scholarly journals Characterization and Evaluation of Bacillus siamensis Isolate for its Growth Promoting Potential in Tomato

2019 ◽  
Vol 65 (2) ◽  
pp. 42-50 ◽  
Author(s):  
Amanul Islam ◽  
Shahinur Kabir ◽  
Abul Khair
Keyword(s):  
Growth Promotion ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Growth Enhancement ◽  
Sequencing Data ◽  
Fresh Weight ◽  
Tomato Cultivars ◽  
Rrna Gene Sequencing

Abstract In quest of prospective rizospheric bacteria of agricultural importance, one of the isolates from bean (Lablab niger Medikus) was identified as Bacillus siamensis based on morphological, biochemical and 16S rRNA gene sequencing data. Study was carried out to evaluate growth promotion of two tomato cultivars, in vitro and in vivo. Experiments conducted for two consecutive years, following seed treatments revealed that the bacterial isolate increased plant height by 14.66‒15.68%, shoot fresh weight by 34.5‒65.09% and root fresh weight by 75.3‒92.48% over the non-treated control. The bacterial strain showed encouraging results for plant growth promotion in pot study and hence may be useful for the growth enhancement of tomato plant.

scholarly journals Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 140
Author(s):  
Farideh Ghadamgahi ◽  
Saeed Tarighi ◽  
Parissa Taheri ◽  
Ganapathi Varma Saripella ◽  
Alice Anzalone ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Genome Mining ◽  
16S Rrna Gene Sequencing ◽  
Control Agent ◽  
Rrna Gene ◽  
Clavibacter Michiganensis Subsp ◽  
Ability To Act

P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent.

In vitro and in vivo characterization and strain safety of Lactobacillus reuteri NCIMB 30253 for probiotic applications

2012 ◽  
Vol 58 (6) ◽  
pp. 776-787 ◽  
Author(s):  
Imran Sulemankhil ◽  
Mathieu Parent ◽  
Mitchell Lawrence Jones ◽  
Zhenqian Feng ◽  
Alain Labbé ◽  
...  
Keyword(s):  
Lactobacillus Reuteri ◽  
16S Rrna Gene Sequencing ◽  
Human Consumption ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Dose Study ◽  
Clinically Significant ◽  
Rrna Gene Sequencing

Lactobacillus reuteri NCIMB 30253 was shown to have potential as a probiotic by reducing the proinflammatory chemokine interleukin-8. Moreover, this strain was evaluated, by in vitro and in vivo techniques, for its safety for human consumption. The identity of the strain was investigated by metabolic profiling and 16S rRNA gene sequencing, and in vitro safety evaluations were performed by molecular and metabolic techniques. Genetic analysis was confirmed by assessing the minimum inhibitory concentration to a panel of antibiotics, showing that the strain was susceptible to 8 antibiotics tested. The ability of the strain to produce potentially harmful by-products and antimicrobial compounds was evaluated, showing that the strain does not produce biogenic amines and does not show bacteriocin activity or reuterin production. A 28-day repeated oral dose study was conducted in normal Sprague–Dawley rats to support the in vivo strain safety. Oral administration of the strain resulted in no changes in general condition and no clinically significant changes to biochemical and haematological markers of safety relative to vehicle control treated animals. This comprehensive assessment of safety of L. reuteri NCIMB 30253 supports the safety of the strain for use as a probiotic.

scholarly journals Antifouling activities of extracellular polymeric substances produced by marine bacteria associated with the gastropod (Babylonia sp.)

2018 ◽  
Vol 17 (2) ◽  
pp. 115-124 ◽  
Author(s):  
Nadarajan Viju ◽  
Nagarajan Ezhilraj ◽  
Chellamnadar Vaikundavasagom Sunjai Shankar ◽  
Stanislaus Mary Josephine Punitha ◽  
Sathianeson Satheesh
Keyword(s):  
Extracellular Polymeric Substances ◽  
16S Rrna Gene Sequencing ◽  
Bioactive Metabolites ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Ft Ir ◽  
Rrna Gene Sequencing

AbstractBacteria associated with surfaces have been frequently cited as a potential source for the isolation of bioactive metabolites. In this study, bacteria associated with marine gastropod, Babylonia sp. were isolated and screened for antibacterial activity against biofilm-forming bacteria. The antibiofilm and antifouling effect of the selected surface- associated bacterial strains were examined under in vitro and in vivo conditions. Results showed that the extracellular polymeric substances (EPS) of the bacterial strain CML associated with gastropod species considerably reduced the adhesion of biofilm-forming bacteria on glass coupons. Besides, the antifouling coat prepared by incorporating of this EPS into polyurethane varnish prevented the settlement of biofoulers on test substratum submerged in marine waters. The functional groups present in the EPS were analyzed using FT-IR. The bacterium responsible for the production of the bioactive EPS was identified as Bacillus subtilis subsp. by 16S rRNA gene sequencing. More detailed characterization of the identified bioactive EPS could lead to the isolation of a novel natural antifouling product.

scholarly journals The growth response of rice (Oryza sativa L. var. FARO 44) in vitro after inoculation with bacterial isolates from a typical ferruginous ultisol

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Musa Saheed Ibrahim ◽  
Beckley Ikhajiagbe
Keyword(s):  
16S Rrna ◽  
Bacillus Cereus ◽  
Proteus Mirabilis ◽  
Growth Response ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rice Seedlings ◽  
Rrna Gene Sequencing

Abstract Background Rice forms a significant portion of food consumed in most household worldwide. Rice production has been hampered by soil factors such as ferruginousity which has limited phosphorus availability; an important mineral component for the growth and yield of rice. The presence of phosphate-solubilizing bacteria (PSB) in soils has been reported to enhance phosphate availability. In view of this, the present study employed three bacteria species (BCAC2, EMBF2 and BCAF1) that were previously isolated and proved P solubilization capacities as inocula to investigate the growth response of rice germinants in an in vitro setup. The bacteria isolates were first identified using 16S rRNA gene sequencing and then applied as inoculum. The inolula were prepared in three concentrations (10, 7.5 and 5.0 ml) following McFarland standard. Viable rice (var. FARO 44) seeds were sown in petri dishes and then inoculated with the three inocula at the different concentrations. The setup was studied for 28 days. Results 16S rRNA gene sequencing identified the isolates as: isolate BCAC2= Bacillus cereus strain GGBSU-1, isolate BCAF1= Proteus mirabilis strain TL14-1 and isolate EMBF2= Klebsiella variicola strain AUH-KAM-9. Significant improvement in rice germination, morphology, physiology and biomass parameters in the bacteria-inoculated setups was observed compared to the control. Germination percentage after 4 days was 100 % in the inoculated rice germinants compared to 65% in the control (NiS). Similarly, inoculation with the test isolates enhanced water-use efficiency by over 40%. The rice seedlings inoculated with Bacillus cereus strain GGBSU-1 (BiS) showed no signs of chlorosis and necrosis throughout the study period as against those inoculated with Proteus mirabilis strain TL14-1 (PiS) and Klebsiella variicola strain AUH-KAM-9 (KiS). Significant increase in chlorophyll-a, chlorophyll-b and alpha amylase was observed in the rice seedlings inoculated with BiS as against the NiS. Conclusion Inoculating rice seeds with Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 in an in vitro media significantly improved growth parameters of the test plant. Bacillus cereus strain GGBSU-1 showed higher efficiency due to a more improved growth properties observed.

scholarly journals Live Bacillus subtilis natto Promotes Rumen Fermentation by Modulating Rumen Microbiota In Vitro

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1519
Author(s):  
Meinan Chang ◽  
Fengtao Ma ◽  
Jingya Wei ◽  
Junhao Liu ◽  
Xuemei Nan ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
Rumen Fluid ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rumen Fermentation ◽  
Rrna Gene ◽  
Bacillus Subtilis Natto ◽  
Rrna Gene Sequencing

Previous studies have shown that Bacillus subtilis natto affects rumen fermentation and rumen microbial community structure, which are limited to detect a few microbial abundances using traditional methods. However, the regulation of B. subtilis natto on rumen microorganisms and the mechanisms of microbiota that affect rumen fermentation is still unclear. This study explored the effects of live and autoclaved B. subtilis natto on ruminal microbial composition and diversity in vitro using 16S rRNA gene sequencing and the underlying mechanisms. Rumen fluid was collected, allocated to thirty-six bottles, and divided into three treatments: CTR, blank control group without B. subtilis natto; LBS, CTR with 109 cfu of live B. subtilis natto; and ABS, CTR with 109 cfu of autoclaved B. subtilis natto. The rumen fluid was collected after 0, 6, 12, and 24 h of fermentation, and pH, ammonia nitrogen (NH3-N), microbial protein (MCP), and volatile fatty acids (VFAs) were determined. The diversity and composition of rumen microbiota were assessed by 16S rRNA gene sequencing. The results revealed LBS affected the concentrations of NH3-N, MCP, and VFAs (p < 0.05), especially after 12 h, which might be attributed to changes in 18 genera. Whereas ABS only enhanced pH and NH3-N concentration compared with the CTR group (p < 0.05), which might be associated with changes in six genera. Supplementation with live B. subtilis natto improved ruminal NH3-N and propionate concentrations, indicating that live bacteria were better than autoclaved ones. This study advances our understanding of B. subtilis natto in promoting ruminal fermentation, providing a new perspective for the precise utilization of B. subtilis natto in dairy rations.

scholarly journals Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments

2019 ◽  
Author(s):  
Guangyi Su ◽  
Jakob Zopfi ◽  
Haoyi Yao ◽  
Lea Steinle ◽  
Helge Niemann ◽  
...  
Keyword(s):  
Lake Sediments ◽  
16S Rrna Gene Sequencing ◽  
Electron Acceptors ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Sequencing Data ◽  
Oxidation Of Methane ◽  
Freshwater Habitats ◽  
Rrna Gene Sequencing

AbstractAnaerobic oxidation of methane (AOM) by methanotrophic archaea is an important sink of this greenhouse gas in marine sediments. However, evidence for AOM in freshwater habitats is rare, and little is known about the pathways, electron acceptors and microbes involved. Here, we show that AOM occurs in anoxic sediments of a lake in southern Switzerland (Lake Cadagno). Combined AOM-rate and 16S rRNA gene-sequencing data suggest thatCandidatusMethanoperedens archaea are responsible for the observed methane oxidation. Members of the Methanoperedenaceae family were previously reported to conduct nitrate- or iron/manganese-dependent AOM. However, we demonstrate for the first time that the methanotrophic archaea do not necessarily rely upon these oxidants as terminal electron acceptors directly, but mainly perform canonical sulfate-dependent AOM, which under sulfate-starved conditions can be supported by metal (Mn, Fe) oxides through oxidation of reduced sulfur species to sulfate. The correspondence of high abundances of Desulfobulbaceae andCandidatusMethanoperedens at the same sediment depth confirm the interdependence of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria. The relatively high abundance and widespread distribution ofCandidatusMethanoperedens in lake sediments highlight their potentially important role in mitigating methane emissions from terrestrial freshwater environments to the atmosphere, analogous to ANME-1, -2 and -3 in marine settings.

scholarly journals Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

2021 ◽  
Vol 12 ◽  
Author(s):  
Marc Crampon ◽  
Coralie Soulier ◽  
Pauline Sidoli ◽  
Jennifer Hellal ◽  
Catherine Joulian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Treated Wastewater ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Rrna Gene Sequencing

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

scholarly journals Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding

2021 ◽  
Vol 11 ◽  
Author(s):  
Yujie Hou ◽  
Xiong Zhang ◽  
Qinyan Zhou ◽  
Wenxing Hong ◽  
Ying Wang
Keyword(s):  
16S Rrna ◽  
Penaeus Monodon ◽  
Poor Performance ◽  
16S Rrna Gene Sequencing ◽  
Reference Database ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Significant Generalization ◽  
Rrna Gene Sequencing ◽  
Almost All

Matching 16S rRNA gene sequencing data to a metabolic reference database is a meaningful way to predict the metabolic function of bacteria and archaea, bringing greater insight to the working of the microbial community. However, some operational taxonomy units (OTUs) cannot be functionally profiled, especially for microbial communities from non-human samples cultured in defective media. Therefore, we herein report the development of Hierarchical micrObial functions Prediction by graph aggregated Embedding (HOPE), which utilizes co-occurring patterns and nucleotide sequences to predict microbial functions. HOPE integrates topological structures of microbial co-occurrence networks with k-mer compositions of OTU sequences and embeds them into a lower-dimensional continuous latent space, while maximally preserving topological relationships among OTUs. The high imbalance among KEGG Orthology (KO) functions of microbes is recognized in our framework that usually yields poor performance. A hierarchical multitask learning module is used in HOPE to alleviate the challenge brought by the long-tailed distribution among classes. To test the performance of HOPE, we compare it with HOPE-one, HOPE-seq, and GraphSAGE, respectively, in three microbial metagenomic 16s rRNA sequencing datasets, including abalone gut, human gut, and gut of Penaeus monodon. Experiments demonstrate that HOPE outperforms baselines on almost all indexes in all experiments. Furthermore, HOPE reveals significant generalization ability. HOPE's basic idea is suitable for other related scenarios, such as the prediction of gene function based on gene co-expression networks. The source code of HOPE is freely available at https://github.com/adrift00/HOPE.

scholarly journals Findings from the microbiota of tooth apical periodontitis and the search for pathogen forgranulomatous inflammation

2021 ◽  
Author(s):  
Yuanyuan Wang ◽  
Hao Xu ◽  
Minghui Wei ◽  
Yuhong Wang ◽  
Wenzhe Wang ◽  
...  
Keyword(s):  
Granulomatous Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Apical Periodontitis ◽  
Rrna Gene ◽  
Normal Microbiota ◽  
Rrna Gene Sequencing ◽  
Neisseria Subflava ◽  
Foot Pad

Abstract BackgroundOrofacial granulomatosis (OFG) is a granulomatous inflammation (GI) disease in maxillofacial region, the underlying cause of it remains unknown. Our previous study demonstrated that tooth apical periodontitis (AP) plays a significant role in the pathogenesis of OFG, we aimed here to characterize the AP bacterial signatures of OFG patients, and identify bacteria that may be important pathogens capable of inducing OFG.ResultsThe composition of AP microbiota in OFG cases and common AP controls was compared using 16S rRNA gene sequencing, the results showed a specific AP microbiota signature in OFG patients, characterized by domination of phyla Firmicutes and Proteobacteria , notably members of Streptococcus, Lactobacillus and Neisseria. To assess the pathogenicity of the potential pathogens in OFG, we isolated and successfully in vitro cultured Streptococcus, Lactobacillus casei, Neisseria subflava, Veillonella parvula and Actinomyces from OFG patients, and injected the clinical isolates into mice respectively. Ultimately, foot pad injection with N. subflava elicited granulomatous inflammation, and the virulence of N. subflava was verified based on Koch’s postulates.ConclusionsOur findings confirmed the role of bacteria in OFG, and first suggested that the component of the host normal microbiota, N. subflava is likely a pathogen for GI.

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