Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source.

Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures ("py"') demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c- and b-type cytochromes was observed in "py," pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells' photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(-), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE: Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet's history.

Molecular structure and characterization of the Thermochromatium tepidum light-harvesting 1 photocomplex produced in a foreign host.

Purple phototrophic bacteria possess light-harvesting 1 and reaction center (LH1-RC) core complexes that play a key role in converting solar energy to chemical energy. High-resolution structures of LH1-RC and RC complexes have been intensively studied and have yielded critical insight into the architecture and interactions of their proteins, pigments, and cofactors. Nevertheless, a detailed picture of the structure and assembly of LH1-only complexes is lacking due to the intimate association between LH1 and the RC. To study the intrinsic properties and structure of an LH1-only complex, a genetic system was constructed to express the Thermochromatium (Tch.) tepidum LH1 complex heterologously in a modified Rhodospirillum rubrum mutant strain. The heterologously expressed Tch. tepidum LH1 complex was isolated in a pure form free of the RC and exhibited the characteristic absorption properties of Tch. tepidum. Cryo-EM structures of the LH1-only complexes revealed a closed circular ring consisting of either 14 or 15 αß-subunits, making it the smallest completely closed LH1 complex discovered thus far. Surprisingly, the Tch. tepidum LH1-only complex displayed even higher thermostability than that of the native LH1-RC complex. These results reveal previously unsuspected plasticity of the LH1 complex, provide new insights into the structure and assembly of the LH1-RC complex, and show how molecular genetics can be exploited to study membrane proteins from phototrophic organisms whose genetic manipulation is not yet possible.

Calcium and the ecology of photosynthesis in purple sulfur bacteria.

The ecological success of purple sulfur bacteria (PSB) is linked to their ability to collect near-infrared solar energy by membrane-integrated, pigment-protein photocomplexes. These include a Core complex containing both light-harvesting 1 (LH1) and reaction centre (RC) components (called the LH1-RC photocomplex) present in all PSB and a peripheral light-harvesting complex present in most but not all PSB. In research to explain the unusual absorption properties of the thermophilic purple sulfur bacterium Thermochromatium tepidum, Ca2+ was discovered bound to LH1 polypeptides in its LH1-RC; further work showed that calcium controls both the thermostability and unusual spectrum of the Core complex. Since then, Ca2+ has been found in the LH1-RC photocomplexes of several other PSB, including mesophilic species, but not in the LH1-RC of purple non-sulfur bacteria. Here we focus on four species of PSB-two thermophilic and two mesophilic-and describe how Ca2+ is integrated into and affects their photosynthetic machinery and why this previously overlooked divalent metal is a key nutrient for their ecological success.

Diversity of genetic platforms harboring the blaPER-2 gene in Enterobacterales and insights into the role of ISPa12 in its mobilization and dissemination.

The production of PER-like extended-spectrum ß-lactamases has recently been associated with reduced susceptibility to the last resort drugs aztreonam/avibactam and cefiderocol. PER-2 has been mainly confined to Argentina and neighboring countries. Until now, only three plasmids harboring blaPER-2 genes have been characterized but very little is known about the involvement of different plasmid groups in its dissemination. The diversity of genetic platforms associated with blaPER-2 genes from a collection of PER-producing Enterobacterales was analysed by describing the close environment and the plasmid backbones. Full sequences of 11 plasmids were obtained by short read (Illumina) and long read (Oxford Nanopore or PacBio) sequencing technologies. De novo assemblies, annotation and sequence analysis were performed by Unicycler, Prokka and BLAST. Plasmid analysis revealed that the blaPER-2 gene is encoded on plasmids of different incompatibility groups (A, C, FIB, HI1B, N2), indicating that this gene may have been disseminated through a variety of plasmids. Comparison with the few publicly available nucleotide sequences describing the blaPER-2 genetic environment, including those from the environmental species Pararheinheimera spp. (considered as the progenitor of blaPER genes), indicates a role of ISPa12 in blaPER-2 gene mobilization from the chromosome of Pararheinheimera spp. Also, the blaPER-2 gene was carried by a novel ISPa12-composite transposon, Tn7390. In addition, its association with ISKox2-like elements in the close genetic environment in all plasmids analysed suggests a role of these insertion sequence elements in further dissemination of blaPER-2 genes.

Allochromatium tepidum, sp. nov., a hot spring species of purple sulfur bacteria.

We describe a new species of purple sulfur bacteria (Chromatiaceae, anoxygenic phototrophic bacteria) isolated from a microbial mat in the sulfidic geothermal outflow of a hot spring in Rotorua, New Zealand. This phototroph, designated as strain NZ, grew optimally near 45 °C but did not show an absorption maximum at 915 nm for the light-harvesting-reaction center core complex (LH1-RC) characteristic of other thermophilic purple sulfur bacteria. Strain NZ had a similar carotenoid composition as Thermochromatium tepidum, but unlike Tch. tepidum, grew photoheterotrophically on acetate in the absence of sulfide and metabolized thiosulfate. The genome of strain NZ was significantly larger than that of Tch. tepidum but slightly smaller than that of Allochromatium vinosum. Strain NZ was phylogenetically more closely related to mesophilic purple sulfur bacteria of the genus Allochromatium than to Tch. tepidum. This conclusion was reached from phylogenetic analyses of strain NZ genes encoding 16S rRNA and the photosynthetic functional gene pufM, from phylogenetic analyses of entire genomes, and from a phylogenetic tree constructed from the concatenated sequence of 1090 orthologous proteins. Moreover, average nucleotide identities and digital DNA:DNA hybridizations of the strain NZ genome against those of related species of Chromatiaceae supported the phylogenetic analyses. From this collection of properties, we describe strain NZ here as the first thermophilic species of the genus Allochromatium, Allochromatium tepidum NZT, sp. nov.

Complete genome of the thermophilic purple sulfur Bacterium Thermochromatium tepidum compared to Allochromatium vinosum and other Chromatiaceae.

The complete genome sequence of the thermophilic purple sulfur bacterium Thermochromatium tepidum strain MCT (DSM 3771T) is described and contrasted with that of its mesophilic relative Allochromatium vinosum strain D (DSM 180T) and other Chromatiaceae. The Tch. tepidum genome is a single circular chromosome of 2,958,290 base pairs with no plasmids and is substantially smaller than the genome of Alc. vinosum. The Tch. tepidum genome encodes two forms of RuBisCO and contains nifHDK and several other genes encoding a molybdenum nitrogenase but lacks a gene encoding a protein that assembles the Fe-S cluster required to form a functional nitrogenase molybdenum-iron cofactor, leaving the phototroph phenotypically Nif-. Tch. tepidum contains genes necessary for oxidizing sulfide to sulfate as photosynthetic electron donor but is genetically unequipped to either oxidize thiosulfate as an electron donor or carry out assimilative sulfate reduction, both of which are physiological hallmarks of Alc. vinosum. Also unlike Alc. vinosum, Tch. tepidum is obligately phototrophic and unable to grow chemotrophically in darkness by respiration. Several genes present in the Alc. vinosum genome that are absent from the genome of Tch. tepidum likely contribute to the major physiological differences observed between these related purple sulfur bacteria that inhabit distinct ecological niches.

Microbial Community Composition during a Bloom of Purple Bacteria in Intertidal Sediments in Vigo (Northwest Spain).

In summer 2019, a large, bright pink microbial mat was visible on top of macroalgal deposits in muddy sediments of an urban beach (Playa do Adro, Vigo). In order to characterize the dominant organisms in these colored mats, results from microscopic observations, photosynthetic pigments, and molecular analysis were gathered. Light microscopy examination revealed pinkish microbial aggregates with minor contributions of larger protists and cyanobacteria. High-performance liquid chromatography (HPLC) pigment analysis documented the dominance of bacteriochlorophyll a and carotenoids whose spectra were compatible with those described in photosynthetic purple bacteria. 16S rRNA gene amplicon sequencing confirmed that the vast majority of reads belonged to Proteobacteria (73.5%), and among them, nearly 88% of those reads belonged to purple sulfur bacteria (Gammaproteobacteria). A single family, Chromatiaceae, constituted the bulk of this assemblage, including the genera Thiohalocapsa (32%), Marichromatium (12.5%), Phaeochromatium (5%), and Halocromatium (2%) as main contributors. Nonetheless, a considerable number of sequences could not be assigned to a particular genus, stressing the large biological diversity in these microbial mats and the potential presence of novel taxa of purple sulfur bacteria. IMPORTANCE Urban beaches are valuable recreational areas particularly vulnerable to human disturbance. In these areas, the intertidal sediments harbor a diverse community of microorganisms, including virus, bacteria, fungi, and protozoa. In this sense, pollution events can introduce pathogenic allochthonous microbes which may constitute a human health risk. Visual and sensory observations, such as a weird color or bad smell, are usually appreciated as a warning by beachgoers and authorities, as indeed was the case at do Adro beach in 2019. The observed proliferation seems to be common in summertime, but its dimension alerted beachgoers and media. The obtained results allowed for the identification of purple sulfur bacteria as responsible for the pink-violet top layer staining the intertidal zone. These blooms have never been associated with public health risks. Beyond solving the sanitary concern, other important findings were its diversity and large proportion of novel taxa, illustrating the complexity of these ecosystems.

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake.

The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.

Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue.

Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.

Molecular Physiology of Anaerobic Phototrophic Purple and Green Sulfur Bacteria.

There are two main types of bacterial photosynthesis: oxygenic (cyanobacteria) and anoxygenic (sulfur and non-sulfur phototrophs). Molecular mechanisms of photosynthesis in the phototrophic microorganisms can differ and depend on their location and pigments in the cells. This paper describes bacteria capable of molecular oxidizing hydrogen sulfide, specifically the families Chromatiaceae and Chlorobiaceae, also known as purple and green sulfur bacteria in the process of anoxygenic photosynthesis. Further, it analyzes certain important physiological processes, especially those which are characteristic for these bacterial families. Primarily, the molecular metabolism of sulfur, which oxidizes hydrogen sulfide to elementary molecular sulfur, as well as photosynthetic processes taking place inside of cells are presented. Particular attention is paid to the description of the molecular structure of the photosynthetic apparatus in these two families of phototrophs. Moreover, some of their molecular biotechnological perspectives are discussed.

The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships.

In a conserved culture of the purple sulfur bacterium Thiospirillum jenense DSM216T, cells of this species were easily recognized by cell morphology, large-size spirilla and visible flagellar tuft. The Tsp. jenense genome is 3.22 Mb in size and has a GC content of 48.7 mol%. It was readily identified as a member of the Chromatiaceae by the complement of proteins in its genome. A whole genome comparison clearly placed Tsp. jenense near Thiorhodovibrio and Rhabdochromatium species and somewhat more distant from Thiohalocapsa and Halochromatium species. This relationship was also found with the sequences of the photosynthetic reaction center protein PufM. The genome sequence supported important properties of this bacterium: the presence of ribulose-bisphosphate carboxylase and enzymes of the Calvin cycle of autotrophic carbon dioxide fixation but the absence of carboxysomes, an incomplete tricarboxylic acid cycle and the lack of malate dehydrogenase, the presence of a sulfur oxidation pathway including adenylylsulfate reductase (aprAB) but absence of assimilatory sulfate reduction, the presence of hydrogenase (hoxHMFYUFE), nitrogenase and a photosynthetic gene cluster (pufBALMC). The FixNOP type of cytochrome oxidase was notably lacking, which may be the reason that renders the cells highly sensitive to oxygen. Two minor phototrophic contaminants were found using metagenomic binning: one was identified as a strain of Rhodopseudomonas palustris and the second one has an average nucleotide identity of 82% to the nearest neighbor Rhodoferax antarcticus. It should be considered as a new species of this genus and Rhodoferax jenense is proposed as the name.

A comparative look at structural variation among RC-LH1 'Core' complexes present in anoxygenic phototrophic bacteria.

All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.

Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems.

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the ß-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

Rheinheimera pleomorphica sp. nov., a Novel Alkali-Tolerant Bacteria Isolated from Chilika Lake, India.

A novel Gram-negative gamma-proteobacterium, non-sporulating motile, rod or coccus-shaped bacterium designated as strain PKS7T was isolated from a sediment sample collected from Chilika Lake, Odisha, India and characterized taxonomically using a polyphasic approach. The major quinone was Q8 and major cellular fatty acids were C16:0, C17:0, C15:1w8c, C17:1w8c, C12:03-OH. The chemotaxonomic features confirmed the isolate to be a member of genus Rheinheimera. 16SrRNA gene sequence of strain PKS7T was closest in similarity to R. aquimaris SW-353T (99.36% identity), R. muenzenbergensis E49T (98.63%), R. nanhaiensis E407-8T (98.35%), R. japonica KMM 9513T (98.35%) and R. baltica DSM-14885T (98.08%). The 16S rRNA gene sequence-based phylogenetic analysis and sequence similarity between the isolated strain and type strains also revealed its affiliation to genus Rheinheimera. DNA-DNA relatedness with closest type strain R. aquimaris SW-353T was 25.0% (±3.40) and in silico DDH showed values in the range of 17.7-37.1% with the type strains of the genus Rheinheimera for which whole genome sequence are available. Strain PKS7T was also distinguished by a multi-locus sequence analysis (MLST) by alingning gyrB gene sequences of the closest type strains of Rheinheimera. The draft genome of strain PKS7T contained 32 contigs of total size 3,963,569 bp comprising of 3763 predicted coding sequences with a G + C content of 50.7 mol%. Comparision of phenotypic and genotypic data with its closest neighbours and closely related species confirm the strain PKS7T to be recognised as a novel species within the genus Rheinheimera, for which the name Rheinheimera pleomorphica sp. nov. is proposed. The type strain is PKS7T (= KCTC 42365 = JCM 30460).

A Bidimensional Segregation Mode Maintains Symbiont Chromosome Orientation toward Its Host.

All living organisms require accurate segregation of their genetic material. However, in microbes, chromosome segregation is less understood than replication and cell division, which makes its decipherment a compelling research frontier. Furthermore, it has only been studied in free-living microbes so far. Here, we investigated this fundamental process in a rod-shaped symbiont, Candidatus Thiosymbion oneisti. This gammaproteobacterium divides longitudinally as to form a columnar epithelium ensheathing its nematode host. We hypothesized that uninterrupted host attachment would affect bacterial chromosome dynamics and set out to localize specific chromosomal loci and putative DNA-segregating proteins by fluorescence in situ hybridization and immunostaining, respectively. First, DNA replication origins (ori) number per cell demonstrated symbiont monoploidy. Second, we showed that sister ori segregate diagonally prior to septation onset. Moreover, the localization pattern of the centromere-binding protein ParB recapitulates that of ori, and consistently, we showed recombinant ParB to specifically bind an ori-proximal site (parS) in vitro. Third, chromosome replication ends prior to cell fission, and as the poles start to invaginate, termination of replication (ter) sites localize medially, at the leading edges of the growing septum. They then migrate to midcell, concomitantly with septation progression and until this is completed. In conclusion, we propose that symbiont ParB might drive chromosome segregation along the short axis and that tethering of sister ter regions to the growing septum mediates their migration along the long axis. Crucially, active bidimensional segregation of the chromosome allows transgenerational maintenance of its configuration, and therefore, it may represent an adaptation to symbiosis. VIDEO ABSTRACT.

Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.

Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2-h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant-specific (e.g. phosphate acquisition and alkane-1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.

Rheinheimera riviphila sp. nov., isolated from a freshwater stream.

Strain KYPC3T, isolated from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPC3T belonged to the genus Rheinheimera. Strain KYPC3T exhibited 16S rRNA gene sequence similarity values of 94.8-97.9% to the type strains of species of the genus Rheinheimera. Strain KYPC3T was most closely related to Rheinheimera chironomi K19414T with 16S rRNA gene sequence similarity of 97.9%. Cells of strain KYPC3T were Gram-stain negative, aerobic, motile by means of a single-polar flagellum, non-spore forming, coccoid or short rods surrounded by a thick capsule and forming off-white coloured colonies. Growth occurred at 15-30 °C (optimum, 20-25 °C), at pH 6-8 (optimum, pH 7) and with 0-0.5% NaCl (optimum, 0%). The major fatty acids (> 10%) of strain KYPC3T were C12:0 3-OH, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized lipid. The major isoprenoid quinone was Q-8. The draft genome was approximately 4.75 Mb in size with a G + C content of 49.8 mol%. The DNA-DNA relatedness of strain KYPC3T with respect to recognized species of the genus Rheinheimera was significantly less than 70%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPC3T should be classified as a novel species of the genus Rheinheimera, for which the name Rheinheimera riviphila sp. nov. is presented. The type strain is KYPC3T (= BCRC 81008T = LMG 29729T = KCTC 52440T).

Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters.

Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 µM O2 ·h-1 . Single-cell analyses of lake water incubated with 13 CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved.

PER extended-spectrum ß-lactamases originate from Pararheinheimera spp.

To investigate the origin of PER extended-spectrum ß-lactamases, publicly available sequence databases were searched for blaPER-like genes. Three genomes from Pararheinheimera, a genus associated with water and soil environments, were found to carry blaPER-like genes but lacked the ISCR1/ISPa12/ISPa13 insertion sequences commonly associated with blaPER in clinical isolates. Sequence analysis revealed 78-96% nucleotide identity and conserved synteny between the clinical mobile genetic elements (MGEs) encoding blaPER-1 and the blaPER locus in the Pararheinheimera genomes. Notably, blaPER genes were only identified in 3 of 21 Pararheinheimera and Rheinheimera genomes, whereas the genetic environment of blaPER genes as found in clinical MGEs was conserved in all Pararheinheimera and Rheinheimera genomes. These findings indicate that blaPER genes were likely acquired by a branch of the Pararheinheimera genus long before the antibiotic era. Later, blaPER genes were mobilised, likely through the involvement of insertion sequences, from one or several Pararheinheimera species, allowing their dissemination into human pathogens.

Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics.

The meromictic Lake Cadagno is characterized by a compact chemocline with high concentrations of anoxygenic phototrophic purple and green sulfur bacteria. However, a complete picture of the bacterial diversity, and in particular of effects of seasonality and compartmentalization is missing. To characterize bacterial communities and elucidate relationships between them and their surrounding environment high-throughput 16S rRNA gene pyrosequencing was conducted. Proteobacteria, Chlorobi, Verrucomicrobia, and Actinobacteria were the dominant groups in Lake Cadagno water column. Moreover, bacterial interaction within the chemocline and between oxic and anoxic lake compartments were investigated through fluorescence in situ hybridization (FISH) and flow cytometry (FCM). The different populations of purple sulfur bacteria (PSB) and green sulfur bacteria (GSB) in the chemocline indicate seasonal dynamics of phototrophic sulfur bacteria composition. Interestingly, an exceptional bloom of a cyanobacteria population in the oxic-anoxic transition zone affected the common spatial distribution of phototrophic sulfur bacteria with consequence on chemocline location and water column stability. Our study suggests that both bacterial interactions between different lake compartments and within the chemocline can be a dynamic process influencing the stratification structure of Lake Cadagno water column.