Bacterial diversity of soil samples from the western Himalayas, India

2009 ◽  
Vol 55 (5) ◽  
pp. 564-577 ◽  
Author(s):  
Pooja Gangwar ◽  
Syed Imteyaz Alam ◽  
Sunita Bansod ◽  
Lokendra Singh
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Species ◽  
Hydrolytic Enzymes ◽  
Soil Samples ◽  
Rrna Gene ◽  
Organic Carbon Content ◽  
Western Himalayas ◽  
Bacterial Strains ◽  
Culture Independent ◽  
The One

High-altitude cold habitats of the Himalayas are little explored with respect to bacterial diversity. Diverse bacterial species and phylotypes obtained by culture-dependent and culture-independent approaches are reported here. Phylogenetic analysis and modulation of bacterial diversity with altitude and available organic carbon content are also described. Psychrophilic and psychrotolerant bacteria dominated the Himalayan habitats, accounting for 60% of the cultivated strains. Isolates produced one or more (up to five) hydrolytic enzymes, lipase being the one secreted by most strains (62%). Partial 16S rRNA gene sequences were obtained for 99 bacterial strains and 74 clones obtained from soil samples from the western Himalayas. Forty-five percent of cultured bacterial strains belonged to the Proteobacteria group with 39% belonging to γ-Proteobacteria. Firmicutes was the second most abundant class with 32% of the total isolates followed by Actinobacteria (16%) and Bacteroidetes (6%). Most of the strains belonged to the genus Bacillus (30%) followed by Pseudomonas (24%) and Arthrobacter (12%). In culture-independent studies, phylotypes belonging to the Proteobacteria were dominant (73%) with the majority being β-Proteobacteria (31%). The bacterial diversity exhibited an altitude gradient with a gradual decline in the number of genera with increase in altitude. The isolates exhibited close phylogenetic affinities to bacteria from other cold habitats.

DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

2018 ◽  
Vol 41 (3) ◽  
pp. 255-264 ◽  
Author(s):  
J. Abraham Pérez-Pérez ◽  
David Espinosa-Victoria ◽  
Hilda V. Silva-Rojas ◽  
Lucía López-Reyes
Keyword(s):  
Bacterial Diversity ◽  
Digestive Tract ◽  
Bacterial Species ◽  
Brain Heart Infusion ◽  
Rrna Gene ◽  
Eisenia Foetida ◽  
Bacterial Isolates ◽  
Bacterial Microbiota ◽  
Decomposition Of Organic Matter ◽  
Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

scholarly journals Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Shinya Kageyama ◽  
Mikari Asakawa ◽  
Toru Takeshita ◽  
Yukari Ihara ◽  
Shunsuke Kanno ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Bacterial Diversity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Bacterial Composition ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

Molecular bacterial diversity and bioburden of commercial airliner cabin air

2007 ◽  
Vol 53 (11) ◽  
pp. 1259-1271 ◽  
Author(s):  
Myron T. La Duc ◽  
Tara Stuecker ◽  
Kasthuri Venkateswaran
Keyword(s):  
Bacterial Diversity ◽  
Rrna Gene ◽  
Human Respiratory Tract ◽  
Atp Assay ◽  
Gram Positive Bacteria ◽  
Air Impingement ◽  
Culture Independent ◽  
Bacterial Enumeration ◽  
Gradual Accumulation ◽  
Opportunistic Pathogenic

Culture-independent, biomarker-targeted bacterial enumeration and identification strategies were employed to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Samples from each of 4 flights on 2 commercial carriers were collected via air-impingement. The total viable microbial population ranged from below detection limits to 4.1 × 106cells/m3of air, as assessed by the ATP assay. A gradual accumulation of microbes was observed from the time of passenger boarding through mid-flight, followed by a sharp decline in bacterial abundance and viability from the initiation of descent through landing. Representatives of the α-, β-, and γ-Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Neisseria meningitidis rRNA gene sequences were retrieved in great abundance from Airline A followed by Streptococcus oralis/mitis sequences. Pseudomonas synxantha sequences dominated Airline B clone libraries, followed by those of N. meningitidis and S. oralis/mitis. The cabin air samples examined herein housed low bacterial diversity and were often dominated by a particular subset of bacteria: opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity.

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 Genomic Techniques Used to Investigate the Human Gut Microbiota

2021 ◽  
Author(s):  
Akhlash P. Singh
Keyword(s):  
Gut Microbiota ◽  
High Throughput ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Human Gut ◽  
Culture Independent ◽  
Microbe Interactions ◽  
Next Generation Sequencing Ngs ◽  
Lifestyle Related Diseases ◽  
Gut Microbial Community

The human gut is the complex microbial ecosystem comprises more than 100 trillion microbes also known as microbiota. The gut microbiota does not only include about 400–500 types of bacterial strains, but it also contains archaea, bacteriophage, fungi, and protozoa species. In order to complete the characterization of the gut microbial community, we need the help of many culture-dependent and culture-independent genomic technologies. Recently, next-generation sequencing (NGS), mediated metagenomics that rely on 16S rRNA gene amplification, and whole-genome sequencing (WGS) have provided us deep knowledge related to important interactions such as host-microbiota and microbe-microbe interactions under various perturbation inside the gut. But, we still lack complete knowledge related to unique gene products encoded by gut meta-genome. Hence, it required the application of high-throughput “omics-based” methods to support metagenomics. Currently, a combination of high-throughput culturing and microfluidics assays is providing a new method to characterize non-amenable bacterial strains from the gut environment. The recent additions of artificial intelligence and deep learning to the area of microbiome studies have enhanced the capability of identification of thousand microbes simultaneously. Given above, it is necessary to apply new genome editing tools that can be used to design the personalized microflora which can be used to cure lifestyle-related diseases.

scholarly journals The 16S rRNA Analysis and Enzyme Screening of Bacillus from Rhizosphere Soil of Lombok Island

2021 ◽  
Vol 26 (4) ◽  
pp. 582-590
Author(s):  
Tri Ratna Sulistiyani ◽  
Mia Kusmiati ◽  
Gita Azizah Putri
Keyword(s):  
16S Rrna ◽  
Enzyme Activities ◽  
Hydrolytic Enzyme ◽  
Hydrolytic Enzymes ◽  
Distinct Species ◽  
Soil Samples ◽  
Rrna Gene ◽  
Bacillus Sp ◽  
16S Rrna Analysis ◽  
Lombok Island

Bacillus are commonly found in nature, especially in soil and food. It has the ability to produce bioactive compounds as well as the enzyme. This study was aimed to isolate, identify, and screen their enzyme activities. Four soil samples from Mandalika, Lombok Island, West Nusa Tenggara (NTB), were used for isolation. Bacillus was isolated using the heat-shock method and characterized through Gram staining, endospore staining, and morphological phenotype. Bacillus identification was conducted based on 16S rRNA gene sequence. The hydrolytic enzyme activities were checked qualitatively using selective media, and the enzyme tested including amylase, galactosidase, lipase, protease, and cellulase. As many as twenty-two bacteria isolates were obtained from four soil samples and represented 15 distinct species. The member of bacteria genera successfully identified, consisted of Bacillus sp., Brevibacillus sp., and Fictibacillus sp. Bacillus sp. was the most isolated. Some of the isolated bacteria have the ability to produce lipase, protease, and cellulase that potential to be used in biotechnology processes.   Keywords: Bacillus, hydrolytic enzymes, identification, screening

scholarly journals Identification of a Novel Brevibacillus laterosporus Strain With Insecticidal Activity Against Aedes albopictus Larvae

2021 ◽  
Vol 12 ◽  
Author(s):  
Giulia Barbieri ◽  
Carolina Ferrari ◽  
Stefania Mamberti ◽  
Paolo Gabrieli ◽  
Michele Castelli ◽  
...  
Keyword(s):  
Aedes Albopictus ◽  
Mosquito Control ◽  
Control Strategies ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Morphological Characterization ◽  
Soil Samples ◽  
Rrna Gene ◽  
Breeding Sites ◽  
Brevibacillus Laterosporus

Bacterial species able to produce proteins that are toxic against insects have been discovered at the beginning of the last century. However, up to date only two of them have been used as pesticides in mosquito control strategies targeting larval breeding sites: Bacillus thuringensis var. israelensis and Lysinibacillus sphaericus. Aiming to expand the arsenal of biopesticides, bacterial cultures from 44 soil samples were assayed for their ability to kill larvae of Aedes albopictus. A method to select, grow and test the larvicidal capability of spore-forming bacteria from each soil sample was developed. This allowed identifying 13 soil samples containing strains capable of killing Ae. albopictus larvae. Among the active isolates, one strain with high toxicity was identified as Brevibacillus laterosporus by 16S rRNA gene sequencing and by morphological characterization using transmission electron microscopy. The new isolate showed a larvicidal activity significantly higher than the B. laterosporus LMG 15441 reference strain. Its genome was phylogenomically characterized and compared to the available Brevibacillus genomes. Thus, the new isolate can be considered as a candidate adjuvant to biopesticides formulations that would help preventing the insurgence of resistance.

Assessment of zinc solubilization potential of zinc-resistant Pseudomonas oleovorans strain ZSB13 isolated from contaminated soil

2023 ◽  
Vol 83 ◽  
Author(s):  
H. F. Rehman ◽  
A. Ashraf ◽  
S. Muzammil ◽  
M. H. Siddique ◽  
T. Ali
Keyword(s):  
Contaminated Soil ◽  
Bacterial Strain ◽  
Bacterial Species ◽  
Resistant Bacteria ◽  
Zn Deficiency ◽  
Rrna Gene ◽  
Growth Enhancement ◽  
Pseudomonas Oleovorans ◽  
Human Beings ◽  
Bacterial Strains

Abstract Zinc is an essential micronutrient that is required for optimum plant growth. It is present in soil in insoluble forms. Bacterial solubilization of soil unavailable form of Zn into available form, is an emerging approach to alleviate the Zn deficiency for plants and human beings. Zinc solubilizing bacteria (ZSB) could be a substitute for chemical Zn fertilizer. The present study aimed to isolate and characterize bacterial species from the contaminated soil and evaluate their Zn solubilizing potential. Zn resistant bacteria were isolated and evaluated for their MIC against Zn. Among the 13 isolated bacterial strains ZSB13 showed maximum MIC value upto 30mM/L. The bacterial strain with the highest resistance against Zn was selected for further analysis. Molecular characterization of ZSB13 was performed by 16S rRNA gene amplification which confirmed it as Pseudomonas oleovorans. Zn solubilization was determined through plate assay and broth medium. Four insoluble salts (zinc oxide (ZnO), zinc carbonate (ZnCO3), zinc sulphite (ZnS) and zinc phosphate (Zn3(PO4)2) were used for solubilization assay. Our results shows 11 mm clear halo zone on agar plates amended with ZnO. Likewise, ZSB13 showed significant release of Zn in broth amended with ZnCO3 (17 and 16.8 ppm) and ZnO (18.2 ppm). Furthermore, Zn resistance genes czcD was also enriched in ZSB13. In our study, bacterial strain comprising Zn solubilization potential has been isolated that could be further used for the growth enhancement of crops.

262 Reproductive Microbiomes as Predicators of Fertility in Beef Cattle

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 135-136
Author(s):  
Rebecca K Poole
Keyword(s):  
Beef Cattle ◽  
Pathogenic Bacteria ◽  
Reproductive Tract ◽  
Bacterial Species ◽  
Uterine Disease ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Sequencing Studies ◽  
Culture Independent ◽  
Genus Lactobacillus

Abstract Over the past decade, a multitude of research has sought to understand the complexity and role of the reproductive microbiome as it pertains to fertility. Previously, the reproductive microbiome was evaluated using culture-dependent methods; however, recent advancements in culture-independent, 16S rRNA gene amplicon community sequencing have vastly expanded our understanding of the reproductive tract microbiome. Early sequencing studies sought to compare the vaginal microbiome of cattle to the vaginal microbiome of healthy women, which predominantly consists of bacteria in the genus Lactobacillus and believed to be an indicator of fertility. In the vagina of beef cattle, however, there are incredibly low abundances of Lactobacillus and a greater diversity of bacterial species present. Beta-diversity, which examine differences in bacterial communities between samples, does not appear to differ in the vagina between unbred, open, or pregnant cattle. In postpartum beef cattle just prior to breeding, there are greater levels of diversity and increased bacterial species richness in the vagina compared to the uterus. Research on bacterial species within the uterus have primarily focused on pathogenic bacteria in postpartum cattle diagnosed with uterine disease. Fewer studies have investigated uterine bacterial species in presumed healthy postpartum beef cattle and the subsequent effects on fertility outcomes (e.g., pregnant vs. open at day 30). When evaluating the uterine microbiome during an industry standard estrus synchronization protocol, bacterial community abundance and diversity reduce over time regardless of resulting fertility outcomes. The greatest difference in uterine bacterial abundance between resulting pregnant and non-pregnant cattle appears to occur just prior to breeding. Numerous mechanisms could be contributing to the fluctuations in the uterine microbiome in beef cattle including circulating hormone concentrations or local immunoregulation. This presentation will focus on recent research investigating potential mechanisms that may alter the reproductive microbiome and ultimately impact fertility.

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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