scholarly journals Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (Picea mariana) Seedlings Grown in a Nursery

2004 ◽  
Vol 70 (6) ◽  
pp. 3541-3551 ◽  
Author(s):  
M. Filion ◽  
R. C. Hamelin ◽  
L. Bernier ◽  
M. St-Arnaud
Keyword(s):  
Picea Mariana ◽  
Root Rot ◽  
Black Spruce ◽  
Restriction Analysis ◽  
Phylogenetic Analyses ◽  
Methodological Approach ◽  
Rrna Gene ◽  
Wide Range ◽  
Bacteria And Fungi ◽  
Evenness Indices

ABSTRACT Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.

scholarly journals Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1900-1905 ◽  
Author(s):  
Jun Kun Lu ◽  
Ya Jing Dou ◽  
Ya Jie Zhu ◽  
Sheng Kun Wang ◽  
Xin Hua Sui ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
Phylogenetic Analyses ◽  
Jiangxi Province ◽  
Rrna Gene ◽  
Symbiotic Gene ◽  
Content Type ◽  
Acacia Melanoxylon ◽  
Link Type

Three slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium . To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium , indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium . Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium , for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (T m).

scholarly journals Metagenomic Insights Into the Microbial Assemblage Capable of Quorum Sensing and Quorum Quenching in Particulate Organic Matter in the Yellow Sea

2021 ◽  
Vol 11 ◽  
Author(s):  
Ying Su ◽  
Yuanzhi Yang ◽  
Xiao-Yu Zhu ◽  
Xiao-Hua Zhang ◽  
Min Yu
Keyword(s):  
Organic Matter ◽  
Quorum Sensing ◽  
Particulate Organic Matter ◽  
Yellow Sea ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Quorum Quenching ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Wide Range

Quorum sensing (QS) is a density-dependent communicating mechanism that allows bacteria to regulate a wide range of biogeochemical important processes and could be inhibited by quorum quenching (QQ). Increasing researches have demonstrated that QS can affect the degradation of particulate organic matter (POM) in the photic zone. However, knowledge of the diversity and variation of microbial QS and QQ systems in sinking POM is scarce. Here, POM samples were collected from surface seawater (SW), bottom seawater (BW), and surficial sediment (SS) in the Yellow Sea of China. 16S rRNA gene amplicon and metagenome sequencing were performed to analyze the community structure of particle-associated microorganisms and distribution of QS genes [acylated homoserine lactone (AHL) synthesizing gene luxI and AHL sensing gene luxR] and QQ genes (genes encoding for AHL lactonase and acylase) in POM. Shifting community structures were observed at different sampling depths, with an increase of microbial abundance and diversity from SW to BW. Along with the variation of microbial communities, the abundances of luxI and luxR decreased slightly but were restored or even exceeded when POM arrived at SS. Comparatively, abundances of AHL lactonase and acylase remained constant during the transportation process from SW to BW but increased dramatically in SS. Correlation tests indicated that abundances of luxI and luxR were positively correlated with temperature, while those of AHL acylase were positively correlated with depth, SiO42–, PO43–, and NO3–, but negatively correlated with temperature and pH. According to phylogenetic analyses, the retrieved QS and QQ genes are more diverse and distinctive than ever experimentally identified. Besides, the vertical transmission of QS and QQ genes along with POM sinking was observed, which could be one of the key factors leading to the prevalence of QS and QQ genes in marine ecosystems. Overall, our results increase the current knowledge of QS and QQ metabolic pathways in marine environment and shed light on the intertwined interspecies relationships to better investigate their dynamics and ecological roles in POM cycling.

scholarly journals Grouping of Pseudomonas spp. isolated from dieback- affected sissoo (Dalbergia sissoo Roxb.) using phylogenetic analyses

2015 ◽  
Vol 24 (2) ◽  
pp. 141-153
Author(s):  
HP Mühlbach ◽  
H Tantau ◽  
A Stubbe ◽  
D Palm ◽  
J Schulze ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Disease ◽  
Restriction Analysis ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Dalbergia Sissoo ◽  
Thin Sections ◽  
Specific Antibodies ◽  
Histological Studies ◽  
Dna Restriction

Dieback of sissoo (Dalbergia sissoo Roxb.) is a devastating plant disease, whose causative biotic agents were not yet identified unequivocally. Our previous studies revealed that bacteria belonging to the genus Pseudomonas were associated with dieback?affected sissoo trees. To study the bacterial community associated with dieback-affected sissoo trees, DNA based approaches were used in the present work. Sequencing almost the complete 16S rRNA gene of 33 selected Pseudomonas isolates allowed them to be grouped into two main clusters only. The major group consisted of 19 isolates related to P. oryzihabitans, while in the minor one ten isolates related to P. putida were found together with very few other pseudomonads. Almost the same clustering was obtained a with the independent grouping methods of amplified ribosomal DNA restriction analysis (ARDRA). These results strongly indicate that mainly bacteria strains related to Pseudomonas oryzihabitans were associated with dieback-affected Dalbergia sissoo trees. Immuno-histological studies with thin-sections of sissoo roots using Pseudomonas-specific antibodies showed that bacteria had invaded the root parenchyma. Plant Tissue Cult. & Biotech. 24(2): 141-153, 2014 (December)

scholarly journals A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

2017 ◽  
Vol 66 (1) ◽  
pp. 39-56
Author(s):  
Nilgun Tekin ◽  
Arzu Coleri Cihan ◽  
Basar Karaca ◽  
Cumhur Cokmus
Keyword(s):  
16S Rrna ◽  
Alkaline Protease ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Protease Production ◽  
Rrna Gene ◽  
Wide Range ◽  
Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

scholarly journals The Polyextreme Ecosystem, Salar de Huasco at the Chilean Altiplano of the Atacama Desert Houses Diverse Streptomyces spp. with Promising Pharmaceutical Potentials

Diversity ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 69 ◽  
Author(s):  
Carlos Cortés-Albayay ◽  
Johanna Silber ◽  
Johannes F. Imhoff ◽  
Juan A. Asenjo ◽  
Barbara Andrews ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Atacama Desert ◽  
Fibroblast Cell ◽  
Mouse Fibroblast ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The North ◽  
Streptomyces Spp ◽  
Chilean Altiplano ◽  
Bacteria And Fungi

Salar de Huasco at the Chilean Altiplano of the Atacama Desert is considered a polyextreme environment, where solar radiation, salinity and aridity are extremely high and occur simultaneously. In this study, a total of 76 bacterial isolates were discovered from soil samples collected at two different sites in the east shoreline of Salar de Huasco, including H0 (base camp next to freshwater stream in the north part) and H6 (saline soils in the south part). All isolated bacteria were preliminarily identified using some of their phenotypic and genotypic data into the genera Streptomyces (86%), Nocardiopsis (9%), Micromonospora (3%), Bacillus (1%), and Pseudomonas (1%). Streptomyces was found dominantly in both sites (H0 = 19 isolates and H6 = 46 isolates), while the other genera were found only in site H0 (11 isolates). Based on the genotypic and phylogenetic analyses using the 16S rRNA gene sequences of all Streptomyces isolates, 18% (12 isolates) revealed <98.7% identity of the gene sequences compared to those in the publicly available databases and were determined as highly possibly novel species. Further studies suggested that many Streptomyces isolates possess the nonribosomal peptide synthetases-coding gene, and some of which could inhibit growth of at least two test microbes (i.e., Gram-positive and Gram-negative bacteria and fungi) and showed also the cytotoxicity against hepatocellular carcinoma and or mouse fibroblast cell lines. The antimicrobial activity and cytotoxicity of these Streptomyces isolates were highly dependent upon the nutrients used for their cultivation. Moreover, the HPLC-UV-MS profiles of metabolites produced by the selected Streptomyces isolates unveiled apparent differences when compared to the public database of existing natural products. With our findings, the polyextreme environments like Salar de Huasco are promising sources for exploring novel and valuable bacteria with pharmaceutical potentials.

scholarly journals Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell

2007 ◽  
Vol 57 (4) ◽  
pp. 701-707 ◽  
Author(s):  
Dawn E. Holmes ◽  
Kelly P. Nevin ◽  
Trevor L. Woodard ◽  
Aaron D. Peacock ◽  
Derek R. Lovley
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Acid Fermentation ◽  
Mixed Acid ◽  
Phylogenetic Cluster ◽  
Wide Range ◽  
Novel Genus And Species

A Gram-negative, non-motile, filamentous, rod-shaped, non-spore-forming bacterium (strain F2T) was isolated from the surface of an electricity-harvesting electrode incubated in marine sediments. Strain F2T does not contain c-type cytochromes, flexirubin or carotenoids. It is a facultative anaerobe that can ferment sugars by using a mixed acid fermentation pathway and it can grow over a wide range of temperatures (4–42 °C). The DNA G+C (44.9 mol%) content and chemotaxonomic characteristics (major fatty acids, a-15 : 0 and 15 : 0) were consistent with those of species within the phylum Bacteroidetes. Phylogenetic analysis of the 16S rRNA nucleotide and elongation factor G amino acid sequences indicated that strain F2T represents a unique phylogenetic cluster within the phylum Bacteroidetes. On the basis of 16S rRNA gene sequence phylogeny, the closest relative available in pure culture, Alkaliflexus imshenetskii, is only 87.5 % similar to strain F2T. Results from physiological, biochemical and phylogenetic analyses showed that strain F2T should be classified as a novel genus and species within the phylum Bacteroidetes, for which the name Prolixibacter bellariivorans gen. nov., sp. nov. is proposed. The type strain is F2T (=ATCC BAA-1284T=JCM 13498T).

scholarly journals Identification and characterisation of oil sludge degrading bacteria isolated from compost

2016 ◽  
Vol 42 (2) ◽  
pp. 67-77 ◽  
Author(s):  
Onyedikachi Ubani ◽  
Harrison Ifeanyichukwu Atagana ◽  
Mapitsi Silvester Thantsha ◽  
Adeleke Rasheed
Keyword(s):  
Phylogenetic Analyses ◽  
Oil Sludge ◽  
Bacterial Degradation ◽  
Rrna Gene ◽  
Molecular Weights ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic ◽  
Polymerase Chain ◽  
Bacteria And Fungi ◽  
The 16S Rrna Gene

AbstractCompounds present in oil sludge such as polycyclic aromatic hydrocarbons (PAHs) are known to be cytotoxic, mutagenic and potentially carcinogenic. Microorganisms including bacteria and fungi have been reported to degrade oil sludge components to innocuous compounds such as carbon dioxide, water and salts. In the present study, we isolated different bacteria with PAH-degrading capabilities from compost prepared from oil sludge and animal manures. These bacteria were isolated on a mineral base medium and mineral salt agar plates. A total of 31 morphologically distinct isolates were carefully selected from 5 different compost treatments for identification using polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (universal forward 16S-P1 PCR and reverse 16S-P2 PCR). The amplicons were sequenced and sequences were compared with the known nucleotides from the GenBank. The phylogenetic analyses of the isolates showed that they belong to 3 different clades; Firmicutes, Proteobacteria and Actinobacteria. These bacteria identified were closely related to the generaBacillus, Arthrobacter, Staphylococcus, Brevibacterium, Variovorax, Paenibacillus, Ralstonia and Geobacillus.The results showed thatBacillus species were predominant in all composts. Based on the results of the degradation of the PAHs in the composts and results of previous studies on bacterial degradation of hydrocarbons in oil, the characteristics of these bacterial isolates suggests that they may be responsible for the breakdown of PAHs of different molecular weights in the composts. Thus, they may be potentially useful for bioremediation of oil sludge during compost bioremediation.

scholarly journals Thalassobacillus devorans gen. nov., sp. nov., a moderately halophilic, phenol-degrading, Gram-positive bacterium

2005 ◽  
Vol 55 (5) ◽  
pp. 1789-1795 ◽  
Author(s):  
María Teresa García ◽  
Virginia Gallego ◽  
Antonio Ventosa ◽  
Encarnación Mellado
Keyword(s):  
Enrichment Culture ◽  
Phylogenetic Analyses ◽  
Halophilic Bacteria ◽  
Halophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gram Positive ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium ◽  
Wide Range

A novel moderately halophilic bacterium, strain G-19.1T, has been isolated from a phenol enrichment of samples collected in hypersaline habitats of southern Spain. This enrichment culture was a part of a screening programme to isolate halophilic bacteria able to degrade various aromatic compounds. Strain G-19.1T has been characterized as a potential phenol-degrader over a wide range of saline conditions. Strain G-19.1T was found to be an aerobic, Gram-positive, endospore-forming, non-pigmented, moderately halophilic rod that grew optimally in media containing 7·5–10 % NaCl at pH 7·0. The DNA G+C content was 42·4 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences indicated that the closest relatives were Halobacillus species (96·2–97·0 %), although this novel isolate constitutes a separate line of descent within the radiation of Gram-positive rods. The cell-wall peptidoglycan contained meso-diaminopimelic acid, indicating that this strain does not share the main characteristic that differentiates members of the genus Halobacillus (which contain Orn–d-Asp) from other related genera. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. On the basis of phenotypic, genotypic and phylogenetic analyses, this isolate should be classified in a novel genus and species, for which the name Thalassobacillus devorans gen. nov., sp. nov. is proposed. The type strain is strain G-19.1T (=DSM 16966T=CECT 7046T=CCM 7282T).

scholarly journals Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales

2006 ◽  
Vol 56 (4) ◽  
pp. 855-859 ◽  
Author(s):  
Jang-Cheon Cho ◽  
Stephen J. Giovannoni
Keyword(s):  
Marine Bacterium ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Sargasso Sea ◽  
Wide Range ◽  
Novel Genus And Species ◽  
Distinct Lineage ◽  
The 16S Rrna Gene

A Gram-negative, chemoheterotrophic, facultatively anaerobic, slightly halophilic, oval-shaped marine bacterium, designated HTCC2601T, was isolated from the western Sargasso Sea by high-throughput culturing involving dilution to extinction. Although the 16S rRNA gene sequence similarity between the isolate and Salipiger mucosus was 96·5 %, phylogenetic analyses using different treeing algorithms clearly indicated that the strain forms a distinct lineage within a clade containing the recently classified genera Salipiger and Palleronia in the order Rhodobacterales of the Alphaproteobacteria. The DNA–DNA relatedness between strain HTCC2601T and S. mucosus was 26·3 %. Strain HTCC2601T utilized a wide range of carbohydrates, including hexose monomers, sugar alcohols, organic acids and amino acids, as sole carbon sources. The DNA G+C content of strain HTCC2601T was 65·4 mol%, and the predominant constituents of the cellular fatty acids were 18 : 1ω7c (79·7 %) and 11-methyl 18 : 1ω7c (7·5 %). The strain differed from members of the closely related genera Salipiger and Palleronia in its morphological, biochemical and ecological characteristics. On the basis of the taxonomic data obtained in this study, a novel genus and species, Pelagibaca bermudensis gen. nov., sp. nov., is proposed; HTCC2601T (=KCTC 12554T=JCM 13377T) is the type strain of Pelagibaca bermudensis.

scholarly journals Morphologic and Molecular Characterization of a Demodex (Acari: Demodicidae) Species from White-Tailed Deer (Odocoileus virginianus)

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Michael J. Yabsley ◽  
Sarah E. Clay ◽  
Samantha E. J. Gibbs ◽  
Mark W. Cunningham ◽  
Michaela G. Austel
Keyword(s):  
Odocoileus Virginianus ◽  
18S Rrna ◽  
Association Studies ◽  
Phylogenetic Analyses ◽  
Skin Irritation ◽  
Black Bear ◽  
Distinct Species ◽  
Rrna Gene ◽  
Adult Males ◽  
Wide Range

Demodex mites, although usually nonpathogenic, can cause a wide range of dermatological lesions ranging from mild skin irritation and alopecia to severe furunculosis. Recently, a case of demodicosis from a white-tailed deer (Odocoileus virginianus) revealed a Demodex species morphologically distinct from Demodex odocoilei. All life cycle stages were considerably larger than D. odocoilei and although similar in size to D. kutzeri and D. acutipes from European cervids, numerous morphometrics distinguished the four species. Adult males and females were 209.1±13.1 and 225.5±13.4 μm in length, respectively. Ova, larva, and nymphs measured 65.1±4.1, 124.9±11.6, and 205.1±19.4 μm in length, respectively. For phylogenetic analyses, a portion of the 18S rRNA gene was amplified and sequenced from samples of the WTD Demodex sp., two Demodex samples from domestic dogs, and Demodex ursi from a black bear. Phylogenetic analyses indicated that the WTD Demodex was most similar to D. musculi from laboratory mice. A partial sequence from D. ursi was identical to the WTD Demodex sequence; however, these two species can be differentiated morphologically. This paper describes a second Demodex species from white-tailed deer and indicates that 18S rRNA is useful for phylogenetic analysis of most Demodex species, but two morphologically distinct species had identical partial sequences. Additional gene targets should be investigated for phylogenetic and parasite-host association studies.

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