scholarly journals Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

2021 ◽  
Author(s):  
Sameh H. Youseif ◽  
Fayrouz H. Abd El-Megeed ◽  
Ethan A. Humm ◽  
Maskit Maymon ◽  
Akram H. Mohamed ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Bacterial Community ◽  
Plant Growth ◽  
Soil Health ◽  
Natural Environments ◽  
Beneficial Effects ◽  
Wheat Rhizosphere ◽  
Culture Independent ◽  
Total Bacterial Community ◽  
Culture Dependent

Bacteria colonizing the rhizosphere, a narrow zone of soil surrounding the root system, are known to have beneficial effects in improving the growth and stress tolerance of plants. However, most bacteria in natural environments, especially those in rhizosphere soils, are recalcitrant to cultivation using traditional techniques, and thus their roles in soil health and plant growth remain unexplored.

scholarly journals The bacterial community of the lone star tick (Amblyomma americanum)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
L. Paulina Maldonado-Ruiz ◽  
Saraswoti Neupane ◽  
Yoonseong Park ◽  
Ludek Zurek
Keyword(s):  
Bacterial Community ◽  
Amblyomma Americanum ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Core Microbiome ◽  
Lone Star Tick ◽  
Animal Pathogens ◽  
Wide Range ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low. Methods We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks. Results We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin. Conclusions No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

scholarly journals A Culture-Independent and Culture-Dependent Study of the Bacterial Community from the Bedrock Soil Interface

2015 ◽  
Vol 05 (13) ◽  
pp. 842-857 ◽  
Author(s):  
Karen Olsson-Francis ◽  
Carl P. Boardman ◽  
Victoria K. Pearson ◽  
Paul F. Schofield ◽  
Anna Oliver ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Culture Independent ◽  
Soil Interface ◽  
Culture Dependent

Bacterial Communities Associated with Retail Alfalfa Sprouts

2008 ◽  
Vol 71 (1) ◽  
pp. 200-204 ◽  
Author(s):  
CINDY LOUI ◽  
GRIGOR GRIGORYAN ◽  
HAOHAO HUANG ◽  
LEE W. RILEY ◽  
SANGWEI LU
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Fresh Produce ◽  
Growth Conditions ◽  
Human Pathogens ◽  
Culture Independent ◽  
Foodborne Outbreaks ◽  
Total Bacterial Community ◽  
Alfalfa Sprouts ◽  
Alfalfa Sprout

Fresh produce, including salad, is increasingly implicated in foodborne outbreaks. Although studies have been carried out to detect specific human pathogens from fresh produce, the total bacterial community associated with fresh produce is poorly understood. In this study, we characterized the bacterial community associated with alfalfa sprouts, using a culture-independent method. Four retail-purchased alfalfa sprout samples were obtained from different producers, and the bacterial community associated with each sample was determined by 16S rDNA profiling. Our results indicate that alfalfa sprouts sampled in our study shared significant similarities in their bacterial communities. Proteobacteria was the dominant phylum detected from all alfalfa sprout samples, with Enterobacteriaceae, Oxalobacteraceae, Moraxellaceae, and Sphingomonadaceae as the most frequently detected families. These results indicate that growth conditions of alfalfa sprouts should be taken into consideration to prevent the proliferation of pathogenic proteobacteria such as Escherichia coli O157 and Salmonella.

scholarly journals Culture-dependent and culture-independent characterization of bacterial community diversity in different types of sandy lands: the case of Minqin County, China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yali Wei ◽  
Fang Wang ◽  
Jiangli Gao ◽  
Yaolong Huang ◽  
Wei Ren ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Biological Diversity ◽  
Plant Growth Promoting Rhizobacteria ◽  
Nutrient Content ◽  
Community Diversity ◽  
Sandy Land ◽  
Different Types ◽  
Culture Independent ◽  
Plant Growth Promoting ◽  
Culture Dependent

Abstract Background Minqin is suffering from a serious desertification, whereas the knowledge about its bacterial community is limited. Herein, based on Nitraria tangutorum and Haloxylon ammodendron from Minqin, the bacterial community diversities in fixed sandy land, semi-fixed sandy land and shifting sandy land were investigated by combining with culture-dependent and culture-independent methods. Results Minqin stressed with high salinity and poor nutrition is an oligotrophic environment. Bacterial community in Minqin was shaped primarily by the presence of host plants, whereas the type of plant and sandy land had no marked effect on those, which displayed a better survival in the rhizospheres of N. tangutorum and H. ammodendron. The dominant groups at phyla level were Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria and Candidate_division_TM7. The abundance of Firmicutes with ability of desiccation-tolerance was significantly higher in harsh environment, whereas Bacteroidetes were mainly distributed in areas with high nutrient content. The abundances of Proteobacteria and Bacteroidetes were relatively high in the rhizospheres of N. tangutorum and H. ammodendron, which had more plant-growth promoting rhizobacteria. A large number of Actinobacteria were detected, of which the most abundant genus was Streptomyces. The physicochemical factors related to the diversity and distribution of the bacterial community were comprehensively analyzed, such as pH, electrical conductivity, soil organic matter, C/N and sand, and the results indicated that Minqin was more suitable for the growth of N. tangutorum, which should be one of most important sand-fixing plants in Minqin. Conclusions The bacterial community diversities in different types of sandy lands of Minqin were comprehensively and systematically investigated by culture-dependent and culture-independent approaches, which has a great significance in maintaining/restoring biological diversity.

scholarly journals Bacterial Community Profiling of the Eastern Oyster (Crassostrea virginica): Comparison of Culture-Dependent and Culture-Independent Outcomes

2009 ◽  
Vol 28 (4) ◽  
pp. 827-835 ◽  
Author(s):  
Kenneth J. La Valley ◽  
Steve Jones ◽  
Marta Gomez-Chiarri ◽  
Joseph Dealteris ◽  
Michael Rice
Keyword(s):  
Bacterial Community ◽  
Crassostrea Virginica ◽  
Eastern Oyster ◽  
Community Profiling ◽  
Culture Independent ◽  
Culture Dependent

scholarly journals Incorporation of Multi-Strain Probiotic Preparation in a Traditional Brazilian Cheese: Effects on Microbiological Safety and Bacterial Community

2019 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Moysés Estevão de S. F. Pehrson ◽  
Viviane Lívia C. Souza ◽  
Ismael M. Mancilha
Keyword(s):  
Bacterial Community ◽  
Consumer Preference ◽  
Raw Milk ◽  
Microbiological Safety ◽  
Off Flavors ◽  
Culture Independent ◽  
Probiotic Preparation ◽  
Raw Milk Cheese ◽  
Sensory Profiles ◽  
Culture Dependent

Consumer preference for raw milk cheeses has increased in the past few years. This occurred partly due to their more diverse, enjoyable characteristics, but also due to claims that certain members of the autochthonous microbiota of milk can be beneficial to human health. These microorganisms can inhibit the growth of undesirable microorganisms and may also be used to establish a biogeographic identity for these products. The aim of this study was to assess the effect of a multi-strain probiotic preparation on the microbiological safety and composition of bacterial community of a traditional Brazilian raw milk cheese by means of culture dependent and methods and pyrosequencing. Probiotic enriched cheeses presented an average of 50% less sequence reads belonging to Enterobacteriaceae than control cheeses. Total and thermotolerant coliforms cell viability decreased throughout ripening in two seasons (summer and autumn), while in the winter the presence of these microorganisms was negligible since the beginning of ripening. Results obtained through culture dependent method did not correlate with culture independent method, which pointed to a relatively constant number of Enterobacteriaceae reads during ripening. Viable cells of coagulase positive Staphylococcus aureus stayed within legal limits in both groups of cheeses since the first day and decreased to zero at the 15th day in probiotic enriched cheeses. Salmonella sp. and Listeria sp. were absent in both control and probiotic groups. Our results support that enriching raw milk cheeses with probiotic bacteria or other bioprotective bacteria may help mitigate off flavors produced by Enterobacteriaceae and result in safer products by inhibiting the growth of these microorganisms, while maintaining the microbial diversity that may be beneficial to sensory profiles and health-promoting characteristics. We also showed that this traditional cheese, if made under right the conditions, can meet legal parameters in much less than 60 days of ripening.

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