scholarly journals Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria

2004 ◽  
Vol 70 (7) ◽  
pp. 4363-4366 ◽  
Author(s):  
Liesbeth Schoenborn ◽  
Penelope S. Yates ◽  
Bronwyn E. Grinton ◽  
Philip Hugenholtz ◽  
Peter H. Janssen
Keyword(s):  
Soil Bacteria ◽  
Serial Dilution ◽  
Bacterial Phyla ◽  
Pasture Soil ◽  
Solid Media ◽  
Dilution Culture ◽  
Serial Dilution Culture ◽  
Bacterial Lineages

ABSTRACT Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of Acidobacteria, Verrucomicrobia, and Gemmatimonadetes and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media. We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.

scholarly journals Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria

2003 ◽  
Vol 69 (12) ◽  
pp. 7210-7215 ◽  
Author(s):  
Shayne J. Joseph ◽  
Philip Hugenholtz ◽  
Parveen Sangwan ◽  
Catherine A. Osborne ◽  
Peter H. Janssen
Keyword(s):  
Soil Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phylogenetic Groups ◽  
Bacterial Phyla ◽  
New Family ◽  
Solid Media ◽  
Family Level ◽  
Petri Dishes ◽  
High Degree

ABSTRACT Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from soil by using simple solid media in petri dishes. These isolates were assigned to 60 family-level groupings in nine bacterial phyla on the basis of a comparative analysis of their 16S rRNA genes. Ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied bacterial classes and phyla. They included members of subdivisions 1, 2, 3, and 4 of the phylum Acidobacteria, subdivision 3 of the phylum Verrucomicrobia, subdivision 1 of the phylum Gemmatimonadetes, and subclasses Acidimicrobidae and Rubrobacteridae of the phylum Actinobacteria. In addition, members of 10 new family-level groupings of subclass Actinobacteridae of the phylum Actinobacteria and classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were obtained. The high degree of phylogenetic novelty and the number of isolates affiliated with so-called unculturable groups show that simple cultivation methods can still be developed further to obtain laboratory cultures of many phylogenetically novel soil bacteria.

scholarly journals Inter-laboratory validation of the serial dilution culture—most probable number method for enumerating viable phytoplankton

2018 ◽  
Vol 31 (1) ◽  
pp. 491-503
Author(s):  
Hugh L. MacIntyre ◽  
John J. Cullen ◽  
Shannah Rastin ◽  
Magdalena Waclawik ◽  
Kimberly J. Franklin ◽  
...  
Keyword(s):  
Serial Dilution ◽  
Most Probable Number ◽  
Probable Number ◽  
Dilution Culture ◽  
Serial Dilution Culture

scholarly journals Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Amir Erez ◽  
Jaime G Lopez ◽  
Benjamin G Weiner ◽  
Yigal Meir ◽  
Ned S Wingreen
Keyword(s):  
Resource Competition ◽  
Nutrient Supply ◽  
Serial Dilution ◽  
Community Diversity ◽  
Ecosystem Stability ◽  
Early Bird ◽  
Trade Offs ◽  
Dilution Culture ◽  
Serial Dilution Culture ◽  
High Diversity

Microbial communities feature an immense diversity of species and this diversity is linked to outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, community diversity shifts due to an 'early-bird' effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.

Evaluation of the comparability of the results of determining drug resistance in staphylococci by the method of diffusion in agar and systems MS-2, MiC-2000

1993 ◽  
Vol 74 (3) ◽  
pp. 233-235
Author(s):  
L. T. Musina ◽  
I. A. Semina ◽  
K. K. Gladkova ◽  
N. F. Makarova
Keyword(s):  
Drug Resistance ◽  
Serial Dilution ◽  
Disk Diffusion ◽  
Diffusion Method ◽  
Laboratory Practice ◽  
Traditional Methods ◽  
Disk Diffusion Method ◽  
Solid Media

In everyday laboratory practice, the method of serial dilution in liquid or solid media and the disk diffusion method are usually used to determine the sensitivity of a microbe to antibiotics. Unfortunately, traditional methods are laborious and can produce results within 18-24 hours after isolation of the pathogen.

scholarly journals Legionella antimicrobial sensitivity testing: comparison of microbroth dilution with BCYE and LASARUS solid media

2020 ◽  
Author(s):  
Edward Portal ◽  
Kirsty Sands ◽  
Artjoms Portnojs ◽  
Victoria J Chalker ◽  
Owen B Spiller
Keyword(s):  
Legionella Pneumophila ◽  
Solid Medium ◽  
Bacterial Species ◽  
Serial Dilution ◽  
Sensitivity Testing ◽  
Antimicrobial Sensitivity ◽  
Solid Media ◽  
Agar Dilution ◽  
Microbroth Dilution ◽  
Serial Dilutions

Abstract Objectives There is a lack of international unification for AST methodology for Legionella pneumophila. Current literature contains multiple possible methods and this study compares each of them to determine methodological concordance. Methods Antibiotic susceptibility of 50 L. pneumophila strains was determined using broth microdilution (BMD), serial antimicrobial dilution in traditional buffered charcoal yeast extract (BCYE) agar (as well as comparison with gradient strip overlay on BCYE) and in a novel charcoal-free agar (LASARUS) for rifampicin, azithromycin, levofloxacin and doxycycline. Results The deviation of tested media relative to BMD highlighted the overall similarity of BMD and LASARUS across all antimicrobials tested (within one serial dilution). BCYE agar dilution showed an increased MIC of up to five serial dilutions relative to BMD, while MICs by gradient strip overlay on BCYE were elevated by two to three serial dilutions, with the exception of doxycycline, which was decreased by three serial dilutions relative to MIC values determined by BMD. The MIC range for azithromycin was wider than for other antimicrobials tested and found to be caused by the presence or absence of the lpeAB gene. Conclusions BMD-based antimicrobial susceptibility testing (AST) methodology should be the internationally agreed gold standard for Legionella spp. AST, as is common for other bacterial species. Traditional BCYE gave significantly elevated MIC results and its use should be discontinued for Legionella spp., while MIC determination using LASARUS solid medium gave results concordant (within one serial dilution) with BMD for all antimicrobials tested. To the best of our knowledge, this study is the first to identify the lpeAB gene in UK isolates.

scholarly journals Effective soil extraction method for cultivating previously uncultured soil bacteria

2018 ◽  
Author(s):  
Tuan Manh Nguyen ◽  
Chan Seo ◽  
Moongi Ji ◽  
Man-Jeong Paik ◽  
Seung-Woon Myung ◽  
...  
Keyword(s):  
Soil Bacteria ◽  
Soil Extract ◽  
Low Molecular Weight ◽  
Critical Problem ◽  
Soil Extraction ◽  
Soil Extracts ◽  
Single Cell Sequencing ◽  
Uncultured Bacteria ◽  
Solid Media ◽  
Microbial Strains

ABSTRACTHere, a new medium named as intensive soil extract medium (ISEM) based on new soil extract (NSE) using 80% ethanol was used to efficiently isolate previously uncultured bacteria and new taxonomic candidates, which accounted for 49% and 55% of the total isolates examined (n=258), respectively. The new isolates were affiliating with seven phyla such asProteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, andBacteroidetes. The result of chemical analysis showed that NSE included more diverse components of low-molecular-weight organic substances than two conventional soil extracts using distilled water. Cultivation of previously uncultured bacteria is expected to extend knowledge through the discovery of new phenotypic, physiological and functional properties, and even roles of unknown genes.IMPORTANCEEither metagenomics or single-cell sequencing can detect unknown genes from uncultured microbial strains in environments and may find their significant potential metabolites and roles. However, such gene/genome-based techniques still have a critical problem making impossible for further applications through cultivation. To solve this problem, various approaches for cultivation of uncultured bacteria have been developed, but they still have lack of skill to grow them on solid media for isolation and subculture.

scholarly journals Novel bacterial lineages associated with boreal moss species

2017 ◽  
Author(s):  
Hannah Holland-Moritz ◽  
Julia Stuart ◽  
Lily R. Lewis ◽  
Samantha Miller ◽  
Michelle C. Mack ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Carbon Fixation ◽  
Net Primary Productivity ◽  
Bacterial Community Composition ◽  
Marker Gene ◽  
Metagenomic Sequencing ◽  
Moss Species ◽  
Anoxygenic Phototrophs ◽  
Bacterial Phyla ◽  
Bacterial Lineages

AbstractMosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local environmental conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss species collected near Fairbanks, AK USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbor diverse lineages of potential N2- fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.

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