scholarly journals Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1344
Author(s):  
Naima Lemjiber ◽  
Khalid Naamani ◽  
Annabelle Merieau ◽  
Abdelhi Dihazi ◽  
Nawal Zhar ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Genomic Islands ◽  
Rrna Gene ◽  
In Planta ◽  
Bacterial Strains ◽  
Bacillus Altitudinis ◽  
Genes Encoding ◽  
Bacillus Spp ◽  
Pear Trees ◽  
Rrna Gene Sequencing

Bacterial burn is one of the major diseases affecting pear trees worldwide, with serious impacts on producers and economy. In Morocco, several pear trees (Pyrus communis) have shown leaf burns since 2015. To characterize the causal agent of this disease, we isolated fourteen bacterial strains from different parts of symptomatic pear trees (leaves, shoots, fruits and flowers) that were tested in planta for their pathogenicity on Louise bonne and Williams cultivars. The results showed necrotic lesions with a significant severity range from 47.63 to 57.77% on leaves of the Louise bonne cultivar inoculated with isolate B10, while the other bacterial isolates did not induce any disease symptom. 16S rRNA gene sequencing did not allow robust taxonomic discrimination of the incriminated isolate. Thus, we conducted whole-genome sequencing (WGS) and phylogenetic analyzes based on gyrA, gyrB and cdaA gene sequences, indicating that this isolate belongs to the Bacillus altitudinis species. This taxonomic classification was further confirmed by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) analyzes compared to sixty-five Bacillus spp. type strains. The genome was mined for genes encoding carbohydrate-active enzymes (CAZymes) known to play a role in the vegetal tissue degradation. 177 candidates with functions that may support the in planta phytopathogenicity results were identified. To the best of our knowledge, this is the first data reporting B. altitudinis as agent of leaf burn in P. communis in Morocco. Our dataset will improve our knowledge on spread and pathogenicity of B. altitudinis genotypes that appears as emergent phytopathogenic agent, unveiling virulence factors and their genomic location (i.e., within genomic islands or the accessory genome) to induce trees disease.

scholarly journals Xylanolytic Psychotrophs From Andosolic Sedge Fens and Moss Heaths in Iceland

Fine Focus ◽  
2018 ◽  
Vol 4 (2) ◽  
pp. 171-186
Author(s):  
Olivia J. Rickman ◽  
M. Auður Sigurbjörnsdóttir ◽  
Oddur Vilhemsson
Keyword(s):  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Cold Environments ◽  
Specific Pcr ◽  
Xylanolytic Activity ◽  
Cold Active ◽  
Rrna Gene Sequencing ◽  
Stenotrophomonas Rhizophila

Nine xylanolytic bacterial strains were isolated from fen and heath soils in northern Iceland. They were found by 16S rRNA gene sequencing to belong to the genera Paenibacillus, Bacillus, Pseudomonas, and Stenotrophomonas. Using a simple, plate-based semiquantitative assay with azo-crosslinked xylan as the substrate, it was determined that although isolated from cold environments, most of the strains displayed greater xylanolytic activity under mesophilic conditions, with only the paenibacilli displaying markedly cold-active xylanolytic activity. Indeed, for one isolate, Paenibacillus castaneae OV2122, xylanolytic activity was only detected at 15°C and below under the conditions tested. Of the nine strains, Paenibacillus amylolyticus OV2121 displayed the greatest activity at 5°C. Glycohydrolase family-specific PCR indicated that the paenibacilli produced multiple xylanases of families 10 and 11, whereas a family 8 xylanase was detected in Pseudomonas kilonensis AL1515, and a family 11 xylanase in Stenotrophomonas rhizophila AL1610.

Mechanism of boron tolerance in soil bacteria

2010 ◽  
Vol 56 (1) ◽  
pp. 22-26 ◽  
Author(s):  
Iftikhar Ahmed ◽  
Toru Fujiwara
Keyword(s):  
Soil Bacteria ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Soil Samples ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Tolerance Mechanisms ◽  
Boron Tolerance ◽  
Rrna Gene Sequencing ◽  
Comparative Phylogenetic Analysis

Boron (B) is toxic to living cells at levels above a certain threshold. We isolated several B-tolerant bacterial strains from soil samples and studied them for possible mechanisms of B tolerance. 16S rRNA gene sequencing and comparative phylogenetic analysis demonstrated that the isolates belong to the following 6 genera: Arthrobacter , Rhodococcus , Lysinibacillus , Algoriphagus , Gracilibacillus , and Bacillus . These isolates exhibited B-tolerance levels of 80, 100, 150, 300, 450, and 450 mmol/L, respectively, whilst maintaining a significantly lower intracellular B concentration than in the medium. Statistical analysis showed a negative correlation between the protoplasmic B concentration and the degree of tolerance to a high external B concentration. The kinetic assays suggest that the high B efflux and (or) exclusion are the tolerance mechanisms against a high external B concentration in the isolated bacteria.

scholarly journals Effects of Probiotic Bacteria Lactobacillaceae on the Gut Microbiota in Children With Celiac Disease Autoimmunity: A Placebo-Controlled and Randomized Clinical Trial

2021 ◽  
Vol 8 ◽  
Author(s):  
Elin Oscarsson ◽  
Åsa Håkansson ◽  
Carin Andrén Aronsson ◽  
Göran Molin ◽  
Daniel Agardh
Keyword(s):  
Celiac Disease ◽  
Gut Microbiota ◽  
Tissue Transglutaminase ◽  
16S Rrna Gene Sequencing ◽  
Probiotic Bacteria ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Bacterial Strains ◽  
Probiotic Supplementation ◽  
Rrna Gene Sequencing

Disturbances of the gut microbiota may influence the development of various autoimmune diseases. This study investigated the effects of supplementations with the probiotic bacteria, Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2, on the microbial community in children with celiac disease autoimmunity (CDA). The study included 78 genetically predisposed children for celiac disease with elevated levels of tissue transglutaminase autoantibodies (tTGA) signaling for ongoing CDA. Among those children, 38 received a placebo and 40 received the probiotic supplement daily for 6 months. Fecal and plasma samples were collected at baseline and after 3 and 6 months, respectively. The bacterial community was investigated with 16S rRNA gene sequencing and terminal restriction fragment length polymorphism (T-RFLP), and tTGA levels were measured in radiobinding assays. In children that received probiotic supplementation, the relative abundance of Lactobacillaceae increased over time, while it remained unchanged in the placebo group. There was no overall correlation between tTGA levels and bacterial genus except for a positive correlation between Dialister and IgG-tTG in the probiotic group. The abundance of specific bacterial amplicon sequence variant (ASV:s) changed during the study in both groups, indicating that specific bacterial strains might be affected by probiotic supplementation.

scholarly journals Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder

2019 ◽  
Vol 8 (1) ◽  
pp. 5 ◽  
Author(s):  
Anshul Sharma ◽  
Jasmine Kaur ◽  
Sulhee Lee ◽  
Young-Seo Park
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gene Sequence ◽  
Random Amplified Polymorphic Dna ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Sequence Alignments ◽  
Gene Sequence Analysis ◽  
Rrna Gene Sequencing

The present work aimed at tracking intentionally inoculated lactic acid bacteria (LAB) strains in yogurt and probiotic powder. Leuconostoc (Leu.) mesenteroides (11251), Lactobacillus (L.) brevis (B151), and Lactobacillus plantarum (LB41K) strains were tracked in yogurt, and L. plantarum (LB41P) was tracked in a commercial probiotic powder. The yogurt was intentionally inoculated with the selected bacterial strains. Two types of yogurt with known and unknown bacterial pools were utilized. The standard 16S rRNA gene sequencing was used to evaluate the initial screening. The molecular typing tools, random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative gene sequence analysis of selected housekeeping loci were used to track the inoculated dubious strains. Out of 30 random selections for each inoculation, the developed method identified seven (11251), nine (B151), and five (LB41K) colonies in the yogurt. The validation was performed by identifying 7 colonies (LB41P) out of 30 in the probiotic powder. The DNA banding profiles and the gene sequence alignments led to the identification of the correct inoculated strains. Overall, the study summarizes the use of molecular tools to identify the deliberately inoculated LAB strains. In conclusion, the proposed polyphasic approach effectively tracked the intentionally inoculated strains: Leu. mesenteroides, L. brevis, and L. plantarum (LB41K) in yogurt and L. plantarum (LB41P) in probiotic powder. The study demonstrates how to track industrially relevant misused LAB strains in marketable food products.

scholarly journals Isolation and characterization of Bacillus spp. strains as potential probiotics for poultry

2019 ◽  
Vol 65 (10) ◽  
pp. 762-774 ◽  
Author(s):  
Alejandro Penaloza-Vazquez ◽  
Li Maria Ma ◽  
Patricia Rayas-Duarte
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Antibiotic Use ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Broiler Chicks ◽  
Long Term Stability ◽  
Isolation And Characterization ◽  
Sporulation Efficiency ◽  
Bacillus Spp ◽  
Rrna Gene Sequencing

Probiotics have become one of the potential solutions to global restriction on antibiotic use in food animal production. Bacillus species have been attractive probiotics partially due to their long-term stability during storage. In this study, 200 endospore-forming bacteria isolates were recovered from sourdough and the gastrointestinal tract (GIT) of young broiler chicks. Based on the production of a series of exoenzymes and survivability under stress conditions similar to those in the poultry GIT, 42 isolates were selected and identified by 16S rRNA gene sequencing. Seven strains with a profile of high enzymatic activities were further evaluated for sporulation efficiency, biofilm formation, compatibility among themselves (Bacillus spp.), and antagonistic effects against three bacteria pathogenic to poultry and humans: Enterococcus cecorum, Salmonella enterica, and Shiga-toxin-producing Escherichia coli. The strains from sourdough were identified as Bacillus amyloliquefaciens whereas the ones from the chicks’ GIT were Bacillus subtilis. These strains demonstrated remarkable potential as probiotics for poultry.

scholarly journals Animal fat and glycerol bioconversion to polyhydroxyalkanoate by produced water bacteria

e-Polymers ◽  
2020 ◽  
Vol 20 (1) ◽  
pp. 92-102
Author(s):  
Rafeya Sohail ◽  
Nazia Jamil ◽  
Iftikhar Ali ◽  
Sajida Munir
Keyword(s):  
Produced Water ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Ftir Analysis ◽  
Bacterial Strains ◽  
Future Studies ◽  
Animal Fat ◽  
Bacillus Tequilensis ◽  
Rrna Gene Sequencing

AbstractOil reservoirs contain large amounts of hydrocarbon rich produced water, trapped in underground channels. Focus of this study was isolation of PHA producers from produced water concomitant with optimization of production using animal fat and glycerol as carbon source. Bacterial strains were identified as Bacillus subtilis (PWA), Pseudomonas aeruginosa (PWC), Bacillus tequilensis (PWF), and Bacillus safensis (PWG) based on 16S rRNA gene sequencing. Similar amounts of PHA were obtained using animal fat and glycerol in comparison to glucose. After 24 h, high PHA production on glycerol and animal fat was shown by strain PWC (5.2 g/ L, 6.9 g/ L) and strain PWF (12.4 g/ L, 14.2 g/ L) among all test strains. FTIR analysis of PHA showed 3-hydroxybutyrate units. The capability to produce PHA in the strains was corroborated by PhaC synthase gene sequencing. Focus of future studies can be the use of lipids and glycerol on industrial scale.

scholarly journals Diversity of Nematode Microbial Antagonists from Algeria Shows Occurrence of Nematotoxic Trichoderma spp.

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 941
Author(s):  
Nawal Benttoumi ◽  
Mariantonietta Colagiero ◽  
Samira Sellami ◽  
Houda Boureghda ◽  
Abdelaziz Keddad ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Fusarium Spp ◽  
Trichoderma Spp ◽  
Bacillus Spp ◽  
Phytoparasitic Nematodes ◽  
Meloidogyne Spp ◽  
Rrna Gene Sequencing

Fungi and bacteria associated to phytoparasitic nematodes Globodera rostochiensis and Meloidogyne spp. in Algeria were identified and characterized. Trichoderma spp. showed the highest prevalence in the cysts of G. rostochiensis. A number of isolates were identified through PCR amplification and the sequencing of the internal transcribed spacer (ITS)1-2 and Rpb2 gene regions. The most represented species were T. harzianum and T. afroharzianum. The latter and T. hirsutum were reported for the first time in Algeria. Fusarium spp., including F. oxysporum and F. solani, comprised a second group of fungi found in cysts. Taxa associated to females of Meloidogyne spp. included T. harzianum, Fusarium spp. and other hyphomycetes. To assess the efficacy of Trichoderma spp., two assays were carried out in vitro with the culture filtrates of two T. afroharzianum and T. harzianum isolates, to check their toxicity versus the second stage juveniles of M. incognita. After 24–48 h exposure, a mortality significantly higher than the control was observed for both filtrates at 1% dilutions. The TRI genes involved in the production of trichothecenes were also amplified with the PCR from some Trichoderma spp. isolates and sequenced, supporting a putative role in nematode toxicity. Bacteria isolated from the cysts of G. rostochiensis included Brucella, Rhizobium, Stenotrophomonas and Bacillus spp., identified through 16S rRNA gene sequencing. The potential of the microbial isolates identified and their mechanisms of action are discussed, as part of a sustainable nematode management strategy.

Selection of Bacillus thuringiensis against Pathogenic Nematodes Attacking Pepper Tree

2020 ◽  
Vol 36 (3) ◽  
pp. 57-62
Author(s):  
Minh Vo Van ◽  
Tuan Vo Chau ◽  
My Pham Тhi ◽  
Ha Do Thu ◽  
Trang Le Vu Khanh
Keyword(s):  
Bacillus Thuringiensis ◽  
16S Rrna Gene Sequencing ◽  
Inhibitory Effect ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Nematode Eggs ◽  
Science And Education ◽  
Pepper Tree ◽  
Rrna Gene Sequencing ◽  
Meloidogyne Sp

Nine strains belonging to the Bacillus genus have been isolated from soil samples in Tien Phuoc district, Quang Nam province. They were capable of surviving at 42°C, and the Bl, B4, B7 and B9 strains could produce toxic crystals at this temperature. B7 had the most promising characteristics in terms of spore-forming ability. The result of the 16S rRNA gene sequencing showed that B7 belongs to the Bacillus thuringiensis species, which is known to effectively control root-knot Meloidogyne sp. nematodes attacking pepper tree. This study was aimed at evaluating the inhibitory effect of the bacterial isolate under study on root-knot eggs and juveniles. It was shown that the highest inhibitory activity of the cultures of the bacterial strains under study was observed at their concentration of 109cells/mL; in this case, up to 89.67% of nematode eggs and 100% of juveniles J2 were killed after 10 h of treatment. Bacillus thuringiensis, Meloidogyne sp., pepper tree, root-knot, nematodes We are grateful to the Danang University of Science and Education and Duy Tan University for supporting this study.

scholarly journals Isolation and characterisation of endocrine disruptor nonylphenol-using bacteria from South Africa

2017 ◽  
Vol 113 (5/6) ◽  
Author(s):  
Lehlohonolo B. Qhanya ◽  
Ntsane T. Mthakathi ◽  
Charlotte E. Boucher ◽  
Samson S. Mashele ◽  
Chrispian W. Theron ◽  
...  
Keyword(s):  
South Africa ◽  
Bacterial Species ◽  
Endocrine Disrupting Chemicals ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Mpumalanga Province ◽  
Synthetic Chemicals ◽  
Phylogenetic Identification ◽  
Rrna Gene Sequencing

Endocrine disrupting chemicals (EDCs) are synthetic chemicals that alter the function of endocrine systems in animals including humans. EDCs are considered priority pollutants and worldwide research is ongoing to develop bioremediation strategies to remove EDCs from the environment. An understanding of indigenous microorganisms is important to design efficient bioremediation strategies. However, much of the information available on EDCs has been generated from developed regions. Recent studies have revealed the presence of different EDCs in South African natural resources, but, to date, studies analysing the capabilities of microorganisms to utilise/degrade EDCs have not been reported from South Africa. Here, we report for the first time on the isolation and enrichment of six bacterial strains from six different soil samples collected from the Mpumalanga Province, which are capable of utilising EDC nonylphenol as a carbon source. Furthermore, we performed a preliminary characterisation of isolates concerning their phylogenetic identification and capabilities to degrade nonylphenol. Phylogenetic analysis using 16S rRNA gene sequencing revealed that four isolates belonged to Pseudomonas and the remaining two belonged to Enterobacteria and Stenotrophomonas. All six bacterial species showed degradation of nonylphenol in broth cultures, as HPLC analysis revealed 41–46% degradation of nonylphenol 12 h after addition. The results of this study represent the beginning of identification of microorganisms capable of degrading nonylphenol, and pave the way for further exploration of EDC-degrading microorganisms from South Africa.

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