Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat

Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds

Six metagenome-assembled genomes (JB008Ts, JB007, JB015, JB003, JB004, and JB002) belonging to the order Spirochaetales were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008Ts and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2-93.4 %, respectively with uncultivated Spirochaetaceae family members, and < 90 % identity with Marispirochaeta aestuari JC444T. While, the bin JB015 showed 99.1 % identity with Pleomorphochaeta naphthae SEBR 4209T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008Ts confirmed that these members belong to the family Spirochaetaceae and bins JB015, JB002, JB003, and JB004 belong to the genus Pleomorphochaeta within the family Sphaerochaetaceae. The AAI values of the binned genomes JB007 and JB008Ts compared to other members of the Spirochaetaceae family were between 53.9- 56.8 % and 53.8-57.1 %, respectively. Furthermore, the comparison of ANI, dDDH, and POCP metrics of the binned genomes JB007 and JB008Ts, both among themselves and with the members of Spirochaetaceae, was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008Ts is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name Thalassospirochaeta sargassi gen. nov. sp. nov., in the family Spirochaetaceae while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other Pleomorphochaeta members.

Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales

A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone (Haliotis rufescens) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae. We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone (Haliotis sorenseni). In addition, we highlight the need for better classification of taxa within the class Spirochaetia.

Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia

Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.

Thermospira aquatica gen. nov., sp. nov., a novel thermophilic spirochete isolated from a Tunisian hot spring, and description of the novel family Thermospiraceae

A novel thermophilic, anaerobic bacterium, strain F1F22^T, was isolated from hot spring water collected in northern Tunisia. The cells were non-motile, Gram-negative and helical with hooked ends, 0.5×10-32 µm in size. Growth of the strain was observed at 45-70 °C (optimum, 55 °C), in 0.0-1.0 % (w/v) NaCl (optimum without NaCl) and at pH 6.5-8.5 (optimum, pH 7.5). Yeast extract was required for growth, and the strain grew on glucose, sucrose and maltose. The major fatty acids were C_16:0 (40.2 %), iso-C_16: 0 (30.2 %) and C_16 :0 DMA (14.5 %). The genome consisted of a circular chromosome (2.5 Mb) containing 2672 predicted protein-encoding genes with a G+C content of 43.15 mol %. Based on a comparative 16S rRNA gene sequence analysis, strain F1F22^T formed a deeply branching lineage within the phylum Spirochaetota, class Spirochaetia, order Brevinematales, and had only low sequence similarity to other species of the phylum (lower than 83 %). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain F1F22^T with Treponema caldarium DSM 7334^T, Brevinema andersonii ATCC 43811^T and Spirochaeta thermophila DSM 6578^T showed values between 63.26 and 63.52 %, and between 20 and 25 %. Hence, we propose strain F1F22^T as a representative of a novel family (Thermospiraceae fam. nov.), genus and species of Brevinematales: Thermospira aquatica gen. nov., sp. nov. (type strain F1F22^T=JCM 31314^T=DSM 101182^T).

Aminithiophilus ramosus gen. nov., sp. nov., a sulphur-reducing bacterium isolated from a pyrite-forming enrichment culture, and taxonomic revision of the family Synergistaceae

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2^T could be affiliated with the phylum Synergistota. Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2^T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C_15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2^T (=DSM 107166^T=NBRC 114655^T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith's Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

Response of anaerobic granular sludge to long-term loading of roxarsone: From macro- to micro-scale perspective

Extensive use of organoarsenic feed additives such as roxarsone has caused organoarsenicals to occur in livestock wastewater and further within anaerobic wastewater treatment systems. Currently, information on the long-term impacts of roxarsone on anaerobic granular sludge (AGS) activity and the underlying mechanisms is very limited. In this study, the response of AGS to long-term loading of roxarsone was investigated using a laboratory up-flow anaerobic sludge blanket reactor spiked with 5.0 mg L^-1 of roxarsone. Under the effect of roxarsone, methane production decreased by ∼40% due to the complete inhibition on acetoclastic methanogenic activity on day 260, before being restored eventually. Over 30% of the influent arsenic was accumulated in the AGS and the capability of AGS to prevent intracellular As(III) accumulation increased with time. The AGS size was reduced by ∼30% to 1.20‒1.26 mm. Based on morphology and confocal laser scanning microscopy analysis, roxarsone exposure stimulated the excretion of extracellular polymeric substances and the surface spalling of AGS. High-throughput sequencing analysis further indicated roxarsone initially altered the acidogenic pathway and severely inhibited the acetoclastic methanogen Methanothrix. Acetogenic bacteria and Methanothrix were finally enriched and became the main contributor for a full restoration of the initial methane production. These findings provide a deeper understanding on the effect of organoarsenicals on AGS, which is highly beneficial for the effective anaerobic treatment of organoarsenic-bearing wastewater.

Interplay of microbial communities with mineral environments in coralline algae

Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO₂ world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.

Spirochetes isolated from arthropods constitute a novel genus Entomospira genus novum within the order Spirochaetales

Spirochetal bacteria were successfully isolated from mosquitoes (Culex pipiens, Aedes cinereus) in the Czech Republic between 1999 and 2002. Preliminary 16S rRNA phylogenetic sequence analysis showed that these strains differed significantly from other spirochetal genera within the family Spirochaetaceae and suggested a novel bacterial genus in this family. To obtain more comprehensive genomic information of these isolates, we used Illumina MiSeq and Oxford Nanopore technologies to sequence four genomes of these spirochetes (BR151, BR149, BR193, BR208). The overall size of the genomes varied between 1.68 and 1.78 Mb; the GC content ranged from 38.5 to 45.8%. Draft genomes were compared to 36 publicly available genomes encompassing eight genera from the class Spirochaetes. A phylogeny generated from orthologous genes across all taxa and the percentage of conserved proteins (POCP) confirmed the genus status of these novel spirochetes. The genus Entomospira gen. nov. is proposed with BR151 selected as type species of the genus. For this isolate and the closest related isolate, BR149, we propose the species name Entomospira culicis sp. nov. The two other isolates BR208 and BR193 are named Entomospira nematocera sp. nov. (BR208) and Entomospira entomophilus sp. nov. (BR193). Finally, we discuss their interesting phylogenetic positioning.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field

A Gram-stain-negative oval-rod-shaped, spore-forming anaerobic bacterium, designated as strain MCWD5^T, was isolated from sediment of a salt pond in the Republic of Korea (35° 7' 18″ N 126° 19' 4″ E). The 16S rRNA gene sequence analysis revealed that strain MCWD5^T had low similarity values to members in the family Lachnospiraceae, such as Robinsoniella peoriensis PPC31^T (94.8 %), Ruminococcusgauvreauii CCRI-16110^T (94.2 %) and Lachnotalea glycerini DLD10^T (94.0 %), and its phylogenetic position is unstable. The strain could grow at 20-42 °C (optimum, 38-42 °C), pH 5.5-10.0 (pH 7.0) and with 0-6 % (2.0 %) NaCl. Strain MCWD5^T could not use nitrate, nitrite, sulfate or sulfite as electron acceptors. The strain could utilize various carbohydrates, such as arabinose, cellobiose, glucose, etc., and polymers such as pectin and starch. The major fatty acids of strain MCWD5^T were C14 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7c DMA and summed feature 8 (C17 : 1ω8c and/or C17 : 2), which was clearly different from those of related genera. The major polar lipids were diphosphatidyglycerol, phosphatidyglycerol and an unknown phospholipid. Based on the results of phylogenetic, physiologic and chemotaxonomic studies, Anaerosacchariphilus polymeriproducens gen. nov., sp. nov. with the type strain MCWD5^T (=KCTC 15595^T=DSM 105757^T) is proposed in the family Lachnospiraceae.

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah

Microbialites, organosedimentary carbonate structures, cover approximately 20% of the basin floor in the south arm of Great Salt Lake, which ranges from ~12 to 15% salinity. Photosynthetic microbial mats associated with these benthic mounds contribute biomass that supports secondary production in the ecosystem, including that of the brine shrimp, Artemia franciscana. However, the effects of predicted increases in the salinity of the lake on the productivity and composition of these mats and on A. franciscana fecundity is not well documented. In the present study, we applied molecular and microcosm-based approaches to investigate the effects of changing salinity on (1) the primary productivity, abundance, and composition of microbialite-associated mats of GSL, and (2) the fecundity and survivability of the secondary consumer, A. franciscana. When compared to microcosms incubated closest to the in situ measured salinity of 15.6%, the abundance of 16S rRNA gene templates increased in microcosms with lower salinities and decreased in those with higher salinities following a 7-week incubation period. The abundance of 16S rRNA gene sequences affiliated with dominant primary producers, including the cyanobacterium Euhalothece and the diatom Navicula, increased in microcosms incubated at decreased salinity, but decreased in microcosms incubated at increased salinity. Increased salinity also decreased the rate of primary production in microcosm assays containing mats incubated for 7 weeks and decreased the number of A. franciscana cysts that hatched and survived. These results indicate that an increase in the salinity of GSL is likely to have a negative impact on the productivity of microbialite communities and the fecundity and survivability of A. franciscana. These observations suggest that a sustained increase in the salinity of GSL and the effects this has on primary and secondary production could have an upward and negative cascading effect on higher-trophic-level ecological compartments that depend on A. franciscana as a food source, including a number of species of migratory birds.

Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts

The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU0.03 ), while a second OTU0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria

The anaerobic, mesophilic and moderately halophilic strain L21-Spi-D4^T was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein-rich extracts of Arthrospira (formerly Spirulina) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR-022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21-Spi-D4^T revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes. A distinct and reproducible co-occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR-022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21-Spi-D4^T , and Salinivirgaceae fam. nov., comprising sequences of the MgMjR-022 clade.

Description of 'Candidatus Marispirochaeta associata' and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov

Strain JC231 was isolated from a coastal saline habitat of Gujarat and was identified based on 16S rRNA gene sequence analysis as a member belonging to the genus Spirochaeta and showed highest sequence similarity (<91 %) with Spirochaeta bajacaliforniensis DSM 16054T and other members of the family Spirochaetaceae. Intensive attempts to culture strain JC231 in pure culture have failed and were associated with only one species of a Desulfovibrio. However, presence of fosmidomycin inhibited the growth of Desulfovibrio sp. and strain JC231 was characterized in its presence. Strain JC231 was an obligate anaerobe, helical shaped and Gram-stain-negative with catalase and oxidase negative. Draft genome sequence analysis of strain JC231 indicated the full complement of genes for both 2-C-methyl-d-erythritol 4-phosphate and 3-hydroxy-3-methylglutaryl-CoA pathways of terpenogenesis. C14 : 0, iso-C15 : 0, C16 : 0, iso-C15 : 1H/C13 : 0 3OH and iso-C14 : 0 are the major (>5 %) fatty acids. Strain JC231 contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and six unidentified lipids (L1-L6). G+C content of strain JC231 was 55.7 mol%. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC231 as a representative of a new genus and species in the family Spirochaetaceae, for which the name 'CandidatusMarispirochaeta associata' is proposed. Strain JC231 is deposited as a defined co-culture with Desulfovibrio sp. JC271 to DSMZ (DSM 29857) and KCTC (KCTC 15472). Based on phenotypic, genotypic and phylogenetic analyses, we also propose the reclassification of Spirochaeta bajacaliforniensis as Sediminispirochaeta bajacaliforniensis gen. nov., comb. nov., Spirochaeta smaragdinae as Sediminispirochaeta smaragdinae comb. nov. and Spirochaeta sinaica as Sediminispirochaeta sinaica comb. nov.

Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum

The recently isolated strain L21-Fru-AB^T represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-AB^T represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-AB^T and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.

Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment

A Gram-staining-negative, thin rod-shaped, anaerobic bacterium designated MCWD3(T) was isolated from sediment of the deep sea in Ulleung Basin, East Sea, Korea. The ranges of temperature, pH and NaCl for growth of this strain were 15-40°C (optimum 29°C), 5.0-10.0 (optimum pH 6.5), and 1-5%, respectively. The major fatty acids were iso-C(15:0) (30%) and iso-C(15:0) dimethyl acetal (17%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipids, phospholipids, and aminolipids. The fermentation product from yeast extract was acetate. Phylogenetic analysis based on 16S rRNA genes indicated that the isolate was related to Sporosalibacterium faouarense (92.8% sequence identity), Clostridiisalibacter paucivorans (92.6%), and Brassicibacter mesophilus (92.4%). However, the isolate was differentiated from these genera by both physiological and chemotaxonomical properties. On the basis of a polyphasic taxonomic analysis, we propose that MCWD3(T) represents a novel taxon with the name Abyssisolibacter fermentans gen. nov. sp. nov.

High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture

Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535^T, was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535^T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. The strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535^T did not form spore.

Planctomycetes do possess a peptidoglycan cell wall

Most bacteria contain a peptidoglycan (PG) cell wall, which is critical for maintenance of shape and important for cell division. In contrast, Planctomycetes have been proposed to produce a proteinaceous cell wall devoid of PG. The apparent absence of PG has been used as an argument for the putative planctomycetal ancestry of all bacterial lineages. Here we show, employing multiple bioinformatic methods, that planctomycetal genomes encode proteins required for PG synthesis. Furthermore, we biochemically demonstrate the presence of the sugar and the peptide components of PG in Planctomycetes. In addition, light and electron microscopic experiments reveal planctomycetal PG sacculi that are susceptible to lysozyme treatment. Finally, cryo-electron tomography demonstrates that Planctomycetes possess a typical PG cell wall and that their cellular architecture is thus more similar to that of other Gram-negative bacteria. Our findings shed new light on the cellular architecture and cell division of the maverick Planctomycetes.

Planctomycetes appear to differ from all other bacteria in their cellular organization and their apparent lack of a peptidoglycan (PG) cell wall. Here Jeske et al. show that Planctomycetes do possess a typical PG cell wall and that their cellular architecture resembles that of Gram-negative bacteria.

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. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. 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.