Bacterial Community of Galchi-Baechu Kimchi Based on Culture-Dependent Investigations and Selection of Starter Candidates

AbstractThermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.

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

Parasites & Vectors ◽

10.1186/s13071-020-04550-z ◽

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.

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Selection of antibiotic resistance by metals in a riverine bacterial community

Chemosphere ◽

10.1016/j.chemosphere.2020.127936 ◽

2021 ◽

Vol 263 ◽

pp. 127936

Author(s):

Isabel Silva ◽

Marta Tacão ◽

Isabel Henriques

Keyword(s):

Antibiotic Resistance ◽

Bacterial Community ◽

Selection Of

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Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing

Journal of Marine Science and Engineering ◽

10.3390/jmse8080604 ◽

2020 ◽

Vol 8 (8) ◽

pp. 604

Author(s):

Meng-Qi Ye ◽

Guan-Jun Chen ◽

Zong-Jun Du

Keyword(s):

Antibiotic Resistance ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Antibiotic Resistance Genes ◽

Control Group ◽

Rrna Gene ◽

Metabolic Functions ◽

Culture Dependent

The effect of antibiotics on the diversity and functioning of indigenous microorganisms in the environment has attracted much attention. In this study, effects of exposure to six different antibiotics on the bacterial community, metabolic functions and antibiotic resistance genes (ARGs) in marine sediments during enrichment culturing were investigated. Classical culture-dependent method and high-throughput 16S rRNA gene sequencing method were both applied. In the culture-dependent analysis, the obtained 1549 isolates belonged to four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) and 155 genera. Proteobacteria and Firmicutes were the dominant phyla. The diversity and abundance of obtained bacteria after antibiotic processing exhibited different degrees of decrease. Enrichment culturing for different time could also affect the bacterial community composition. Some genera of bacteria were not isolated in the control group, but they could be isolated in the antibiotic-treated groups. In high-throughput 16S rRNA gene amplicon sequencing analyses, all the effective reads were clustered into 2822 OTUs at 97% similarity cutoff; they were annotated to 49 phyla, 103 class, 220 orders, 347 families, 624 genera and 1122 species. An alpha diversity analysis indicated that the community diversity and richness decreased under antibiotic exposure. The changes at the genus level were much more obvious. Only 48 genera of 129 genera were shared by all the samples. A total of 29 genera which were not detected in the initial control sample could be detected in at least one antibiotic-treated group. SIMPER analysis showed that OTU2543 and OTU1450 were the most common taxa to the dissimilarity of bacterial community between antibiotic-treated groups and the control group. OTU2034 and OUT2543 were the most contributive taxa to dissimilarity of groups incubating for different time. Metabolism was the predominant bacterial function. A total of 30 ARGs were detected in the samples. This study mainly focused on the changes of microbiota under the selective pressure of antibiotics for different time and the results demonstrated that the antibiotic could affect the bacterial diversity and richness in the marine ecosystem.

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Comparative analysis of bacterial community composition in bulk tank raw milk by culture-dependent and culture-independent methods using the viability dye propidium monoazide

Journal of Dairy Science ◽

10.3168/jds.2014-8340 ◽

2014 ◽

Vol 97 (11) ◽

pp. 6761-6776 ◽

Cited By ~ 18

Author(s):

Mareike Weber ◽

Janina Geißert ◽

Myriam Kruse ◽

André Lipski

Keyword(s):

Comparative Analysis ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Raw Milk ◽

Propidium Monoazide ◽

Culture Independent ◽

Bulk Tank ◽

Culture Dependent

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Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2012.01339.x ◽

2012 ◽

Vol 80 (3) ◽

pp. 696-708 ◽

Cited By ~ 31

Author(s):

Lucía Ferrando ◽

Jimena Fernández Mañay ◽

Ana Fernández Scavino

Keyword(s):

Oryza Sativa ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Endophytic Bacterial Community ◽

Culture Dependent

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Impact of Organic Acids Supplementation to Hardwood Spent Sulfite Liquor as Substrate for the Selection of Polyhydroxyalkanoates-Producing Organisms

Fermentation ◽

10.3390/fermentation4030058 ◽

2018 ◽

Vol 4 (3) ◽

pp. 58 ◽

Cited By ~ 3

Author(s):

Diogo Queirós ◽

Catarina Rangel ◽

Paulo Costa Lemos ◽

Simona Rossetti ◽

Luísa Seuanes Serafim

Keyword(s):

Bacterial Community ◽

Organic Acids ◽

Production Process ◽

Paper Industry ◽

Short Chain ◽

Fish Analysis ◽

Microbial Culture ◽

Mixed Microbial Culture ◽

Selection Of ◽

Spent Sulfite Liquor

The effectiveness of polyhydroxyalkanoates (PHAs) production process from a waste stream is determined by the selection of a suitable mixed microbial culture (MMC). In this work, a feedstock from the paper industry, hardwood spent sulfite liquor (HSSL), supplemented with short-chain organic acids (SCOAs) to simulate a fermented effluent, was used as substrate to enrich a MMC in PHA-storing microorganisms. A stable culture was quickly established, and during the accumulation step the selected MMC reached a maximum PHA content of 34.6% (3HB:3HV-76:24). The bacterial community was analyzed through FISH analysis. Bacteria belonging to the four main classes were identified: Betaproteobacteria (44.7 ± 2.7%), Alphaproteobacteria (13.6 ± 1.3%) and Gammaproteobacteria (2.40 ± 1.1%) and Bacteroidetes (9.20 ± 3.8%). Inside the Betaproteobacteria class, Acidovorax (71%) was the dominant genus.

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The Effect of Antibiotic Treatment on the Bacterial Community of the Brown Planthopper and Its Correlation with Rice Virulence

Agronomy ◽

10.3390/agronomy11112327 ◽

2021 ◽

Vol 11 (11) ◽

pp. 2327

Author(s):

Xiaorong Xu ◽

Liang Chen ◽

Hantao Zhou ◽

Ming Tang

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Brown Planthopper ◽

Nilaparvata Lugens ◽

Biological Processes ◽

Rna Seq ◽

Phenylpropanoid Biosynthesis ◽

And Control ◽

Selection Of

The prevention and control of planthoppers represent important issues for rice production. Current long-term control methods rely on pesticides, which raise concerns about environmental pollution. Recently, evidence has suggested that bacterial symbionts are important factors influencing the formation of Hemiptera insect biotypes and the selection of host plants for insects, which suggesting that targeting bacterial communities may be an effective alternative method for planthopper control. In this study, we perturbed the bacterial communities of the brown planthopper, Nilaparvata lugens, by feeding antibiotic-treated rice and used RNA-seq to examine the transcriptome of normal rice fed with perturbed BPHs by RNA-seq. Our results showed that the composition of the bacterial communities significantly changed after the perturbation, which was accompanied by changes in distinct biological processes of rice, especially the phenylpropanoid biosynthesis pathway, compared with the effect of the BPH feeding on rice without bacterial communities perturbation. Our work establishes a protocol for bacterial communities perturbation in BPH, demonstrating the link between bacterial community and the responses to BPH feeding and providing new insights into the interaction between BPH and rice.

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