultrastructural Organization of Multicellular Filamentous Chloroflexota (Chloroflexi) Bacteria.

The cell biology of Chloroflexota is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic Roseiflexus castenholzii and Chloroflexus aggregans, and mesophilic "Ca. Viridilinea mediisalina." These species represent the three main lineages within a group of multicellular filamentous anoxygenic phototrophic Chloroflexota bacteria belonging to the Chloroflexales order. We found surprising structural complexity in the Chloroflexales. As with filamentous cyanobacteria, cells of C. aggregans and "Ca. Viridilinea mediisalina" share the outer membrane-like layers of their intricate multilayer cell envelope. Additionally, cells of R. castenholzii and "Ca. Viridilinea mediisalina" are connected by septal channels that resemble cyanobacterial septal junctions. All three strains possess long pili anchored close to cell-to-cell junctions, a morphological feature comparable to that observed in cyanobacteria. The cytoplasm of the Chloroflexales bacteria is crowded with intracellular organelles such as different types of storage granules, membrane vesicles, chlorosomes, gas vesicles, chemoreceptor-like arrays, and cytoplasmic filaments. We observed a higher level of complexity in the mesophilic strain compared to the thermophilic strains with regards to the composition of intracellular bodies and the organization of the cell envelope. The ultrastructural details that we describe in these Chloroflexales bacteria will motivate further cell biological studies, given that the function and evolution of the many discovered morphological traits remain enigmatic in this diverse and widespread bacterial group.

Genome Sequences of Green- and Brown-Colored Strains of Chlorobium phaeovibrioides with Gas Vesicles.

The draft genomes of green-colored Chlorobium phaeovibrioides GrKhr17 and brown-colored Chlorobium phaeovibrioides BrKhr17, green sulfur bacteria with gas vesicles isolated from Lake Bolshye Khruslomeny, are presented. These sequences contribute to genomic analyses of the Chlorobiaceae family that are part of ongoing research seeking to better understand their ecosystem-specific adaptations.

Prosthecochloris marina sp. nov., a new green sulfur bacterium from the coastal zone of the South China Sea.

A Gram-negative, anaerobic photoautotroph, nonmotile, oval bacterium possessing gas vesicles and having no prosthecae, designated as V1, was isolated from the South China Sea coastal zone. It had chlorosomes as photosynthetic structures, and bacteriochlorophyll c as the major photosynthetic pigment. The strain was found to grow at 20-35 °C, pH 6.3-8.0 (optimum, pH 7.1) and with 0.7-5.8% (w/v) NaCl (optimum, 1-1.8%). In the presence of sulfide and bicarbonate, acetate, and fructose promoted growth. The DNA G+C content was 47 mol%. While the new isolate belonged to the Chlorobiaceae genus Prosthecochloris, it exhibited low similarity of the 16S rRNA gene sequences (96.21-96.78%) to other members of this genus. Comparison of the genome nucleotide sequences of strain V1 revealed that the new isolate was remote from the Chlorobiaceae type strains both in dDDH (16.8-18.9%) and in ANI (75.2-77.8%). We propose to assign the isolate to a new species, Prosthecochloris marina sp. nov., with the type strain V1T ( = VKM-3301T = KCTC 15824T).

'Candidatus Oscillochloris fontis': a novel mesophilic phototrophic Chloroflexota bacterium belonging to the ubiquitous Oscillochloris genus.

We present the results of a study of mesophilic anoxygenic phototrophic Chloroflexota bacteria from Mechigmen hot spring (the Chukotka Peninsula) and Siberia. According to 16S rRNA phylogenetic analysis, these bacteria belong to Oscillochloris trichoides. However, sequencing the draft genome of the bacterium from the Chukotka and analysis of the average nucleotide identity, as well as in silico DNA-DNA hybridization, reveal that this bacterium belongs to a novel species within the Oscillochloris genus. We, therefore, propose 'Candidatus Oscillochloris fontis' as a novel taxon to represent this mesophilic alkaliphilic anaerobic anoxygenic phototrophic bacterium. Spectrophotometry and high-performance liquid chromatography analysis show that the bacterium possesses bacteriochlorophylls c and a, as well as lycopene, ß-carotene and γ-carotene. In addition, transmission electron microscopy shows the presence of chlorosomes, polyhydroxyalkanoate- and polyphosphate-like granules. The genome of 'Ca. Oscillochloris fontis' and the Siberian strains of Oscillochloris sp. possess the key genes for nitrogenase complex (nifH) and ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbL), as previously described for O. trichoides DG-6. The results presented here, and previously published data, show that Oscillochloris bacteria from different aquatic environments have the potential for CO2 and N2 fixation. Additionally, we describe a new primer system for the detection of RuBisCo form I.

'Candidatus Viridilinea mediisalina', a novel phototrophic Chloroflexi bacterium from a Siberian soda lake.

In this article, we present the description of a novel mesophilic phototrophic Chloroflexi bacterium, 'Candidatus Viridilinea mediisalina' Kir15-3F. We have isolated an anaerobic, highly enriched culture of this bacterium from the Kiran soda lake (Siberia) and optimized its cultivation. Metagenomic sequencing revealed that 'Ca. Viridilinea mediisalina' Kir15-3F is a bacteriochlorophyll-containing Chloroflexi bacterium in the enrichment culture. Fluorescent in situ hybridisation demonstrated a link between the phenotype described here and the 'Ca. Viridilinea mediisalina' Kir15-3F genome. Spectrophotometry and high-performance liquid chromatography analyses showed the presence of bacteriochlorophylls d, c and a, as well as lycopene, γ-carotene and ß-carotene. Transmission electron microscopy showed chlorosomes, gas vesicles, polyhydroxyalkanoate-like and polyphosphate-like granules. Our results illustrated that 'Ca. Viridilinea mediisalina' Kir15-3F is an alkaliphilic, salt-tolerant, obligately mesophilic, anaerobic, phototrophic bacterium. The genome sequences lack genes of the Calvin cycle and a sulphide:quinone reductase gene for sulphide oxidation. Owing to the lack of an axenic culture and based on the genomic and phenotypic data, we have presented the description of the bacterium in the Candidatus category.

Genome Sequence of Prosthecochloris sp. Strain ZM and Prosthecochloris sp. Strain ZM-2, Isolated from an Arctic Meromictic Lake.

Draft genome sequences of green-colored and brown-colored green sulfur bacteria (GSB), Prosthecochloris sp. ZM and Prosthecochloris sp. ZM-2, respectively, which were isolated from the Arctic meromictic lake Zeleny Mys, were sequenced. The genomes' differing gene compositions determine the differences in the bacteriochlorophyllic compositions of these bacteria.

Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications.

'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. Viridilinea mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures with a fold coverage 86.3× and 163.8×, respectively. The B7-9 (5.8 Mb) and the Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding genes, respectively. In this article, we analyzed the phylogeny of representatives of the Chloroflexineae suborder in view of the appearance of new genomic data. These data were used for the revision of earlier published group-specific conserved signature indels and for searching for novel signatures for taxons in the Chloroflexineae suborder.

Sharp water column stratification with an extremely dense microbial population in a small meromictic lake, Trekhtzvetnoe.

Located on the shore of Kandalaksha Bay (the White Sea, Russia) and previously separated from it, Trekhtzvetnoe Lake (average depth 3.5 m) is one of the shallowest meromictic lakes known. Despite its shallowness, it features completely developed water column stratification with high-density microbial chemocline community (bacterial plate) and high rates of major biogeochemical processes. A sharp halocline stabilizes the stratification. Chlorobium phaeovibrioides dominated the bacterial plate, which reached a density of 2 × 108 cell ml-1 and almost completely intercepts H2 S diffusion from the anoxic monimolimnion. The resulting anoxygenic photosynthesis rate reached 240 µmol C l-1 day-1 , exceeding the oxygenic photosynthesis rate in the mixolimnion. The rates of other processes are also high, reaching 4.5 µmol CH4 l-1 day-1 for methane oxidation and 35 µmol S l-1 day-1 for sulfate reduction. Metagenomic analysis demonstrated that the Chl. phaeovibrioides population in the bacterial plate layer had nearly clonal homogeneity, although some fraction of these cells harbour a plasmid. The Chlorobium population was associated with bacteriophages that share homology with CRISPR spacers in the host. These features make the ecosystem of the Trekhtzvetnoe Lake a valuable model for studying regulation and evolution processes in natural high-density microbial systems.

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.

Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from a geyser.

A novel, thermophilic filamentous anoxygenic phototrophic bacterium, strain isl-2T, was isolated from the Strokkur Geyser, Iceland. Strain isl-2T formed unbranched multicellular filaments with gliding motility. The cells formed no spores and stained Gram-negative. The existence of pili was described in a species of the genus Chloroflexus for the first time, to our knowledge. Optimal growth occurred at a pH range of 7.5-7.7 and at a temperature of 55 °C. Strain isl-2T grew photoheterotrophically under anaerobic conditions in the light and chemoheterotrophically under aerobic conditions in the dark. The major cellular fatty acids were C18 : 1ω9, C16 : 0, C18 : 0 and C18 : 0-OH. The major quinone was menaquinone-10. The photosynthetic pigments were bacteriochlorophylls c and a as well as ß- and γ-carotenes. The results of phylogenetic analysis of the 16S rRNA gene sequences placed strain isl-2T into the genus Chloroflexus of the phylum Chloroflexi with Chloroflexus aggregans DSM 9485T as the closest relative (97.0 % identity). The whole-genome sequence of isl-2T was determined. Average nucleotide identity values obtained for isl-2T in comparison to available genomic sequences of other strains of members of the genus Chloroflexus were 81.4 % or less and digital DNA-DNA hybridisation values 22.8 % or less. The results of additional phylogenetic analysis of the PufLM and BchG amino acid sequences supported the separate position of the isl-2T phylotype from the phylotypes of other members of the genus Chloroflexus. On the basis of physiological and phylogenetic data as well as genomic data, it was suggested that isl-2T represents a novel species within the genus Chloroflexus, with the proposed name Chloroflexus islandicus sp. nov. The type strain of the species is isl-2T (=VKM B-2978T,=DSM 29225T,=JCM 30533T).

Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser, Iceland.

We report here the draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain isl-2, which was isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C content of 59.65%. The annotated genome sequence offers the genetic basis for understanding the strain's ecological role as a phototrophic bacterium within the bacterial community.

Biogeography of thermophilic phototrophic bacteria belonging to Roseiflexus genus.

Isolated environments such as hot springs are particularly interesting for studying the microbial biogeography. These environments create an 'island effect' leading to genetic divergence. We studied the phylogeographic pattern of thermophilic anoxygenic phototrophic bacteria, belonging to the Roseiflexus genus. The main characteristic of the observed pattern was geographic and geochronologic fidelity to the hot springs within Circum-Pacific and Alpine-Himalayan-Indonesian orogenic belts. Mantel test revealed a correlation between genetic divergence and geographic distance among the phylotypes. Cluster analysis revealed a regional differentiation of the global phylogenetic pattern. The phylogeographic pattern is in correlation with geochronologic events during the break up of Pangaea that led to the modern configuration of continents. To our knowledge this is the first geochronological scenario of intercontinental prokaryotic taxon divergence. The existence of the modern phylogeographic pattern contradicts with the existence of the ancient evolutionary history of the Roseiflexus group proposed on the basis of its deep-branching phylogenetic position. These facts indicate that evolutionary rates in Roseiflexus varied over a wide range.

Filamentous anoxygenic phototrophic bacteria from cyanobacterial mats of Alla hot springs (Barguzin Valley, Russia).

Alkaline hydrotherms of the Baikal rift zone are unique systems to study the diversity of thermophilic bacteria. In this study, we present data on the phototrophic bacterial community of cyanobacterial mats from the alkaline Alla hot spring. Using a clonal analysis approach, this study evaluated the species diversity, the proportion of oxygenic and anoxygenic phototrophs and their distribution between various areas of the spring. Novel group-specific PCR primers were designed and applied to detect representatives of the Chloroflexus and Roseiflexus genera in mat samples. For the first time, the presence of Roseiflexus-like bacteria was detected in the Baikal rift zone.