Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.

The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.

The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism (SNPs) markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B. xylophilus isolates, from Continental Portugal (4), China (1), Japan (1) and USA (1), were sequenced in the next generation platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic locations: Madeira Island (2), China (1), USA (1), Japan (2) and South Korea (2). The analysis identified 136 polymorphic positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification.

Deep-sea environments are largely unexplored habitats where a surprising number of species may be found in large communities, thriving regardless of the darkness, extreme cold, and high pressure. Their unique geochemical features result in reducing environments rich in methane and sulfides, sustaining complex chemosynthetic ecosystems that represent one of the most surprising findings in oceans in the last 40 years. The deep-sea Lucky Strike hydrothermal vent field, located in the Mid Atlantic Ridge, is home to large vent mussel communities where Bathymodiolus azoricus represents the dominant faunal biomass, owing its survival to symbiotic associations with methylotrophic or methanotrophic and thiotrophic bacteria. The recent transcriptome sequencing and analysis of gill tissues from B. azoricus revealed a number of genes of bacterial origin, hereby analyzed to provide a functional insight into the gill microbial community. The transcripts supported a metabolically active microbiome and a variety of mechanisms and pathways, evidencing also the sulfur and methane metabolisms. Taxonomic affiliation of transcripts and 16S rRNA community profiling revealed a microbial community dominated by thiotrophic and methanotrophic endosymbionts of B. azoricus and the presence of a Sulfurovum-like epsilonbacterium.

Gaiella occulta strain F2‐233T (=CECT 7815 = LMG 26412), isolated from a 150 meter deep mineral water aquifer, was deemed a candidate for high‐quality draft genome sequencing because of the rare environment from which it was isolated. The draft genome sequence (QQZY00000000) of strain F2‐233T is composed of approximately 3 Mb, predicted 3,119 protein‐coding genes of which 2,545 were assigned putative functions. Genome analysis was done by comparison with the other deep‐branching Actinobacteria neighbors Rubrobacter radiotolerans, Solirubrobacter soli and Thermoleophilum album. The genes for the tricarboxylic acid cycle, gluconeogenesis and pentose phosphate pathway, were identified in G. occulta, R. radiotolerans, S. soli and T. album genomes. Genes of the Embden–Meyerhof–Parnas pathway and nitrate reduction were identified in G. occulta, R. radiotolerans and S. soli, but not in the T. album genome. Alkane degradation is precluded by genome analysis in G. occulta. Genes involved in myo‐inositol metabolism were found in both S. soli and G. occulta genomes. A Calvin–Benson–Bassham (CBB) cycle with a type I RuBisCO was identified in G. occulta genome, as well. However, experimental growth under several conditions was negative and CO2 fixation could not be proven in G. occulta.

Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. Alexandre Lobo-da-Cunha, 4,5 Conceição Egas 1,2 and Milton S. da Costa 1, * AbstractAn isolate, designated SPSPC-11 T , with an optimum growth temperature of about 50 C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso-C 15:0, iso-C 15 : 0 2-OH and iso-C 17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11 T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11 T . Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11 T (=CECT 9012 T =LMG 29233 T ) for which we propose the name Raineya orbicola gen. nov., sp. nov. We also describe the family Raineyaceae to accommodate this new genus and species.The vast majority of the species of the phylum Bacteroidetes have optimum growth temperatures that range from about 25 C and 45 C, while slightly thermophilic or thermophilic species are very rare. Some organisms, such as Pseudozobellia thermophila We recently isolated one strain of a slightly thermophilic organism with an optimum growth temperature of around 50 C and a maximum growth temperature of 60 C. Phylogenetic analysis of the 16S rRNA gene sequence showed that this organism represents a distinct lineage within the phylum Bacteroidetes. Based on phylogenetic, physiological and biochemical parameters, we are of the opinion that strain SPSPC-11 T represents a novel genus and species, for which we propose the name Raineya orbicola gen. nov., sp. nov. We also propose that this organism represents a new Abbreviations: CAPSO, 3-(Cyclohexylamino)-2-hydroxy-1-propanesulfonic acid; CECT, Colección Española de Cultivos Tipo; COG, clusters of orthologous groups; CRISPR, clustered regularly interspaced short palindromic repeats; G+C, guanine plus cytosine; HEPES, 4-(2-hydroxyethyl)-1-piperazinethanesulfonic acid; LMG, Laboratorium voor Microbiologie Universiteit Gent; MIGS, minimum information genome sequence; SEM, scanning electron microscopy; TAPS, N-[Tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid; TEM, transmission electron microscopy. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strain T are KY990922, MF125287 and MF125288, respectively. The draft genome acc...

Forest decline diseases are complex processes driven by biotic and abiotic factors. Although information about host–microbiome–environment interactions in agricultural systems is emerging rapidly, similar studies on tree health are still in their infancy. We used acute oak decline (AOD) as a model system to understand whether the rhizosphere physicochemical properties and microbiome are linked to tree health by studying these two factors in healthy and diseased trees located in three sites in different AOD stages—low, mid and severe. We found significant changes in the rhizosphere properties and microbiome composition across the different AOD sites and between the tree health conditions. Rhizosphere pH correlated with microbiome composition, with the microbial assemblages changing in more acidic soils. At the severe AOD site, the oak trees exhibited the lowest rhizosphere pH and distinct microbiome, regardless of their health condition, whereas, at the low and mid-stage AOD sites, only diseased trees showed lower pH and the microbial composition differed significantly from healthy trees. On these two sites, less extreme soil conditions and a high presence of host-beneficial microbiota were observed in the healthy oak trees. For the first time, this study gathers evidence of associations among tree health conditions, rhizosphere properties and microbiome as well as links aboveground tree decline symptoms to the belowground environment. This provides a baseline of rhizosphere community profiling of UK oak trees and paves the way for these associations to be investigated in other tree species suffering decline disease events.

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus Meiothermus with validly published names to reclassify this genus. The results indicate that the species of the genus Meiothermus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus Meiothermus to the species Meithermus ruber, Meiothermus cateniformans, Meiothermus taiwanensis, Meiothermus cerbereus, Meiothermus hypogaeus, Meiothermus luteus, Meiothermus rufus and Meiothermus granaticius, for which it is necessary to emend the genus Meiothermus. The species Meiothermus silvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species Meiothermus chliarophilus, Meiothermus timidus, Meiothermus roseus and Meiothermus terrae as species of a novel genus for which we propose the epithet Calidithermus gen. nov. The genus Meiothermus was proposed [1] to reclassify three species included in the genus Thermus that grew at lower temperatures, formed red-or yellow-pigmented colonies and possessed two variants of glycolipid 1 (GL-1). The species of the genus Meiothermus comprise 13 species with validly published names, namely Meithermus ruber [2], Meiothermus chliarophilus [1, 3], Meiothermus silvanus [1, 3], Meiothermus cerbereus [4], Meiothermus taiwanensis [5], Meiothermus timidus [6] Meiothermus rufus [7], Meiothermus cateniformans [8], Meiothermus granaticius [9], Meiothermus hypogaeus [10], Meiothermus terrae [11], Meiothermus roseus [12] and Meiothermus luteus [13]. Most of the type strains of species of the genus Meiothermus are red-pigmented but the type strains of M. chliarophilus, M. timidus, M. terrae and M. roseus form yellow-pigmented colonies. The name M. roseus refers to the colour of a diffusible pink pigment on solid R2A medium, although the colonies are yellow-pigmented.