Showing papers in "Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology in 2016"
TL;DR: The negative correlation between Roseburia spp.
Abstract: The human gut microbiota plays an important role in human health and might also be implicated in kidney disease. The interest in butyrate producing bacteria has recently increased and is a poorly understood faecal condition in chronic kidney disease (CKD). Therefore, we evaluated differences of the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii in the faeces of Chinese patients with CKD. A case-control study was carried out for 65 CKD patients and 20 healthy controls. Differences were quantitatively validated using quantitative real-time polymerase chain reaction (qPCR). Spearman rank correlation was used to analyse the correlation between gut microbiota and clinical variables. Roseburia spp. and F. prausnitzii were significantly different in CKD patients and controls (p = 0.001; p = 0.025, respectively) and reduced more markedly in end stage renal disease (p = 0.000; p = 0.003, respectively) and microinflammation (p = 0.004; p = 0.001, respectively). Roseburia spp. and F. prausnitzii were negatively associated with C-reactive protein in plasma (r = -0.493, p = 0.00; r = -0.528, p = 0.000; respectively) and Cystatin C (r = -0.321, p = 0.006; r = -0.445, p = 0.000; respectively). They were positively associated with eGFR (r = 0.347, p = 0.002; r = 0.416, p = 0.000; respectively). The negative correlation between Roseburia spp., F. prausnitzii and CRP and renal function suggested that the depletion of butyrate producing bacteria may contribute to CKD-associated inflammation and CKD progression. Roseburia spp. and F. prausnitzii may thus serve as 'microbiomarkers'.
102 citations
TL;DR: A comprehensive comparative analysis of 129 sequenced genomes from members of the class Halobacteria is completed in order to identify shared molecular characteristics, in the forms of conserved signature insertions/deletions (CSIs) and Conserved signature proteins (CSPs), which can provide reliable evidence, independent of phylogenetic trees, that the species from the groups in which they are found are specifically related to each other due to common ancestry.
Abstract: The evolutionary interrelationships between the archaeal organisms which comprise the class Halobacteria have proven difficult to elucidate using traditional phylogenetic tools. The class currently contains three orders. However, little is known about the family level relationships within these orders. In this work, we have completed a comprehensive comparative analysis of 129 sequenced genomes from members of the class Halobacteria in order to identify shared molecular characteristics, in the forms of conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which can provide reliable evidence, independent of phylogenetic trees, that the species from the groups in which they are found are specifically related to each other due to common ancestry. Here we present 20 CSIs and 31 CSPs which are unique characteristics of infra-order level groups of genera within the class Halobacteria. We also present 40 CSIs and 234 CSPs which are characteristic of Haloarcula, Halococcus, Haloferax, or Halorubrum. Importantly, the CSIs and CSPs identified here provide evidence that the order Haloferacales contains two main groups, one consisting of Haloferax and related genera supported by four CSIs and five CSPs and the other consisting of Halorubrum and related genera supported by four CSPs. We have also identified molecular characteristics that suggest that the polyphyletic order Halobacteriales contains at least two large monophyletic clusters of organisms in addition to the polyphyletic members of the order, one cluster consisting of Haloarcula and related genera supported by ten CSIs and nineteen CSPs and the other group consisting of the members of the genus Halococcus supported by nine CSIs and 23 CSPs. We have also produced a highly robust phylogenetic tree based on the concatenated sequences of 766 proteins which provide additional support for the relationships identified by the CSIs and CSPs. On the basis of the phylogenetic analyses and the identified conserved molecular characteristics presented here, we propose a division of the order Haloferacales into two families, an emended family Haloferacaceae and Halorubraceae fam. nov. and a division of the order Halobacteriales into three families, an emended family Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov.
71 citations
TL;DR: The usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. caviae is highlighted.
Abstract: Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.
57 citations
TL;DR: The data in this report suggest that this carboxylic acid may be a potent reductive force against oxidative stress in the nutritionally-versatile Pseudomonas fluorescens.
Abstract: The interaction of keto-acids with reactive oxygen species (ROS) is known to produce the corresponding carboxylic acid with the concomitant formation of CO2. Formate is liberated when the keto-acid glyoxylate neutralizes ROS. Here we report on how formate is involved in combating oxidative stress in the nutritionally-versatile Pseudomonas fluorescens. When the microbe was subjected to hydrogen peroxide (H2O2), the levels of formate were 8 and two-fold higher in the spent fluid and the soluble cell-free extracts obtained in the stressed cultures compared to the controls respectively. Formate was subsequently utilized as a reducing force to generate NADPH and succinate. The former is mediated by formate dehydrogenase (FDH-NADP), whose activity was enhanced in the stressed cells. Fumarate reductase that catalyzes the conversion of fumarate into succinate was also markedly increased in the stressed cells. These enzymes were modulated by H2O2. While the stressed whole cells produced copious amounts of formate in the presence of glycine, the cell-free extracts synthesized ATP and succinate from formate. Although the exact role of formate in anti-oxidative defence has to await further investigation, the data in this report suggest that this carboxylic acid may be a potent reductive force against oxidative stress.
44 citations
TL;DR: In this study, Corynebacterium glutamicum ATCC 13032 was metabolically engineered for methionine production and random mutagenesis was performed to remove feedback inhibition by metabolic end-products.
Abstract: Relieving the feedback inhibition of key enzymes in a metabolic pathway is frequently the first step of producer-strain construction by genetic engineering. However, the strict feedback regulation exercised by microorganisms in methionine biosynthesis often makes it difficult to produce methionine at a high level. In this study, Corynebacterium glutamicum ATCC 13032 was metabolically engineered for methionine production. First, the metD gene encoding the methionine uptake system was deleted to achieve extracellular accumulation of methionine. Then, random mutagenesis was performed to remove feedback inhibition by metabolic end-products. The resulting strain C. glutamicum ENM-16 was further engineered to block or decrease competitive branch pathways by deleting the thrB gene and changing the start codon of the dapA gene, followed by point mutations of lysC (C932T) and pyc (G1A, C1372T) to increase methionine precursor supply. To enrich the NADPH pool, glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase in the pentose phosphate pathway were mutated to reduce their sensitivity to inhibition by intracellular metabolites. The resultant strain C. glutamicum LY-5 produced 6.85 ± 0.23 g methionine l−1 with substrate-specific yield (Y
P/S) of 0.08 mol per mol of glucose after 72 h fed-batch fermentation. The strategies described here will be useful for construction of methionine engineering strains.
43 citations
TL;DR: A novel Gram-stain negative, aerobic, non-flagellated, rod-shaped gliding bacterial strain was isolated from a skin lesion of a diseased Atlantic salmon in Finnmark, Norway and showed high 16S rRNA gene sequence similarity values to Tenacibaculum dicentrarchi NCIMB 14598T.
Abstract: A novel Gram-stain negative, aerobic, non-flagellated, rod-shaped gliding bacterial strain, designated HFJ(T), was isolated from a skin lesion of a diseased Atlantic salmon (Salmo salar L.) in Finnmark, Norway. Colonies were observed to be yellow pigmented with entire and/or undulating margins and did not adhere to the agar. The 16S rRNA gene sequence showed that the strain belongs to the genus Tenacibaculum (family Flavobacteriaceae, phylum 'Bacteroidetes'). Strain HFJ(T) exhibits high 16S rRNA gene sequence similarity values to Tenacibaculum dicentrarchi NCIMB 14598(T) (97.2 %). The strain was found to grow at 2-20 °C and only in the presence of sea salts. The respiratory quinone was identified as menaquinone 6 and the major fatty acids were identified as summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH), iso-C15:0, anteiso-C15:0, iso-C15:1 and iso-C15:0 3-OH. The DNA G+C content was determined to be 34.1 mol%. DNA-DNA hybridization and comparative phenotypic and genetic tests were performed with the phylogenetically closely related type strains, T. dicentrarchi NCIMB 14598(T) and Tenacibaculum ovolyticum NCIMB 13127(T). These data, as well as phylogenetic analyses, suggest that strain HFJ(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum finnmarkense sp. nov. is proposed; the type strain is HFJ (T) = (DSM 28541(T) = NCIMB 42386(T)).
42 citations
TL;DR: The majority of Botryosphaeriaceae species found represent new records and contribute to knowledge of the distribution, host associations and impacts of these fungi on trees in urban environments.
Abstract: Extensive die-back and mortality of various ornamental trees and shrubs has been observed in parts of the Western Balkans region during the past decade. The disease symptoms have been typical of those caused by pathogens residing in the Botryosphaeriaceae. The aims of this study were to isolate and characterize Botryosphaeriaceae species associated with diseased ornamental trees in Serbia, Montenegro, Bosnia and Herzegovina. Isolates were initially characterized based on the DNA sequence data for the internal transcribed spacer rDNA and six major clades were identified. Representative isolates from each clade were further characterized using DNA sequence data for the translation elongation factor 1-alpha, β-tubulin-2 and large subunit rRNA gene regions, as well as the morphology of the asexual morphs. Ten species of the Botryosphaeriaceae were identified of which eight, i.e., Dothiorella sarmentorum, Neofusicoccum parvum, Botryosphaeria dothidea, Phaeobotryon cupressi, Sphaeropsis visci, Diplodia seriata, D. sapinea and D. mutila were known taxa. The remaining two species could be identified only as Dothiorella spp. Dichomera syn-asexual morphs of D. sapinea, Dothiorella sp. 2 and B. dothidea, as well as unique morphological characters for a number of the known species are described. Based on host plants and geographic distribution, the majority of Botryosphaeriaceae species found represent new records. The results of this study contribute to our knowledge of the distribution, host associations and impacts of these fungi on trees in urban environments.
41 citations
TL;DR: It became obvious during this study that the production of antibiotic substances not only is strain-specific, but in many cases also depends on the media composition and growth conditions.
Abstract: It is well recognized that microorganisms associated with marine invertebrates, in particular sponges and hard corals, are an excellent source of new natural products. Therefore, the diversity of bacteria associated with marine invertebrates and their potential to produce bioactive compounds have received much attention in recent years. We report here for the first time on the biodiversity of bacteria associated with the soft coral Alcyonium digitatum, which is abundant in the Baltic Sea. In order to increase the cultured diversity, bacteria were isolated using four different media, identified with support of 16S rRNA gene sequences and screened for antimicrobial activity using two different media. Activity of crude extracts was tested against Bacillus subtilis, Staphylococcus epidermidis, Escherichia coli, and the yeast Candida albicans. A total of 251 coral-associated bacterial isolates were classified and found to belong to 41 species in 14 genera of the Firmicutes, Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria. The genus Bacillus was most abundant and diverse with 17 recognized species. Forty-eight percent of all 251 isolates exhibited antimicrobial activity. All isolates of Bacillus methylotrophicus and Bacillus amyloliquefaciens displayed inhibition of at least three out of the four tested microorganisms. It became obvious during this study that the production of antibiotic substances not only is strain-specific, but in many cases also depends on the media composition and growth conditions. In addition, the antimicrobial potential of bacteria associated with A. digitatum may represent a promising source for antimicrobial substances.
37 citations
TL;DR: Evidence supports the transient nature of the genus Trichoderma in the attine ant colonies as the discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science.
Abstract: Fungus-growing “attine” ants forage diverse substrates to grow fungi for food. In addition to the mutualistic fungal partner, the colonies of these insects harbor a rich microbiome composed of bacteria, filamentous fungi and yeasts. Previous work reported some Trichoderma species in the fungus gardens of leafcutter ants. However, no studies systematically addressed the putative association of Trichoderma with attine ants, especially in non-leafcutter ants. Here, a total of 62 strains of Trichoderma were analyzed using three molecular markers (ITS, tef1 and rpb2). In addition, 30 out of 62 strains were also morphologically examined. The strains studied correspond to the largest sampling carried out so far for Trichoderma in the attine ant environment. Our results revealed the richness of Trichoderma in this environment, since we found 20 Trichoderma species, including three new taxa described in the present work (Trichoderma attinorum, Trichoderma texanum and Trichoderma longifialidicum spp. nov.) as well as a new phylogenetic taxon (LESF 545). Moreover, we show that all 62 strains grouped within different clades across the Trichoderma phylogeny, which are identical or closely related to strains derived from several other environments. This evidence supports the transient nature of the genus Trichoderma in the attine ant colonies. The discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science.
36 citations
TL;DR: AC7 BS significantly prohibits the initial deposition of C. albicans and slows biofilm growth, suggesting a potential role of biosurfactant coatings for preventing fungal infection associated with silicone medical devices.
Abstract: Candida albicans is the major fungus that colonises medical implants, causing device-associated infections with high mortality. Antagonistic bacterial products with interesting biological properties, such as biosurfactants, have recently been considered for biofilm prevention. This study investigated the activity of lipopeptide biosurfactant produced by Bacillus subtilis AC7 (AC7 BS) against adhesion and biofilm formation of C. albicans on medical-grade silicone elastomeric disks (SEDs). Chemical analysis, stability, surface activities of AC7 BS crude extract and physicochemical characterisation of the coated silicone disk surfaces were also carried out. AC7 BS showed a good reduction of water surface tension, low critical micelle concentration, good emulsification activity, thermal resistance and pH stability. Co-incubation with 2 mg ml(-1) AC7 BS significantly reduced adhesion and biofilm formation of three C. albicans strains on SEDs in a range of 67-69 % and of 56-57 %, respectively. On pre-coated SEDs, fungal adhesion and biofilm formation were reduced by 57-62 % and 46-47 %, respectively. Additionally, AC7 BS did not inhibit viability of C. albicans strains in both planktonic and sessile form. Chemical analysis of the crude extract revealed the presence of two families of lipopeptides, principally surfactin and a lower percentage of fengycin. The evaluation of surface wettability indicated that AC7 BS coating of SEDs surface was successful although uneven. AC7 BS significantly prohibits the initial deposition of C. albicans and slows biofilm growth, suggesting a potential role of biosurfactant coatings for preventing fungal infection associated with silicone medical devices.
35 citations
TL;DR: This study showed that strains of R. solanacearum phylotype IV strains had high isDDH values, indicating it may be not appropriate to classify these closely related strains into different subspecies, and confirmed that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of the genus Ralstonia.
Abstract: The genus Ralstonia contains species that are devastating plant pathogens, opportunistic human pathogens, and/or important degraders of xenobiotic and recalcitrant compounds. However, significant nomenclature problems exist, especially for the Ralstonia solanacearum species complex which consists of four phylotypes. Phylogenomics of the Ralstonia genus was investigated via a comprehensive analysis of 39 Ralstonia genomes as well as four genomes of Cupriavidus necator (more commonly known by its previous name Ralstonia eutropha). These data revealed 686 single-copy orthologs that could be extracted from the Ralstonia core-genome and used to reconstruct the phylogeny of the genus Ralstonia. The generated tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome. Our data confirmed that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of the genus Ralstonia, e.g. strains of Ralstonia solanacearum phylotype IIA and IIB may represent two subspecies of R. solanacearum, and strains of R. solanacearum phylotype I and III may be classified into two subspecies of Ralstonia pseudosolanacearum. Recently, strains of R. solanacearum phylotype IV were proposed to be reclassified into different subspecies of Ralstonia syzygii; our study, however, showed that phylotype IV strains had high isDDH values (83.8-96.1 %), indicating it may be not appropriate to classify these closely related strains into different subspecies. We also evaluated the performance of six chromosomal housekeeping genes (gdhA, mutS, adk, leuS, rplB and gyrB) used in Ralstonia phylogenetic inference. The multilocus sequence analysis of these six marker genes was able to reliably infer the phylogenetic relationships of the genus Ralstonia.
TL;DR: The gene (1608-bp) encoding a GH6 endo-β-1,4-glucanase (CelL) from the earthworm-symbiotic bacterium Cellulosimicrobium funkei HY-13 was cloned from its whole genome sequence, expressed recombinantly, and biochemically characterized.
Abstract: The gene (1608-bp) encoding a GH6 endo-β-1,4-glucanase (CelL) from the earthworm-symbiotic bacterium Cellulosimicrobium funkei HY-13 was cloned from its whole genome sequence, expressed recombinantly, and biochemically characterized. CelL (56.0 kDa) is a modular enzyme consisting of an N-terminal catalytic GH6 domain (from Val57 to Pro396), which is 71 % identical to a GH6 protein (accession no.: WP_034662937) from Cellulomonas sp. KRMCY2, together with a C-terminal CBM 2 domain (from Cys429 to Cys532). The highest catalytic activity of CelL toward carboxymethylcellulose (CMC) was observed at 50 °C and pH 5.0, and was relatively stable at a broad pH range of 4.0-10.0. The enzyme was capable of efficiently hydrolyzing the cellulosic polymers in the order of barley β-1,3-1,4-D-glucan > CMC > lichenan > Avicel > konjac glucomannan. However, cellobiose, cellotriose, p-nitrophenyl derivatives of mono- and disaccharides, or structurally unrelated carbohydrate polymers including β-1,3-D-glucan, β-1,4-D-galactomannan, and β-1,4-D-xylan were not susceptible to CelL. The enzymatic hydrolysis of cellopentaose resulted in the production of a mixture of 68.6 % cellobiose and 31.4 % cellotriose but barley β-1,3-1,4-D-glucan was 100 % degraded to cellotriose by CelL. The enzyme strongly bound to Avicel, ivory nut mannan, and chitin but showed relatively weak binding affinity to lichenan, lignin, or poly(3-hydroxybutyrate) granules.
TL;DR: The distribution of the endophytic bacterial species in Eucalyptus was distinct and specific to the development stages under study, and many of the species had the potential for nitrogen fixation, raising the question of whether these bacteria could contribute to overall nitrogen metabolism of Eucallyptus.
Abstract: The relationships between plants and endophytic bacteria significantly contribute to plant health and yield. However, the microbial diversity in leaves of Eucalyptus spp. is still poorly characterized. Here, we investigated the endophytic diversity in leaves of hybrid Eucalyptus grandis x E. urophylla (Eucalyptus “urograndis”) by using culture-independent and culture-dependent approaches, to better understand their ecology in leaves at different stages of Eucalyptus development, including bacteria with N2 fixation potential. Firmicutes, Proteobacteria (classes alpha-, beta- and gamma-) and Actinobacteria were identified in the Eucalyptus “urograndis” endophytic bacterial community. Within this community, the species Novosphingobium barchaimii, Rhizobium grahamii, Stenotrophomonas panacihumi, Paenibacillus terrigena, P. darwinianus and Terrabacter lapilli represent the first report these bacteria as endophytes. The diversity of the total endophytic bacteria was higher in the leaves from the ‘field’ (the Shannon–Wiener index, 2.99), followed by the indices obtained in the ‘clonal garden’ (2.78), the ‘recently out from under shade (2.68), ‘under shade’ (2.63) and ‘plants for dispatch’ (2.51). In contrast, for diazotrophic bacteria, the highest means of these indices were obtained from the leaves of plants in the ‘under shade’ (2.56), ‘recently out from under shade (2.52)’ and ‘field’ stages (2.54). The distribution of the endophytic bacterial species in Eucalyptus was distinct and specific to the development stages under study, and many of the species had the potential for nitrogen fixation, raising the question of whether these bacteria could contribute to overall nitrogen metabolism of Eucalyptus.
TL;DR: The roots of diseased tomato plants are a potential reservoir of biological control actinomycetes, and Streptomyces sp.
Abstract: Plant endophytes play important roles in biocontrol of plant diseases. Actinomycetes are used for biocontrol of fungal diseases caused by Verticillium dahliae. Many studies have focused on the endophytic actinomycetes isolated from the roots of healthy plants, but few on those from the roots of diseased plants. In the present research, actinomycetes were isolated from the roots of diseased and healthy tomato plants, respectively. The results showed that, in total, 86 endophytic actinomycetes were isolated for screening of their antimicrobial activities, 8 of which showed antagonism to V. dahliae in vitro. Among the 8 antagonistic strains, 5 (out of 36) were from the roots of diseased plants, with inhibition diameter zones ranging from 11.2 to 18.2 mm, whereas 3 (out of 50) were from the roots of healthy plants, with inhibition diameter zones ranging from 11.5 to 15.5 mm. Endophytic strain DHV3-2 was isolated from the root of a diseased plant and demonstrated a potent effect against V. dahliae and other pathogenic fungi by showing the largest inhibition diameter zones among all the eight antagonistic strains. Thus, strain DHV3-2 was chosen to investigate its biological control efficacies in vivo. Further study showed that the disease incidence and disease severity indices of tomato Verticillium wilt decreased significantly (P < 0.05). We also found that the plant shoot fresh weight and height increased greatly (P < 0.05) upon treatment with strain DHV3-2 compared to the plants uninoculated in greenhouse conditions. Root colonization showed that strain DHV3-2 had the higher root-colonizing capacity in the roots of infected plants compared with the roots of healthy plants. This isolate was identified as Streptomyces sp. based on morphological characteristics and 16S rRNA gene analysis. In conclusion, the roots of diseased tomato plants are a potential reservoir of biological control actinomycetes, and Streptomyces sp. strain DHV3-2 is a potential biocontrol agent against V. dahliae and growth elicitor in tomato.
TL;DR: DNA–DNA relatedness studies showed that the two strains belong to different genomic species, and based on the genotypic and phenotypic data, the novel species Microvirga makkahensis sp.
Abstract: The taxonomic positions of two Gram-negative strains, SV1470(T) and SV2184P(T), isolated from arid soil samples, were determined using a polyphasic approach. Analysis of the 16S rRNA gene and the concatenated sequences of three housekeeping gene loci (dnaK, rpoB and gyrB) confirmed that the strains belong to the genus Microvirga. Strain SV1470(T) was found to be closely related to Microvirga vignae BR3299(T) (98.8 %), Microvirga flocculans TFB(T) (98.3 %) and Microvirga lupini Lut6(T) (98.2 %), whilst similarity to other type strains of the genus ranged from 97.8 to 96.3 %; strain SV2184P(T) was found to be closely related to Microvirga aerilata 5420S-16(T) (98.0 %), Microvirga zambiensis WSM3693(T) (97.8 %) and M. flocculans ATCC BAA-817(T) (97.4 %), whilst similarity to other type strains of the genus ranged from 97.2 to 95.9 %. The G + C content of the genomic DNA was determined to be 61.5 mol % for strain SV1470(T) and 62.1 mol % for strain SV2184P(T). Both strains were found to have the same quinone system, with Q-10 as the major ubiquinone. The polar lipid profile of strain SV1470(T) was found to consist of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and one unidentified aminolipid, while that of strain SV2184P(T) consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid and two unidentified phospholipids. DNA-DNA relatedness studies showed that the two strains belong to different genomic species. The strains were also distinguished using a combination of phenotypic properties. Based on the genotypic and phenotypic data, the novel species Microvirga makkahensis sp. nov. (type strain SV1470(T) = DSM 25394(T) = KCTC 23863(T) = NRRL-B 24875(T)) and Microvirga arabica sp. nov. (type strain SV2184P(T) = DSM 25393(T) = KCTC 23864(T) = NRRL-B 24874(T)) are proposed.
TL;DR: The putative peptide ABC transporter SppABCD, which is co-transcribed with the TonB-dependent receptor SppR in Pseudomonas aeruginosa PA14, is characterised and it is found that rhamnolipid synthesis was decreased while biofilm and exopolysaccharide synthesis was slightly increased upon overexpression of the spp operon.
Abstract: In the present study, we characterised the putative peptide ABC transporter SppABCD, which is co-transcribed with the TonB-dependent receptor SppR in Pseudomonas aeruginosa PA14. However, our data show that this transporter complex is not involved in the uptake of peptides. The fact that the TonB-dependent receptor SppR is regulated by an iron starvation ECF sigma factor suggested that this transporter is probably involved in the uptake of xenosiderophores. Therefore, we screened culture supernatants of 23 siderophore-producing bacteria for their ability to induce the expression of the SppR-regulating ECF sigma factor. However, none of them had an effect on the expression of this ECF sigma factor. Since the spp operon is not expressed under standard laboratory conditions, we overexpressed it from plasmids in PA14, which led to an impairment of its swarming motility on semisolid agar. Since we excluded the possibility that the uptake of a culture medium component was responsible for the observed phenotype, we hypothesize that the Spp transport system is involved in the uptake of a compound from the periplasmic space or a compound secreted by P. aeruginosa. Furthermore, we found that rhamnolipid synthesis was decreased while biofilm and exopolysaccharide synthesis was slightly increased upon overexpression of the spp operon. Moreover, we observed an impact of spp overexpression on regulation of genes involved in siderophore and phenazine biosynthesis.
TL;DR: This is the first study revealing the pathogenic robustness of F SSC 11 in causing root rot among Fabaceae crops and also the association of clinically important members of the FSSC with roots of a widely grown field crop in the United States.
Abstract: The Fusarium solani species complex (FSSC) includes important root pathogens of soybean in the United States, but the evolutionary lineages associated with soybean root rot are unknown. A multilocus phylogeny based on 93 isolates from soybean and pea roots from North Dakota and Minnesota revealed that root rot was associated with three known phylogenetic species, FSSC 3 + 4 (=Fusarium falciforme) (3 % of isolates), FSSC 5 (60 %), FSSC 11 (34 %), and one unknown species, FSSC X (2 %). Of these species FSSC 5 and FSSC 3 + 4 are clinically important while FSSC 11 is a plant pathogen. Isolates from FSSC 11 were pathogenic on soybean, dry bean, pea and lentil, and did not grow at 37 °C. However, isolates from FSSC 5 were weakly to non-pathogenic, but grew at 37 °C. Isolates from both FSSC 5 and FSSC 11 were highly resistant to fludioxonil in vitro. This is the first study revealing the pathogenic robustness of FSSC 11 in causing root rot among Fabaceae crops and also the association of clinically important members of the FSSC with roots of a widely grown field crop in the United States.
TL;DR: Phenotypic and chemotaxonomic features allowed a separation from the type strains of their phylogenetic neighbours, and useful phenotypic features for discriminating CBAS 572T and CBAs 573 from E. numazuensis and E. montiporae.
Abstract: The taxonomic position of strains Ab112(T) (CBAS 572(T)) and Ab227_MC (CBAS 573) was evaluated by means of genomic taxonomy. These isolates represent the dominant flora cultured from the healthy marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro. Strains CBAS 572(T) and CBAS 573 shared >98 % 16S rRNA sequence identity with Endozoicomonas numazuensis and Endozoicomonas montiporae. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), amino acid identity (AAI) and average nucleotide identity (ANI) further showed that these strains had <70 %, at maximum 71.1 and 78 % of identity, respectively, to their closest neighbours E. numazuensis and E. montiporae. The DNA G+C content of CBAS 572(T) and CBAS 573 were 47.6 and 47.7 mol%, respectively. Phenotypic and chemotaxonomic features also allowed a separation from the type strains of their phylogenetic neighbours. Useful phenotypic features for discriminating CBAS 572(T) and CBAS 573 from E. numazuensis and E. montiporae species include C8 esterase, N-acetyl-β-glucosaminidase, citric acid, uridine and siderophore. The species Endozoicomonas arenosclerae sp. nov. is proposed to harbour the new isolates. The type strain is CBAS 572(T) (=Ab112(T)).
TL;DR: The gene tree based on rpoB is more compatible with the currently accepted classification of Klebsiella than those based on 16S rRNA and khe genes, showing that rPoB can be a powerful tool for identification of K. pneumoniae isolates.
Abstract: The present work aimed to evaluate 16S rRNA, khe and rpoB gene sequencing for the identification of Klebsiella pneumoniae in comparison with phenotypic methods. Fifteen clinical isolates were examined, which were initially identified as K. pneumoniae subsp. pneumoniae using the automated VITEK 32 system in two hospitals in Enshi City, China. Their identity was further supported by conventional phenotypic methods on the basis of morphological and biochemical characteristics. Using Bayesian phylogenetic analyses and haplotypes network reconstruction, 13 isolates were identified as K. pneumoniae, whereas the other two isolates (K19, K24) were classified as Shigella sp. and Enterobacter sp., respectively. Of the three genes, 16S rRNA and khe gene could discriminate the clinical isolates at the genus level, whereas rpoB could discriminate Klebsiella at the species and even subspecies level. Overall, the gene tree based on rpoB is more compatible with the currently accepted classification of Klebsiella than those based on 16S rRNA and khe genes, showing that rpoB can be a powerful tool for identification of K. pneumoniae isolates. Above all, our study challenges the utility of khe as a species-specific marker for identification of K. pneumoniae.
TL;DR: The internal transcribed spacer region in both species of Ceraceosorus is highly heterogeneous containing multiple disparate copies that can vary intragenomically by up to 3.5 %, which may indicate that members of this lineage are potentially underdetected by current sampling methods.
Abstract: Ceraceosorales is a monotypic order in Ustilaginomycotina. Its namesake, Ceraceosorus bombacis, was described as a phytopathogen of Bombax ceiba in India. In this study, we describe Ceraceosorus guamensis sp. nov., collected on the South Pacific island of Guam, which appears to represent the second isolation of any member of this order in over 40 years. Ceraceosorus species are monokaryotic and filamentous in culture, producing conidia on potato dextrose agar. However, both species behave yeast-like when cultured on corn meal agar. The internal transcribed spacer (ITS) region (spanning the ITS1-5.8S-ITS2) in both species of Ceraceosorus is highly heterogeneous containing multiple disparate copies that can vary intragenomically by up to 3.5 %. Moreover, this region could not be amplified using the fungal ITS primers most frequently used for culture-independent methods of assessing fungal biodiversity. This fact, combined with the extremely slow growth rates on commonly employed media, may indicate that members of this lineage are potentially underdetected by current sampling methods.
TL;DR: Phylogenetic analyses of the ITS, βT, TEF-1α and CAL gene sequences revealed that the investigated isolates represent a complex of seven cryptic species, and confirmed that ITS data is insufficient to delineate species in some Ophiostoma species clusters.
Abstract: Two species of blue-stain fungi with similar morphologies, Ophiostoma brunneo-ciliatum and Ophiostoma clavatum, are associates of bark beetles infesting Pinus spp. in Europe. This has raised questions whether they represent distinct taxa. Absence of herbarium specimens and contaminated or mistakenly identified cultures of O. brunneo-ciliatum and O. clavatum have accentuated the uncertainty regarding their correct identification. The aim of this study was to reconsider the identity of European isolates reported as O. brunneo-ciliatum and O. clavatum by applying DNA-based identification methods, and to provide appropriate type specimens for them. Phylogenetic analyses of the ITS, βT, TEF-1α and CAL gene sequences revealed that the investigated isolates represent a complex of seven cryptic species. The study confirmed that ITS data is insufficient to delineate species in some Ophiostoma species clusters. Lectotypes and epitypes were designated for O. clavatum and O. brunneo-ciliatum, and three new species, Ophiostoma brunneolum, Ophiostoma macroclavatum and Ophiostoma pseudocatenulatum, are described in the newly defined O. clavatum-complex. The other two species included in the complex are Ophiostoma ainoae and Ophiostoma tapionis. The results suggest co-evolution of these fungi in association with specific bark beetles. The results also confirm the identity of the fungus associated with the pine bark beetle Ips acuminatus as O. clavatum, while O. brunneo-ciliatum appears to be mainly associated with another pine bark beetle, Ips sexdentatus.
TL;DR: The phenotypic, genotypic and genomic data presented here clearly place these strains as a coherent group within the genus Photobacteria, for which the name Photobacterium sanguinicancri sp.
Abstract: Six strains were isolated from the hemolymph of the spider crab Maja brachydactyla, captured in Spain, and one from a diseased blue mussel, Mytilus edulis. The 16S rRNA gene sequences showed close similarity to the recently described Photobacterium swingsii (98.1 %) and to a lesser degree to Photobacterium aquimaris (97.8 %). MLSA analyses showed a monophyletic group including P. swingsii that form a new subclade. All genomic analyses (Average Nucleotide Identity, Average Amino Acid Identity, and in silico DNA-DNA) clearly separate the strains analysed from P. swingsii with values below the thresholds to delimit a new species. The phenotypic, genotypic and genomic data presented here clearly place these strains as a coherent group within the genus Photobacterium, for which we propose the name Photobacterium sanguinicancri sp. nov. Strain CAIM 1827(T) (=CECT 7579(T), =DSM 24670(T)) is proposed as the type strain of the species.
TL;DR: Results of the culturing based method confirmed that A. melanogenum is predominant within the Aureobasidium population of biofinishes on pine sapwood treated with raw linseed oil and the outdoor placement in the Netherlands.
Abstract: The genus Aureobasidium, which is known as a wood staining mould, has been detected on oil treated woods in the specific stain formation called biofinish. This biofinish is used to develop a new protective, self-healing and decorative biotreatment for wood. In order to understand and control biofinish formation on oil treated wood, the occurrence of different Aureobasidium species on various wood surfaces was studied. Phenotypic variability within Aureobasidium strains presented limitations of morphological identification of Aureobasidium species. PCR amplification and Sanger sequencing of ITS and RPB2 were used to identify the culturable Aureobasidium species composition in mould stained wood surfaces with and without a biofinish. The analysed isolates showed that several Aureobasidium species were present and that Aureobasidium melanogenum was predominantly detected, regardless of the presence of a biofinish and the type of substrate. A. melanogenum was detected on wood samples exposed in the Netherlands, Cameroon, South Africa, Australia and Norway. ITS-specific PCR amplification, cloning and sequencing of DNA extracted from biofinish samples confirmed results of the culturing based method: A. melanogenum is predominant within the Aureobasidium population of biofinishes on pine sapwood treated with raw linseed oil and the outdoor placement in the Netherlands.
TL;DR: The mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest is depicted, and the bacteria with highest response to such a specific niche are identified, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.
Abstract: This study focuses on the selection exerted on bacterial communities in the mycospheres of mushrooms collected in the Brazilian Atlantic Rainforest. A total of 24 paired samples (bulk soil vs. mycosphere) were assessed to investigate potential interactions between fungi and bacteria present in fungal mycospheres. Prevalent fungal families were identified as Marasmiaceae and Lepiotaceae (both Basidiomycota) based on ITS partial sequencing. We used culture-independent techniques to analyze bacterial DNA from soil and mycosphere samples. Bacterial communities in the samples were distinguished based on overall bacterial, alphaproteobacterial, and betaproteobacterial PCR-DGGE patterns, which were different in fungi belonging to different taxa. These results were confirmed by pyrosequencing the V4 region of the 16S rRNA gene (based on five bulk soil vs. mycosphere pairs), which revealed the most responsive bacterial families in the different conditions generated beneath the mushrooms, identified as Bradyrhizobiaceae, Burkholderiaceae, and Pseudomonadaceae. The bacterial families Acetobacteraceae, Chrhoniobacteraceae, Planctomycetaceae, Conexibacteraceae, and Burkholderiaceae were found in all mycosphere samples, composing the core mycosphere microbiome. Similarly, some bacterial groups identified as Koribacteriaceae, Acidobacteria (Solibacteriaceae) and an unclassified group of Acidobacteria were preferentially present in the bulk soil samples (found in all of them). In this study we depict the mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest, and identify the bacteria with highest response to such a specific niche, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.
TL;DR: The value of multi-locus sequence analysis for the relatively rapid, simple and sensitive molecular identification of Streptomyces strains held in culture collections is demonstrated.
Abstract: Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 strains identified as Streptomyces scabiei deposited at various times since the 1950s and these were subjected to multi-locus sequence analysis utilising partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB and trpB. Phylogenetic analyses confirmed the identity of 17 of these strains as Streptomyces scabiei, 9 of the strains as the potato-pathogenic species Streptomyces europaeiscabiei and 6 strains as potentially new phytopathogenic species. Of the 16 other strains, 12 were identified as members of previously described non-pathogenic Streptomyces species while the remaining 4 strains may represent heretofore unrecognised non-pathogenic species. This study demonstrated the value of this technique for the relatively rapid, simple and sensitive molecular identification of Streptomyces strains held in culture collections.
TL;DR: Survival studies indicated that strain MLST1T remains viable after exposure to adverse conditions, particularly in the prolonged absence of a carbon source, at low temperatures and with no NaCl.
Abstract: An aerobic haloalkaliphilic bacterium, designated strain MLST1(T), was isolated from filtered (0.22 µm) Mono Lake (USA) waters. The isolate was observed to grow primarily on yeast extract, peptone and tryptone. Optimal growth occurred in media at pH 9.5 containing 5-11 g/l yeast extract, and 70-100 g/l NaCl. When in log phase of growth, cells were found to be mostly curved motile rods (1-3 µm length by 0.4-1 µm diameter). Phylogenetic analysis of the 16S rRNA gene and chemotaxonomic data revealed that the isolate belonged to the family Idiomarinaceae, and is closely related to Aliidiomarina maris (96.67 % sequence similarity). The major fatty acids were identified to be iso-C17:1 ω9c (27.1 %), iso-C17:0 (21.3 %) and iso-C15:0 (12.2 %). Predominant polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and the major respiratory quinone was identified as Q8. The DNA base composition was 46.3 mol% G+C. Survival studies indicated that strain MLST1(T) remains viable after exposure to adverse conditions, particularly in the prolonged absence of a carbon source, at low temperatures and with no NaCl. Under these conditions, the cells shrunk to around 0.2 µm in length by 0.1 µm in diameter and passed through 0.22 µm filters. The ultra-small cells could only be resuscitated in media with low levels of yeast extract, up to 0.6 g/l. Once resuscitated, cells were able to grow to full size. Strain MLST1(T) is clearly a unique bacterium in the waters of Mono Lake and the name Aliidiomarina minuta sp. nov. is proposed. The type strain is MLST1(T) (=JCM 17425(T) = KCTC 23357(T)).
TL;DR: A Gram-positive, aerobic, non-motile and extremely halophilic bacterial strain was isolated from kimchi, a Korean fermented food, and is considered to represent a novel species of the genus Lentibacillus, for which the name LentIBacillus kimchii sp.
Abstract: A Gram-positive, aerobic, non-motile and extremely halophilic bacterial strain, designated K9(T), was isolated from kimchi, a Korean fermented food. The strain was observed as endospore-forming rod-shaped cells showing oxidase and catalase activity. It was found to grow at 10.0-30.0 % (w/v) NaCl (optimum, 15.0-20.0 %), pH 7.0-8.0 (optimum, pH 7.5) and 15-40 °C (optimum, 30 °C). The polar lipids of strain K9(T) were identified as phosphatidylglycerol, three unidentified phospholipids and an unidentified glycolipid. The isoprenoid quinone was identified as menaquinone-7. The major cellular fatty acids (>20 % of the total) were found to be anteisio-C15:0 and anteisio-C17:0. The cell wall peptidoglycan composition was determined to contain meso-diaminopimelic acid. The G + C content of genomic DNA was determined to be 48.2 mol %. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolated strain is closely related to Lentibacillus salinarum AHS-1(T) (96.7 % sequence similarity). Based on its phenotypic, chemotaxonomic and phylogenetic data, strain K9(T) is considered to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kimchii sp. nov., is proposed. The type strain is K9(T) (=KACC 18490(T) = JCM 30234(T)).
TL;DR: The diversity of epiphytic yeasts from corn (Zea mays Linn.) phylloplanes in Thailand was investigated using this technique and sequence-based analysis of the D1/D2 domains of the large subunit ribosomal DNA sequences.
Abstract: Culture-independent techniques have recently been used for evaluation of microbial diversity in the environment since it addresses the problem of unculturable microorganisms. In this study, the diversity of epiphytic yeasts from corn (Zea mays Linn.) phylloplanes in Thailand was investigated using this technique and sequence-based analysis of the D1/D2 domains of the large subunit ribosomal DNA sequences. Thirty-seven samples of corn leaf were collected randomly from 10 provinces. The DNA was extracted from leaf washing samples and the D1/D2 domains were amplified. The PCR products were cloned and then screened by colony PCR. A total of 1049 clones were obtained from 37 clone libraries. From this total, 329 clones (213 sequences) were closely related to yeast strains in the GenBank database, and they were clustered into 77 operational taxonomic units (OTUs) with a similarity threshold of 99 %. The majority of sequences (98.5 %) were classified into the phylum Basidiomycota. Sixteen known yeast species were identified. Interestingly, more than 65 % of the D1/D2 sequences obtained by this technique were suggested to be sequences from new yeast taxa. The predominant yeast sequences detected belonged to the order Ustilaginales with relative frequency of 68.0 %. The most common known yeast species detected on the leaf samples were Pseudozyma hubeiensis pro tem. and Moesziomyces antarcticus with frequency of occurrence of 24.3 and 21.6 %, respectively.
TL;DR: It is suggested that subinhibitory concentrations of phloretin attenuate the virulence of S. Typhimurium and protect against S. typhimuria infection.
Abstract: Phloretin, a natural component of many fruits, exhibits anti-virulence effects and provides a new alternative to counter bacterial infection. The aim of this study was to determine the effect of subinhibitory concentrations of phloretin on the virulence of Salmonella typhimurium. At concentrations where growth of Salmonella was not inhibited, phloretin significantly inhibited bacteria biofilm formation and motility. Subinhibitory concentrations of phloretin repressed eight genes involved in the Salmonella pathogenicity island 1 and 3 genes involved in flagella production. Furthermore, subinhibitory concentrations of phloretin inhibited the adhesion and invasion of Salmonella in IEC-6 cells and reduced the LDH levels of S. typhimurium-infected IEC-6 cells. Additionally, phloretin significantly decreased the cecum bacterial loads of the mice infected with live S. typhimurium containing subinhibitory concentrations of phloretin by gavage. These results suggested that subinhibitory concentrations of phloretin attenuate the virulence of S. typhimurium and protect against S. typhimurium infection.
TL;DR: Fungi belonging to the Ophiostomatales were identified based on morphology and comparison of sequence data for the β-tubulin, ITS1-5.8S-ITS2 and LSU gene regions.
Abstract: Euphorbia ingens trees have been dying in large numbers in the Limpopo Province of South Africa for approximately 15 years. The ambrosia beetle Cyrtogenius africus is often found infesting diseased and dying trees. The aim of this study was to identify the ophiostomatoid fungi occurring in the galleries of C. africus. Logs infested with this beetle were collected from the KwaZulu-Natal, Limpopo, Mpumalanga, and North West Provinces of South Africa. Fungi belonging to the Ophiostomatales were identified based on morphology and comparison of sequence data for the β-tubulin, ITS1-5.8S-ITS2 and LSU gene regions. A novel species of Ophiostoma and a novel genus in the Ophiostomatales were identified. Inoculation studies with these fungi produced lesions in the branches of healthy E. ingens trees.