scholarly journals Optimisation of automated ribosomal intergenic spacer analysis for the estimation of microbial diversity in fynbos soil

2010 ◽  
Vol 106 (7/8) ◽  
Author(s):  
Etienne Slabbert ◽  
Carel J. Van Heerden ◽  
Karin Jacobs
Keyword(s):  
Microbial Diversity ◽  
Intergenic Spacer ◽  
Ribosomal Intergenic Spacer

scholarly journals Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities

1999 ◽  
Vol 65 (10) ◽  
pp. 4630-4636 ◽  
Author(s):  
Madeline M. Fisher ◽  
Eric W. Triplett
Keyword(s):  
Microbial Diversity ◽  
Bacterial Communities ◽  
Limit Of Detection ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Cycle Number ◽  
Intergenic Spacer Region ◽  
Automated Method ◽  
Ribosomal Intergenic Spacer

ABSTRACT An automated method of ribosomal intergenic spacer analysis (ARISA) was developed for the rapid estimation of microbial diversity and community composition in freshwater environments. Following isolation of total community DNA, PCR amplification of the 16S-23S intergenic spacer region in the rRNA operon was performed with a fluorescence-labeled forward primer. ARISA-PCR fragments ranging in size from 400 to 1,200 bp were next discriminated and measured by using an automated electrophoresis system. Database information on the 16S-23S intergenic spacer was also examined, to understand the potential biases in diversity estimates provided by ARISA. In the analysis of three natural freshwater bacterial communities, ARISA was rapid and sensitive and provided highly reproducible community-specific profiles at all levels of replication tested. The ARISA profiles of the freshwater communities were quantitatively compared in terms of both their relative diversity and similarity level. The three communities had distinctly different profiles but were similar in their total number of fragments (range, 34 to 41). In addition, the pattern of major amplification products in representative profiles was not significantly altered when the PCR cycle number was reduced from 30 to 15, but the number of minor products (near the limit of detection) was sensitive to changes in cycling parameters. Overall, the results suggest that ARISA is a rapid and effective community analysis technique that can be used in conjunction with more accurate but labor-intensive methods (e.g., 16S rRNA gene cloning and sequencing) when fine-scale spatial and temporal resolution is needed.

Relationships among Brazilian and worldwide isolates of Fusarium oxysporum f. sp. lactucae race 1 inferred from ribosomal intergenic spacer (IGS-rDNA) region and EF-1α gene sequences

2018 ◽  
Vol 152 (1) ◽  
pp. 81-94 ◽  
Author(s):  
Cléia S. Cabral ◽  
Maria Esther de N. Fonseca ◽  
Kátia R. Brunelli ◽  
Mauricio Rossato ◽  
Hélcio Costa ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Intergenic Spacer ◽  
Gene Sequences ◽  
Ribosomal Intergenic Spacer ◽  
Race 1

scholarly journals Cover Crop Impact on Soil Organic Carbon, Nitrogen Dynamics and Microbial Diversity in a Mediterranean Semiarid Vineyard

2020 ◽  
Vol 12 (8) ◽  
pp. 3256 ◽  
Author(s):  
Agata Novara ◽  
Valentina Catania ◽  
Marco Tolone ◽  
Luciano Gristina ◽  
Vito Armando Laudicina ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Microbial Diversity ◽  
Cover Crop ◽  
High Throughput Sequencing ◽  
Intergenic Spacer ◽  
Conventional Tillage ◽  
Nitrate Content ◽  
Relevant Effect ◽  
Management Protocol

Cover crop (CC) management in vineyards increases sustainability by improving soil chemical and biological fertility, but knowledge on its effects in semiarid soils is lacking. This study evaluated the effect of leguminous CC management on soil organic carbon (SOC) sequestration, soil nitrate content and microbial diversity in a semiarid vineyard, in comparison to conventional tillage (CT). SOC and nitrate were monitored during vine-growing season; soil respiration, determined by incubation experiments, microbial biomass and diversity was analyzed after CC burial. The microbial diversity was evaluated by bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA) and high-throughput sequencing of 16SrDNA. CC increased nitrate content and, although it had no relevant effect on SOC, almost doubled its active microbial component, which contributes to SOC stabilization. An unexpected stability of the microbial communities under different soil managements was assessed, fungal diversity being slightly enhanced under CT while bacterial diversity increased under CC. The complete nitrifying genus Nitrospira and plant growth-promoting genera were increased under CC, while desiccation-tolerant genera were abundant in CT. Findings showed that temporary CC applied in semiarid vineyards does not optimize the provided ecosystem services, hence a proper management protocol for dry environments should be set up.

scholarly journals Prokaryotic Dynamics in the Meromictic Coastal Lake Faro (Sicily, Italy)

Diversity ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 37 ◽  
Author(s):  
Carmela Raffa ◽  
Carmen Rizzo ◽  
Marc Strous ◽  
Emilio De Domenico ◽  
Marilena Sanfilippo ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Mixing Conditions ◽  
Coastal Lake ◽  
The North ◽  
Ribosomal Intergenic Spacer ◽  
North Eastern ◽  
Clear Identification ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution of the microbial communities in water samples of Lake Faro was performed by both ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and CARD-FISH (Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization) approaches. A correlation between microbial parameters and both environmental variables (i.e., temperature, pH, dissolved oxygen, redox potential, salinity, chlorophyll-a) and mixing conditions was highlighted, with an evident seasonal variability. The most significative differences were detected by ARISA between the mixolimnion and the monimolimnion, and between Spring and Autumn, by considering layer and season as a factor, respectively.

The ribosomal intergenic spacer (IGS) in the potato and tobacco cyst nematodes, Globodera pallida, G. rostochiensis and G. tabacum

2019 ◽  
Vol 48 ◽  
pp. 101441 ◽  
Author(s):  
Mehrdad Madani ◽  
Len Ward ◽  
Andy Vierstraete ◽  
Solke H. De Boer ◽  
Maurice Moens
Keyword(s):  
Intergenic Spacer ◽  
Globodera Pallida ◽  
Cyst Nematodes ◽  
Ribosomal Intergenic Spacer
Sign in / Sign up

Export Citation Format

Share Document