Group-specific PCR primers for the phylum Acidobacteria designed based on the comparative analysis of 16S rRNA gene sequences

Lee, Sanghoon; Cho, Jae-Chang

doi:10.1016/j.mimet.2011.05.003

Cited by 18 publications

(20 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In our study, for Hainich grassland, Schorfheide grassland, and Schorfheide forest, subgroups Gp6 (62%) and Gp4 (20%), Gp6 (59%) and Gp3 (14%), or Gp1 (85%) and Gp3 (10%) were dominating the community, respectively. In contrast, we found members of subgroup Gp5 at an abundance of 10 to 17% in Hainich grassland and Alb soils but missed two important subgroups found in the pyrosequencing approach (Gp7 and Gp16) due to the limitations of primer 31F (4,31,38). In a pyrosequencing analysis of Acidobacteria in 87 soils across the United States, subgroups Gp1 to Gp7 and Gp16 dominated, whereas the clone library approach with 22 of these 87 soils with primer 31F showed a predominance of subgroups Gp1, Gp3, Gp4, Gp5, and Gp6 (29).…”

Section: Discussioncontrasting

confidence: 59%

“…Almost-full-length 16S rRNA genes were amplified from each of the 57 samples using the Acidobacteria-specific forward primer 31F (5) and the universal reverse primer 1492R (36). Primer 31F is highly specific for and covers the most abundant Acidobacteria (subgroups Gp1, Gp3, Gp4, Gp5, and Gp6) but excludes some subgroups also present in soils (4,31,38). For all samples from AEG, AEW, HEG, HEW, and SEW, the 50-l reaction mixture contained 1ϫ PCR buffer including 1.5 mM MgCl 2 (Qiagen, Hilden, Germany), 200 M deoxynucleoside triphosphate (dNTP) mix, 20 g of bovine serum albumin (BSA; Sigma-Aldrich, Steinheim, Germany), 0.2 M (each) primer, 1 unit of Taq polymerase (Qiagen), and 1 to 2 l DNA template (20 to 100 ng).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

Naether

Foesel

Naegele

et al. 2012

Appl Environ Microbiol

299

153

View full text Add to dashboard Cite

In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n ‫؍‬ 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.

show abstract

Section: Discussioncontrasting

confidence: 59%

Section: Methodsmentioning

confidence: 99%

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

Naether

Foesel

Naegele

et al. 2012

Appl Environ Microbiol

299

153

View full text Add to dashboard Cite

show abstract

“…); Korarchaeota (Auchtung et al. ); Acidobacteria (Lee and Cho ; Gans et al. ); Pseudomonas (Widmer et al.…”

Section: Introductionmentioning

confidence: 99%

Exploration of Deinococcus‐Thermus molecular diversity by novel group‐specific PCR primers

et al. 2013

View full text Add to dashboard Cite

The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly, Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deinococcus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum.

show abstract

“…In our soil samples were detected 15 different acidobacterial subgroups among the 26 acidobacterial subgroups classified -subgroups 1-8 according to ; subgroups 9-11 according to and subgroups 12-26 according to . Many researchers have pointed out that not all acidobacterial subgroups could be detected using group-specific primers, such as Acid31F Lee and Cho (2011), the two group-specific primers (Acid31F and ACIDO) do not detect the subgroups 2, 22 and 25, which subgroups were accounted in this study by using the "universal" V4 region primers. In our soil samples, acidobacterial subgroup 2 was one of the most dominant.…”

Section: Magnesium Ions Are Required By Large Number Of Enzymes For Tmentioning

confidence: 69%

“…In our soil samples were detected 15 different acidobacterial subgroups among the 26 acidobacterial subgroups classified -subgroups 1-8 according to ; subgroups 9-11 according to ; and subgroups 12-26 according to . Many researchers have pointed out that not all acidobacterial subgroups could be detected using group-specific primers, such as Acid31F and ACIDO (Lee & Cho, 2011) designed for the selective amplification and detection of members of the phylum Acidobacteria. According to , Ca, and Mg on abundance of Acidobacteria subgroups (4, 6, and 7) relative to all Acidobacteria using pyrosequencing data.…”

Section: Discussionmentioning

confidence: 99%

Bacterial ecology in Amazonian soils under deforestation and agricultural management

Navarrete¹

View full text Add to dashboard Cite

Group-specific PCR primers for the phylum Acidobacteria designed based on the comparative analysis of 16S rRNA gene sequences

Cited by 18 publications

References 24 publications

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

Exploration of Deinococcus‐Thermus molecular diversity by novel group‐specific PCR primers

Bacterial ecology in Amazonian soils under deforestation and agricultural management

Contact Info

Product

Resources

About