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DESCRIPTION OF SPHINGOBACTERIUM PRATI SP. NOV. Sphingobacterium prati (pra'ti L. gen. n. prati of a meadow). Cells are Gram-stain-negative, non-motile, non-sporeforming, strictly aerobic rods, 0.8–1.7 µm long and 0.7–0.9 µm wide. After 2 days incubation on LB agar, colonies are 1.0– 2.5 mm in diameter, slightly yellowish, convex, circular and smooth. Growth occurs at 15–37 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0–4% NaCl (optimum, 0 %). Growth occurs on nutrient agar and LB agar, but not on MacConkey agar. Positive for catalase and oxidase. Acid is produced from sodium lactate, acetoacetic acid, cellobiose, dextrin, D-fructose,D-galactose, D-galacturonic acid,D-gluconic acid, maltose, D-mannose, melibiose, D-salicin, turanose, gelatin, gentiobiose, glycyl-L-proline, guanidine HCl, L-fucose, L-rhamnose, N -acetyl-D-galactosamine, N -acetyl-β-D-mannosamine, nalidixic acid, pectin, sodium butyrate, sucrose, D-glucose and lactose. Acid is not produced from 3-methyl-glucose, bromo-succinic acid, citric acid, D-arabitol,D-aspartic acid, D-fructose-6- PO 4, D-fucose,D-glucose-6- PO 4, D-gluronicacid, D-lactic acid, methyl ester, D-malic acid,D-mannitol, raffinose, D-saccharic acid,D-serine,D-sorbitol, trehalose, formic acid, fusidic acid, glucuronamide, glycerol, inosine, L-alanine, L-arginine, L-aspartic acid, L-galactonic acid, lactone, L-glutamic acid,L-histidine,L-lactic acid,L-malic acid, L-pyroglutamic acid,L-serine, methyl pyruvate, mucic acid, myo-anositol, N -acetyl neuraminic acid, N -acetyl-Dglucosamine, p -hydroxy-phenylacetic acid, propionic acid, quinic acid, stachyose, Tween 40, α-hydroxy-butyric acid, α-keto-butyric acid, α-keto-glutaric acid, β-hydroxy-D acid, L-butyric acid, methyl β-D-glucoside and γ-amino-butyric acid. Resistant to aztreonam, rifamycin and sensitive to lincomycin, minocycline, troleandomycin and vancomycin. Strain arapr2 T harbours β-galactosidase but not lysine decarboxylase, ornithine decarboxylase, urease and tryptophane desaminase (API 10 S). Strain arapr2 T can oxidize glucose and produce NO2 but cannot oxidize arabinose or produce H 2 S (API 10 S). The predominant fatty acids are iso-C 15:0, C 16:0 and C 17:0 iso 3-OH. Menaquinone-7 is the major respiratory quinone. The major polar lipids are glycolipid, aminolipid, phospholipid, phosphatidylethanolamine, phosphoaminolipid and phosphoaminoglycolipid. The type strain, arapr2 T (CIP 111872 T =LMG 31848 T), was isolated from meadow soil collected near Reims, France. The DNA G+C content of the type strain is 40.4 mol%., Published as part of Besaury, Ludovic, Floret, Juliette & Rémond, Caroline, 2021, Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction, pp. 1-8 in International Journal of Systematic and Evolutionary Microbiology (004963) (004963) 71 (8) on page 7, DOI: 10.1099/ijsem.0.004963, http://zenodo.org/record/6224196

A bacterial strain, arapr2T, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Sphingobacteriaceae and more specifically to the genus Sphingobacterium . The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative Sphingobacterium canadense CR11T and 98.25 % to Sphingobacterium pakistanensis NCCP-246T. Genome relatedness indexes revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between arapr2T and its closest relative ( S. canadense CR11T) were 92.97 % and 52.00 %, respectively; for S. pakistanensis NCCP-246T, the ANI and dDDH values were 82.46 and 27.6%, respectively. The genomic DNA of strain arapr2T was 6.02 Mbp long, had a DNA G+C content of 40.4 mol% and had 5504 protein-coding genes. The results obtained in this study suggests that strain arapr2T (CIP 111872T=LMG 31848T) represents a new species for which the name Sphingobacterium prati sp. nov. is proposed. Due to the fact that this strain has been isolated using wheat straw as carbon source, this novel bacterial strain represents a promising biotechnological tool for the fractionation of lignocellulosic biomass in the context of biorefinery development.

A polyphasic taxonomy approach was used to characterize strain YBJ-36T, isolated from a freshwater lake in Taiwan. Phylogenetic analyses, based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters), indicated that strain YBJ-36T formed a phylogenetic lineage in the genus Mucilaginibacter. 16S rRNA gene sequence similarity indicated that strain YBJ-36T is closely related to species within the genus Mucilaginibacter (93.8-97.8% sequence similarity) and is most similar to Mucilaginibacter fluminis TTM-2T (97.8%), followed by Mucilaginibacter roseus TTM-1T (97.2%). Microbiological analyses demonstrated that strain YBJ-36T is Gram-negative, aerobic, non-motile, rod-shaped, surrounded by a thick capsule, and forms pink-colored colonies. Strain YBJ-36T grew between 20-40°C (optimal range, 35-37°C), pH 5.5-7.0 (optimal pH of 6) and 0-2% NaCl (optimal concentration, 0.5%). The predominant fatty acids of strain YBJ-36T are iso-C15:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c), the major polar lipid is phosphatidylethanolamine, the major polyamine is homospermidine, and the major isoprenoid quinone is MK-7. The draft genome is approximately 4.63 Mb in size with a G+C content of 42.8 mol%. Strain YBJ-36T exhibited less than 35% DNA-DNA relatedness with Mucilaginibacter fluminis TTM-2T and Mucilaginibacter roseus TTM-1T. Based on phenotypic and genotypic properties and phylogenetic inference, strain YBJ-36T should be classified in a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter limnophilus sp. nov. is proposed. The type strain is YBJ-36T (= BCRC 81056T = KCTC 52811T = LMG 30058T).

The microbial community in the rhizosphere soil highly affects plant health and vice versa. However, the differences in soil microbial communities associated with different pathogenic statuses in the same field and their causes have not been comprehensively investigated. Here, we deciphered the dissimilarities in the rhizosphere soils of lisianthus (Eustoma grandiflorum) with different pathogenic statuses in a field under uniform management strategies at multiple scales. The rhizosphere soils of diseased plants harbored higher bacterial abundances and diversities compared to that of healthy plants. The relative abundances of three keystone operational taxonomic units (OTUs) and cumulative relative abundance of members in the central module (the largest module) of microbial network significantly decreased by 51.1%, 49.4%, 47.6%, and 42.0% in the rhizosphere soil of infected plants and by 64.3%, 58.8%, 63.4%, and 61.8% in that of dying plants, while the relative abundances of Flavobacteriales, Sphingobacteriales, and Xanthomonadales significantly increased to 4.89-, 1.88-, and 1.44-fold in the rhizosphere soil of infected plants and to 2.89-, 1.55-, and 1.66-fold in that of dying plants, respectively compared with that of healthy plants. Some human disease-related pathways and fluorescein diacetate hydrolysis were more prevalent in the rhizosphere soils of diseased plants. Stochastic processes contributed more than 50.6% and 86.4% to the assembly of different bacterial and fungal communities in these soils, and plants further shaped the bacterial communities, compared to fungal communities, probably by actively recruiting some potential suppressive agents in their rhizosphere when attacked by the pathogen. Overall, here, we firstly reported that the keystone taxa and members in the central module were enriched in the rhizosphere soil of healthy plants, which might be a potential indicator for the soil supporting plant health.

In 2017, the 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. Leaves appeared smaller, turned yellow-brown, and were shed prematurely. Twigs and smaller branches died. Bark was sunken and discolored, often loosened and split. Trunks decayed from the base. Phloem and xylem showed brown necrosis. Ten per cent of trees died in 1–2 months. None of these symptoms was typical for known poplar diseases. Bacteria in soil and the necrotic base of poplar trunk were analysed with Illumina sequencing. Soil and wood were colonized by at least 615 and 249 taxa. The majority of bacteria were common to soil and wood. The most common taxa in soil were: Acidobacteria (14.757%), Actinobacteria (14.583%), Proteobacteria (36.872) with Betaproteobacteria (6.516%), Burkholderiales (6.102%), Comamonadaceae (2.786%), and Verrucomicrobia (5.307%).The most common taxa in wood were: Bacteroidetes (22.722%) including Chryseobacterium (5.074%), Flavobacteriales (10.873%), Sphingobacteriales (9.396%) with Pedobacter cryoconitis (7.306%), Proteobacteria (73.785%) with Enterobacteriales (33.247%) including Serratia (15.303%) and Sodalis (6.524%), Pseudomonadales (9.829%) including Pseudomonas (9.017%), Rhizobiales (6.826%), Sphingomonadales (5.646%), and Xanthomonadales (11.194%). Possible pathogens were Pseudomonas, Rhizobium and Xanthomonas. The initially endophytic character of bacteria is emphasized. Soil and possibly planting material might be the sources of pathogen inoculum.

A Gram-reaction-negative halotolerant bacterial strain, designated Ka21T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, highest similarity was found with Sphingobacterium alkalisoli Y3L14T (96.72%). Cells were observed to be aerobic, non-motile rods. The isolate was found to be able to grow between 0 and 10% of NaCl concentration. The assembled genome of strain Ka21T has a total length of 5.2 Mb with a G + C content of 41.0 mol%. According to the genome analysis, Ka21T encodes several glycoside hydrolases that may play a role in the degradation of accumulated plant biomass in the soil. Based on phenotypic characteristics and phylogenetic analysis, it is concluded that strain Ka21T represents a novel species in the Sphingobacterium genus for which the name Sphingobacterium pedocola sp. nov. is proposed. The type strain of the species is strain Ka21T (= LMG 31575T = NCAIM B.02636T).

Facultative endosymbionts can affect the growth, physiology, and behavior of their arthropod hosts. There are several endosymbionts in the invasive whitefly Bemisia tabaci Mediterranean (MED, Q biotype) that influence host fitness by altering stylet probing behavior. We investigated the probing behavior of B. tabaci MED infected with the facultative endosymbiont Candidatus Cardinium hertigii (Cardinium (Sphingobacteriales: Flexibacteraceae)). We generated genetically similar Cardinium-infected (C*+) and uninfected (C-) clonal sublines and analyzed the probing behavior of newly emerged adult on cotton (Malvales: Malvaceae), Gossypium hirsutum L., using electropenetrography (EPG). The C- subline demonstrated a longer duration of E2 (2.81-fold) and more events of E2 (2.22-fold) than the C*+ subline, indicating a greater level of sustained ingestion of plant phloem. These findings provide insight into the fitness costs (fitness of a particular genotype is lower than the average fitness of the population) of the Cardinium-infected B. tabaci.

The significance of lytic viral lysis in shaping bacterial communities in temperate freshwater systems is less documented. Here we used Illumina sequencing of 16S rRNA genes to examine bacterial community structure and diversity in relation to variable viral lysis in the euphotic zone of 25 temperate freshwater lakes (French Massif Central). We captured a rich bacterial community that was dominated by a few bacterial classes and operational taxonomic units (OTUs) frequently detected in other freshwater ecosystems. In the investigated lakes with contrasting physico-chemical characteristics, the dominant bacterioplankton community was represented by major taxonomical orders, namely Actinomycetales, Burkholderiales, Sphingobacteriales, Acidimicrobiales, Flavobacteriales and Cytophagales covering about 70% of all sequences. Viral lysis was significantly correlated with the bacterial diversity indices (Chao, Shannon, OTUs) which explained about 33% and 45% of the variation in species diversity and observed richness respectively. Anosim and UniFrac analyses indicated a clear distinction of bacterial community structure among the lakes that exhibited high and low lytic viral infection (FIC) rates. Based on our findings, high FIC (10%) supported higher species richness, whereas low FIC (10%) resulted in less diverse community. Our study strongly suggests that lytic activity prevailed over the type of lake ecosystems in shaping bacterioplankton diversity.

Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.

The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N-2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities., Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Start-up of biofilters plays crucial roles in the successful operation of recirculating aquaculture system, and the nature is bacterial community succession. We explored the pattern of bacterial temporal succession during the start-up process of biofilters in a commercial cold-freshwater recirculating aquaculture system (RAS). The whole succession process was divided into three distinct phases: incubation, growth and stability. Phylogenetic diversity and evenness of the bacterial community increased during the start-up process, whereas richness reached its peak at the growth phase. Seven biomarkers were identified, namely Cytophagales, Gemmatimonadales, Sphingomonadales, Sphingobacteriales, Rhizobiales, Clostridiales and Nitrospirales. The relative abundances of these functional bacteria increased, while those with a competitive growth advantage declined. The network interactions were dramatically altered from fairly simple to most complex, and then decreased in complexity during start-up. Positive relationships decreased, while competition increased. The shift in predicted function exhibited a trend from simple to diverse, and converged to idiosyncratic configuration.

International audience; Solid state anaerobic digestion (SSAD) with leachate recirculation is an appropriate method for the valorization of agriculture residues. Rape straw is a massively produced residue with considerable biochemical methane potential, but its degradation in SSAD remains poorly understood. A thorough study was conducted to understand the performance of rape straw as feedstock for laboratory solid state anaerobic digesters. We investigated the methane production kinetics of rape straw in relation to cellulose accessibility to cellulase and the microbial community. Improving cellulose accessibility through milling had a positive influence on both the methane production rate and methane yield. The SSAD of rape straw reached 60% of its BMP in a 40-day pilot-scale test. Distinct bacterial communities were observed in digested rape straw and leachate, with Bacteroidales and Sphingobacteriales as the most abundant orders, respectively. Archaeal populations showed no phase preference and increased chronologically. © 2016 Elsevier Ltd

Bacteria associated with mites influence their fitness, nutrition and reproduction. Previously, we found Solitalea-like (Sphingobacteriales) and Candidatus Cardinium (Cytophagales) bacteria in the stored product mite Acarus siro L. by cloning and using pyrosequencing. In this study, taxon-specific primers targeting 16S rRNA gene were used to detect and quantify the bacteria in mites and eggs of three A. siro populations. The specific probes for fluorescent in situ hybridization (FISH) were used to localize Solitalea-like and Cardinium bacteria in mite bodies. The population growth as an indirect estimator of fitness was used to describe the mite-bacteria interactions on (1) control diet; (2) rifampicin supplemented diet; (3) tetracycline supplemented diet; (4) rifampicin pretreated mites; (5) tetracycline pretreated mites. Solitalea-like 16S rRNA gene sequences from A. siro formed a separate cluster together with sequences from Tyrophagus putrescentiae. qPCR analysis indicated that number of Solitalea-like bacteria 16S rRNA gene copies was ca. 100× higher than that of Cardinium and the numbers differed between populations. FISH analysis localized Solitalea-like bacteria in the parenchymal tissues, mesodeum and food bolus of larvae, nymphs and adults. Solitalea-like, but not Cardinium bacteria were detected by taxon-specific primers in mites and eggs of all three investigated populations. None of the antibiotic treatments eliminated Solitalea-like bacteria in the A. siro populations tested. Rifampicin pretreatment significantly decreased the population growth. The numbers of Solitalea-like bacteria did not correlate with the population growth as a fitness indicator. This study demonstrated that A. siro can host Solitalea-like bacteria either alone or together with Cardinium. We suggest that Solitalea-like bacteria are shared by vertical transfer in A. siro populations.

Despite airborne microorganisms representing a relevant fraction of atmospheric suspended particles, only a small amount of information is currently available on their abundance and diversity and very few studies have investigated the environmental factors influencing the structure of airborne bacterial communities. In this work, we used quantitative PCR and Illumina technology to provide a thorough description of airborne bacterial communities in the urban area of Milan (Italy). Forty samples were collected in 10-day sampling sessions, with one session per season. The mean bacterial abundance was about 10⁴ ribosomal operons per m³ of air and was lower in winter than in the other seasons. Communities were dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and few proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales and Pseudomonadales). Chloroplasts were abundant in all samples. A higher abundance of Actinobacteridae, which are typical soil-inhabiting bacteria, and a lower abundance of chloroplasts in samples collected on cold days were observed. The variation in community composition observed within seasons was comparable to that observed between seasons, thus suggesting that airborne bacterial communities show large temporal variability, even between consecutive days. The structure of airborne bacterial communities therefore suggests that soil and plants are the sources which contribute most to the airborne communities of Milan atmosphere, but the structure of the bacterial community seems to depend mainly on the source of bacteria that predominates in a given period of time.

Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Aims: Bacterial communities in the apple phyllosphere were examined quantitatively and qualitatively by applying culture-dependent and culture-independent methods. Methods and Results: Populations estimated by viewing cells stained with 4¢,6diamidino-2-phenylindole generally were at least 100‐1000 times greater than populations estimated by culturing on tryptic soy agar (TSA). Of the 44 operational taxonomic units (OTUs; cut-off threshold of 97%) detected in total, five bacterial orders containing 23 OTUs were identified by culturing on TSA, whereas nine orders containing 33 OTUs were identified by 16S rRNA gene cloning of DNA extracted from apple leaf surfaces. Twelve of the 44 OTUs were shared between cultured isolates and 16S rRNA gene clones and included the orders Burkholderiales, Pseudomonadales, Rhizobiales and Sphingomonadales. Three OTUs within the genus Sphingomonas accounted for 40% of isolates and 68% of clones. The Actinomycetales were found only among isolates, whereas the Bacteroidales, Enterobacteriales, Myxococales and Sphingobacteriales were represented in the 16S rRNA gene clone libraries but were absent among isolates. Conclusions: Culture-independent methods revealed greater numbers and greater richness of bacteria on apple leaves than found by culturing. Significance and Impact of the Study: This is the first study to directly compare culture-dependent and independent approaches for assessing bacterial communities in the phyllosphere. The biases introduced by different methods will have a significant impact on studies related to phyllosphere ecology, biological control of plant diseases, reservoirs of antibiotic resistance genes and food safety.

Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Ubiquitous microbial communities in river sediments actively govern organic matter decomposition, nutrient recycling, and remediation of toxic compounds. In this study, prokaryotic diversity in two major rivers in central Thailand, the Chao Phraya (CP) and the Tha Chin (TC) distributary was investigated. Significant differences in sediment physicochemical properties, particularly silt content, were noted between the two rivers. Tagged 16S rRNA sequencing on a 454 platform showed that the sediment microbiomes were dominated by Gammaproteobacteria and sulfur/sulfate reducing Deltaproteobacteria, represented by orders Desulfobacteriales and Desulfluromonadales together with organic degraders Betaproteobacteria (orders Burkholderiales and Rhodocyclales) together with the co-existence of Bacteroidetes predominated by Sphingobacteriales. Enrichment of specific bacterial orders was found in the clayey CP and silt-rich TC sediments, including various genera with known metabolic capability on decomposition of organic matter and xenobiotic compounds. The data represent one of the pioneered works revealing heterogeneity of bacteria in river sediments in the tropics. Analysis of bacterial diversity by tagged 16S rRNA sequencing revealed enrichment of specific taxa in CP and TC rivers.

The objectives of this study were to uncover Salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/ polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4- C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose xenobiotic degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.

Bacteria are assumed to efficiently remove organic pollutants from sewage in sewage treatment plants, where antibiotic-resistance genes can move between species via mobile genetic elements known as integrons. Nevertheless, few studies have addressed bacterial diversity and class 1 integron abundance in tropical sewage. Here, we describe the extant microbiota, using V6 tag sequencing, and quantify the class 1 integron-integrase gene (intI1) in raw sewage (RS) and activated sludge (AS). The analysis of 1,174,486 quality-filtered reads obtained from RS and AS samples revealed complex and distinct bacterial diversity in these samples. The RS sample, with 3,074 operational taxonomic units, exhibited the highest alpha-diversity indices. Among the 25 phyla, Proteobacteria, Bacteroidetes and Firmicutes represented 85% (AS) and 92% (RS) of all reads. Increased relative abundance of Micrococcales, Myxococcales, and Sphingobacteriales and reduced pathogen abundance were noted in AS. At the genus level, differences were observed for the dominant genera Simplicispira and Diaphorobacter (AS) as well as for Enhydrobacter (RS). The activated sludge process decreased (55%) the amount of bacteria harboring the intI1 gene in the RS sample. Altogether, our results emphasize the importance of biological treatment for diminishing pathogenic bacteria and those bearing the intI1 gene that arrive at a sewage treatment plant.

Chi.ti.no.pha.ga.ce'a.e. N.L. fem. n. Chitinophaga type genus of the family; suff. -aceae ending to denote a family; N.L. fem. pl. n. Chitinophagaceae the Chitinophaga family. Bacteroidetes / Sphingobacteriia / Sphingobacteriales / Chitinophagaceae Keywords: Chitinophagaceae fam. nov; Chitinophaga; Sphingobacteriia class. nov.; Sphingobacteriales ord. nov

Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes. © 2013 International Society for Microbial Ecology. All rights reserved.

Internal bacterial communities of synanthropic mites Acarus siro, Dermatophagoides farinae, Lepidoglyphus destructor, and Tyrophagus putrescentiae (Acari: Astigmata) were analyzed by culturing and culture-independent approaches from specimens obtained from laboratory colonies. Homogenates of surface-sterilized mites were used for cultivation on non-selective agar and DNA extraction. Isolated bacteria were identified by sequencing of the 16S rRNA gene. PCR amplified 16S rRNA genes were analyzed by terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning sequencing. Fluorescence in situ hybridization using universal bacterial probes was used for direct bacterial localization. T-RFLP analysis of 16S rRNA gene revealed distinct species-specific bacterial communities. The results were further confirmed by cloning and sequencing (284 clones). L. destructor and D. farinae showed more diverse communities then A. siro and T. putrescentiae. In the cultivated part of the community, the mean CFUs from four mite species ranged from 5.2 × 10(2) to 1.4 × 10(3) per mite. D. farinae had significantly higher CFUs than the other species. Bacteria were located in the digestive and reproductive tract, parenchymatical tissue, and in bacteriocytes. Among the clones, Bartonella-like bacteria occurring in A. siro and T. putresecentiae represented a distinct group related to Bartonellaceae and to Bartonella-like symbionts of ants. The clones of high similarity to Xenorhabdus cabanillasii were found in L. destructor and D. farinae, and one clone related to Photorhabdus temperata in A. siro. Members of Sphingobacteriales cloned from D. farinae and A. siro clustered with the sequences of "Candidatus Cardinium hertigii" and as a separate novel cluster.

Endosymbiotic bacteria were identified in the parasitic ciliate Ichthyophthirius multifiliis , a common pathogen of freshwater fish. PCR amplification of DNA prepared from two isolates of I. multifiliis , using primers that bind conserved sequences in bacterial 16S rRNA genes, generated an ∼1,460-bp DNA product, which was cloned and sequenced. Sequence analysis demonstrated that 16S rRNA gene sequences from three classes of bacteria were present in the PCR product. These included Alphaproteobacteria ( Rickettsiales ), Sphingobacteria , and Flavobacterium columnare . DAPI (4′,6-diamidino-2-phenylindole) staining showed endosymbionts dispersed throughout the cytoplasm of trophonts and, in most, but not all theronts. Endosymbionts were observed by transmission electron microscopy in the cytoplasm, surrounded by a prominent, electron-translucent halo characteristic of Rickettsia . Fluorescence in situ hybridization demonstrated that bacteria from the Rickettsiales and Sphingobacteriales classes are endosymbionts of I. multifiliis , found in the cytoplasm, but not in the macronucleus or micronucleus. In contrast, F. columnare was not detected by fluorescence in situ hybridization. It likely adheres to I. multifiliis through association with cilia. The role that endosymbiotic bacteria play in the life history of I. multifiliis is not known.

Sphin.go.bac.te.ri.i'a. N.L. neut. n. Sphingobacterium type genus of the type order; suff. -ia ending proposed by Gibbons and Murray and by Stackebrandt et al. to denote a class; N.L. neut. pl. n. Sphingobacteriia the Sphingobacterium class. Bacteroidetes / Sphingobacteriia Keywords: Sphingobacteriia class. nov.; Sphingobacteriales; Bacteroidetes phyl. nov.

Sphin.go.bac.te.ri'a.les. N.L. neut. n. Sphingobacterium type genus of the order; suff. -ales ending to denote an order; N.L. fem. pl. n. Sphingobacteriales the Sphingobacterium order. Bacteroidetes / Sphingobacteriia / Sphingobacteriales Keywords: Sphingobacteriales ord. nov; Sphingobacterium; Sphingobacteriia class. nov.

Description of Hongiella marincola sp. nov. Hongiella marincola (ma.rin9co.la. L. gen. n. maris of the sea; L. n. incola inhabitant; N.L. n. marincola inhabitant of the sea). Cells are rods, 0��4���0��6��2��0���3��0 ��m on MA. Non-motile. Colonies are circular, smooth, low convex, glistening, moderately reddish-orange in colour and 1��0���2��0 mm in diameter after 3 days incubation at 37 ��C on MA. Optimal growth temperature is 37 ��C. Growth occurs at 10 and 45 ��C, but not at 4 ��C or above 46 ��C. Optimal pH for growth is between 6��5 and 7��5. Growth is observed at pH 5��5, but not at pH 5��0. Optimal growth occurs in the presence of 2���3 % (w/v) NaCl. No growth occurs in the presence of > 9 % (w/v) NaCl. Growth does not occur under anaerobic conditions on MA. Tyrosine is hydrolysed weakly. Hypoxanthine, xanthine and birchwood xylan are not hydrolysed. Acid is produced from D-xylose, melibiose, L-arabinose, D-melezitose, D-glucose, D-galactose, D-mannose, D-cellobiose, lactose, sucrose, maltose, D-trehalose and D-raffinose, but not from D-sorbitol, myo -inositol, D-ribose, D-mannitol, adonitol or L-rhamnose. Acid production from D-fructose is variable (positive for type strain). Formate is not utilized. The predominant isoprenoid quinone is MK-7. The major fatty acids are iso-C15: 0, iso-C17: 0 3 -OH, iso-C16: 0 and C16: 1��7 c and/or iso-C15: 0 2 -OH. The DNA G + C content is 43 mol% (HPLC). Other phenotypic characteristics are given in Table 1. The type strain, SW-2T (= KCTC 12180T = DSM 16067T), was isolated from sea water of the East Sea of Korea. The reference strain is SW-26 (= KCTC 12181 = DSM 16068)., Published as part of Jung-Hoon Yoon, Soo-Hwan Yeo & Tae-Kwang Oh, 2004, Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea, pp. 1845-1848 in International Journal of Systematic and Evolutionary Microbiology 54 on page 1848, DOI: 10.1099/ijs.0.63170-0

Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria. Electronic supplementary material The online version of this article (doi:10.1007/s00248-016-0779-8) contains supplementary material, which is available to authorized users.

Dyadobacter fermentans (Chelius and Triplett, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in aging cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and its annotation. This is the first complete genome sequence of the sphingobacterial genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.