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Rhizosphere competence of biocontrol agent Bacillus subtilis strain SRB28 from sorghum  [cached]
Indian Phytopathology , 2011,
Abstract: Bacillus subtilis SRB28, isolated from sorghum rhizosphere, is a strain known for stimulating sorghum plant growth and antifungal activity against soil-borne fungal pathogens. In this study, the strain was characterized for IAA production and its effects on root development in sorghum. Factors determining rhizosphere competence including root colonization and survival in the sorghum rhizosphere have been assessed. SRB28 produced IAA and influenced the growth of primary root depending on cell concentration. The cells at high concentration (>106 cfu/ml) increased the number of adventitious root and number and length of root hairs in seedlings raised from bacteria treated seed in the presence of tryptophan. The bacteria colonised on sorghum root, formed micro-colonies and survived in the sorghum rhizosphere. The overall results indicated that the B. subtilis SRB28 hold promise as potential biocontrol as well as PGPR for sorghum.
Phosphate Solubilization by Bacillus subtilis and Serratia marcescens Isolated from Tomato Plant Rhizosphere  [PDF]
Eman A. H. Mohamed, Azza G. Farag, Sahar A. Youssef
Journal of Environmental Protection (JEP) , 2018, DOI: 10.4236/jep.2018.93018
Abstract: Plants need phosphorus for many physiological activities in a form of phosphate anions. Three different bacterial strains (Bacillus subtilis PH, Serratia marcescens PH1, and Serratia marcescens PH2), recently isolated from tomato plant rhizosphere, have high phosphate solubilization index (SI from 2.8 to 3.2) on Pikovskaya agar medium (which contains calcium phosphate). Moreover, phosphate release from calcium in Pikovskaya broth over 5 days is increasing with cell growth for the different isolates. The most efficient phosphate solubilization case is the mixed culture of the 3 strains (OD475 is almost 1). On the other hand, pH values decreased dramatically with time due to organic acids secretion and the maximum acidification level is recoded for Serratia marcescens PH2 (pH = 1.94). Interestingly, the isolates are resistance to important pesticides (oxamyl, thiophanate methyl, and captan) that are commonly used in the sampling area. This resistance is very favorable and increases the persistence of the phosphate solubilizing bacteria in contaminated soils. The isolates are therefore plant symbionts and growth promoting agents.
Correctness of Protein Identifications of Bacillus subtilis Proteome with the Indication on Potential False Positive Peptides Supported by Predictions of Their Retention Times
Katarzyna Macur,Tomasz B czek,Roman Kaliszan,Caterina Temporini,Federica Corana,Gabriella Massolini,Jolanta Grzenkowicz-Wydra,Micha Obuchowski
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/718142
Abstract: The predictive capability of the retention time prediction model based on quantitative structure-retention relationships (QSRR) was tested. QSRR model was derived with the use of set of peptides identified with the highest scores and originated from 8 known proteins annotated as model ones. The predictive ability of the QSRR model was verified with the use of a Bacillus subtilis proteome digest after separation and identification of the peptides by LC-ESI-MS/MS. That ability was tested with three sets of testing peptides assigned to the proteins identified with different levels of confidence. First, the set of peptides identified with the highest scores achieved in the search were considered. Hence, proteins identified on the basis of more than one peptide were taken into account. Furthermore, proteins identified on the basis of just one peptide were also considered and, depending on the possessed scores, both above and below the assumed threshold, were analyzed in two separated sets. The QSRR approach was applied as the additional constraint in proteomic research verifying results of MS/MS ion search and confirming the correctness of the peptides identifications along with the indication of the potential false positives.
Bacterial diversity and halotolerant petroleum-degrading bacteria of the rhizosphere of Suaeda salsa (L.) in petroleum-contaminated saline-alkali soil

WANG Xin-Xin,BAI Zhi-Hui,JIN De-Cai,HAN Zhen,ZHUANG Guo-Qiang,

微生物学通报 , 2011,
Abstract: Bacterial community associated with Suaeda salsa (L.) rhizosphere in petroleum-contaminated saline-alkali soil was investigated by 16S rRNA gene clone library analysis. Halotolerant petroleum-degrading bacteria were further isolated by enrichment using petroleum as the sole source of carbon and energy. Marinobacter, Alcanivorax and Pseudomonas dominated Suaeda salsa (L.) rhizosphere in petroleum-contaminated saline-alkali soil as revealed by 16S rRNA gene clone library analysis, which were likely to have a role in the phytoremediation of such soil by Suaeda salsa (L.). Eight halotolerant petroleum-degrading bacterial strains were isolated, which could grow up to 6%?10% NaCl, and could degrade 32.3% ?57.0% petroleum hydrocarbon in 3% NaCl over a period of 14 days. They were identified to belong to the genus of Gordonia, Achromobacter, Dietzia, Bacillus and Pseudomonas by 16S rRNA gene sequence analysis. They may involve in the degradation of petroleum in the phytoremediation of such soil by Suaeda salsa (L.).
Cloning and Expression of a Osmoregulatory Gene pro B from Halotolerant Bacillus subtilis

Zhang Xiaoqing Cao Junwei,Zhai Chao Cheng Jianjun,

微生物学报 , 2002,
Abstract: A 1.3 kb fragment is cloned from halotolerated Bacillus subtilis 93151 with PCR amplification method, and its positively-directionally inserted fragment can complemented with proB-E. coli by function test. Halotolerated ability of E. coli DH5 alpha having this recombination plasmid rises from 2% to 4% in minimal medium. The nucleotide sequence of this fragment is obtained by primer walking method. Nucleotide sequence of this fragment 167-1269 bp translates a protein which has 370 amino acid by sequence analysis through DNAsis program. There are non-typical-10 sequences, typical-35 sequences and a Ribosome binding site of this fragment in its upstream sequence, and there is flanking sequence, which has best efficiency of beginning translating. Homologues comparision, of nucleotide and amino acid sequences of this fragment and those of gene in gene bank shows that homogenous of Nucleotide sequences and amino acid sequences of this fragement and Bacillus subtilis 168 are respectively 81%, 90%, which prove that this gene is certainly a pro B gene. This protein translated by this fragment has several absoluter conservative domain which have been correlating closely with forming active center of enzyme and tri-dimension structure of active center, compared amino acid sequences of this fragment and pro B genes of thirty kinds of different microorganism.
Proteomic analysis of small acid soluble proteins in the spore core of Bacillus subtilis ΔprpE and 168 strains with predictions of peptides liquid chromatography retention times as an additional tool in protein identification
Katarzyna Macur, Caterina Temporini, Gabriella Massolini, Jolanta Grzenkowicz-Wydra, Micha? Obuchowski, Tomasz B?czek
Proteome Science , 2010, DOI: 10.1186/1477-5956-8-60
Abstract: In both strains of B. subtilis, peptides characteristic for SASPs were found, however their identification confidence varied. According to the MS identity parameter Xcorr and difference between predicted and experimental retention times (ΔtR) four groups could be distinguished: correctly and incorrectly identified, potential false positives and false negatives. The ΔprpE strain was characterized by much higher amount of SASPs peptides than standard 168 and their identification confidence was, mostly for alpha- and beta-type SASP, satisfactory.The QSRR-based model for predicting retention times of the peptides, was a useful additional to MS tool, enhancing protein identification. Higher content of SASPs in strain lacking PrpE phosphatase suggests that this enzyme may influence their occurrence in the spores, lowering levels of these proteins.Although bacterial endospores have been studied for over 130 years, there are still questions about basic mechanisms of their unique features, i.e. high resistance to environmental stress, such as high temperatures, chemicals or radiation, which enable them long term survival in unfavorable conditions [1]. Bacillus subtilis (B. subtilis) is a sporulating, model organism often used in the biochemical, genetic and molecular research, concerning Gram positive bacteria. Its sporulation process is very complicated and requires space and time gene expression regulation. About 25% of genes in chromosome of this bacterium are involved in spore formation. What is more, there are already 154 proteins identified, characteristic exclusively for spores, which do not occur in vegetative cells [2]. Small acid soluble spore proteins (SASPs) have been evidenced to be one of specific spore components, which may have an influence on their resistance to unfavorable conditions [3]. The SASPs belong to a group of at least sixteen proteins found in the core of spores produced by B. subtilis [4-6]. Genes coding for those proteins are expressed only duri
Bacillus subtilis Strains with Antifungal Activity against the Phytopathogenic Fungi  [PDF]
Ayslu Mirkasimovna Mardanova, Guzel Fanisovna Hadieva, Marat Tafkilevich Lutfullin, Irina Valer’evna Khilyas, Leyla Farvazovna Minnullina, Adelya Gadelevna Gilyazeva, Lidiya Mikhailovna Bogomolnaya, Margarita Rashidovna Sharipova
Agricultural Sciences (AS) , 2017, DOI: 10.4236/as.2017.81001
Abstract: Bacillus strains isolated from the rhizosphere soil of potato roots were evaluated for the potential antagonistic activity against fungal pathogens in vitro and in vivo. Two bacterial isolates were identified as new Bacillus subtilis strains by 16S rRNA and GyrB gene sequencing and were designated GM2 and GM5, respectively. Strains were characterized by their ability to inhibit growth of a number of phytopathogenic fungi. It was shown that GM5 strain inhibited growth of phytopathogenic fungi more effectively than GM2 strain. Both strains were capable of producing a number of hydrolytic enzymes as well as antimicrobial metabolites (ammonia and HCN). In addition, GM2 strain also produced siderophores. Four genes encoding antimicrobial peptides were identified in the genome of GM2 strain: ituC, bmyB, bacA and srfA. Genome of GM5 contained two genes encoding for antimicrobial peptides, srfA and fenD. Purified lipopeptide fraction from GM5 but not from GM2 strain was able to control Fusarium solani spread in the plate assay. Furthermore, Bacillus subtilis strain GM2 promoted growth of wheat but only GM5 strain was able to protect wheat seedlings from Fusarium oxysporum infection.
Colonization of Potato Rhizosphere by GFP-Tagged Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44 Shown on Large Sections of Roots Using Enrichment Sample Preparation and Confocal Laser Scanning Microscopy  [PDF]
Dorota Krzyzanowska,Michal Obuchowski,Mariusz Bikowski,Michal Rychlowski,Sylwia Jafra
Sensors , 2012, DOI: 10.3390/s121217608
Abstract: The ability to colonize the host plants’ rhizospheres is a crucial feature to study in the case of Plant Growth Promoting Rhizobacteria (PGPRs) with potential agricultural applications. In this work, we have created GFP-tagged derivatives of three candidate PGPRs: Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44. The presence of these strains in the rhizosphere of soil-grown potato (Solanum tuberosum L.) was detected with a classical fluorescence microscope and a confocal laser scanning microscope (CLSM). In this work, we have used a broad-field-of-view CLMS device, dedicated to in vivo analysis of macroscopic objects, equipped with an automated optical zoom system and tunable excitation and detection spectra. We show that features of this type of CLSM microscopes make them particularly well suited to study root colonization by microorganisms. To facilitate the detection of small and scattered bacterial populations, we have developed a fast and user-friendly enrichment method for root sample preparation. The described method, thanks to the in situ formation of mini-colonies, enables visualization of bacterial colonization sites on large root fragments. This approach can be easily modified to study colonization patterns of other fluorescently tagged strains. Additionally, dilution plating of the root extracts was performed to estimate the cell number of MB73/2, P482 and A44 in the rhizosphere of the inoculated plants.
Organic compatible solutes of halotolerant and halophilic microorganisms
Mary F Roberts
Aquatic Biosystems , 2005, DOI: 10.1186/1746-1448-1-5
Abstract: A dynamic and important property of cells is their ability to rapidly adapt to changes in external media, for example, increasing NaCl. To adjust to increased external NaCl, cells in all three kingdoms accumulate a variety of small molecules in the cytoplasm to counteract the external osmotic pressure. Inorganic cations (K+ and in some cells Na+) are often key players in osmotic balance and the osmotic response. However, the diverse collection of organic solutes that organisms accumulate in response to salt stress (also termed osmolytes) is particularly intriguing. Cataloging the occurrence of different molecules and understanding their biosynthesis and regulation by external osmotic pressure have been active areas of research. Studies show that the accumulation of solutes has another role along with osmotic balance. Many osmolytes have been shown to increase the stability of proteins. They appear to act as chemical chaperones in cells, and the mechanism of this stabilization can provide insights into protein folding. The thermostabilizing role of osmolytes has also been exploited for various biotechnology purposes. The aim of this review is an examination of the chemical and biological scope of osmolytes in a wide range of halotolerant and halophilic organisms with an overview of experiments that address why these types of solutes have been naturally selected for osmotic balance. Also included is a brief summary of the biotechnological uses of these organic osmolytes.The types of organic molecules used for osmotic balance include polyols and derivatives, sugars and derivatives, amino acids and derivatives, betaines, and ectoines and occasionally peptides suitably altered to remove charges [1]. As a general rule of thumb, bacteria and eukaryotes usually accumulate neutral compatible solutes whereas archaea prefer negatively charged solutes [2,3]. Interestingly, archaea tend to modify many of the same neutral or zwitterionic solutes accumulated by eukaryotes or bacte
Low Water Activity Induces the Production of Bioactive Metabolites in Halophilic and Halotolerant Fungi  [PDF]
Kristina Sepcic,Polona Zalar,Nina Gunde-Cimerman
Marine Drugs , 2011, DOI: 10.3390/md9010043
Abstract: The aim of the present study was to investigate indigenous fungal communities isolated from extreme environments (hypersaline waters of solar salterns and subglacial ice), for the production of metabolic compounds with selected biological activities: hemolysis, antibacterial, and acetylcholinesterase inhibition. In their natural habitats, the selected fungi are exposed to environmental extremes, and therefore the production of bioactive metabolites was tested under both standard growth conditions for mesophilic microorganisms, and at high NaCl and sugar concentrations and low growth temperatures. The results indicate that selected halotolerant and halophilic species synthesize specific bioactive metabolites under conditions that represent stress for non-adapted species. Furthermore, adaptation at the level of the chemical nature of the solute lowering the water activity of the medium was observed. Increased salt concentrations resulted in higher hemolytic activity, particularly within species dominating the salterns. The appearance of antibacterial potential under stress conditions was seen in the similar pattern of fungal species as for hemolysis. The active extracts exclusively affected the growth of the Gram-positive bacterium tested, Bacillus subtilis. None of the extracts tested showed inhibition of acetylcholinesterase activity.
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