Home LiteratureArticle Details

PMID: 19020558 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Phylogenetic diversity of Acidobacteria in a former agricultural soil.

The ISME journal ·Vol. 3 ·No. 3 ·2009-03-00 ·Pages 378-82

Kielak A, Pijl AS, van Veen JA, Kowalchuk GA

Abstract

Although Acidobacteria represent the most abundant bacterial phylum in many soils, knowledge of acidobacterial diversity is still rather incomplete. We, therefore, examined the diversity of 16S rRNA genes affiliated with this phylum in a former arable soil via three independent approaches: (1) screening of a fosmid metagenome library for inserts containing Acidobacteria-like 16S rRNA genes; (2) PCR-cloning using general bacterial primers; and (3) PCR-cloning with acidobacterial-specific primers. Bacterial-specific libraries compared rhizosphere versus bulk soil samples, revealing a higher proportion of acidobacterial sequences in bulk soil libraries (P<0.001). Bacterial libraries recovered the greatest diversity, and sequence examination suggested that sequence mismatches with the Acidobacteria-specific primers limited the coverage of the metagenome library screening and specific library approaches. Together, these results expand knowledge of the distribution and diversity of Acidobacteria in soil environments and highlight important technical considerations in the molecular analysis of Acidobacteria diversity.

MeSH Terms

Bacteria/classification,isolation & purification Biodiversity Cloning, Molecular DNA Primers/genetics DNA, Bacterial/chemistry,genetics DNA, Ribosomal/chemistry,genetics Gene Library Genes, rRNA Molecular Sequence Data Phylogeny RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Sequence Homology, Nucleic Acid Soil Microbiology

Chemicals

DNA Primers DNA, Bacterial DNA, Ribosomal RNA, Bacterial RNA, Ribosomal, 16S

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Kielak Anna

Department of Terrestrial Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands.

Pijl Agata S

van Veen Johannes A

Kowalchuk George A

Article Info

Journal

The ISME journal

Abbr.

ISME J

ISSN

1751-7370

DOI

10.1038/ismej.2008.113

Published

2009-03-00

Epub

2008-00-20

Pages

378-82

Language

English

Region

England

NLM ID

101301086

Subset

Databases

GENBANK

FJ004643, FJ004644, FJ004645, FJ004646, FJ004647, FJ004648, FJ004649, FJ004650, FJ004651, FJ004652, FJ004653, FJ004654, FJ004655, FJ004656, FJ004657, FJ004658, FJ004659, FJ004660, FJ004661, FJ004662, FJ004663, FJ004664, FJ004665, FJ004666, FJ004667, FJ004668, FJ004669, FJ004670, FJ004671, FJ004672, FJ004673, FJ004674, FJ004675, FJ004676, FJ004677, FJ004678, FJ004679, FJ004680, FJ004681, FJ004682, FJ004683, FJ004684, FJ004685, FJ004686, FJ004687, FJ004688, FJ004689, FJ004690, FJ004691, FJ004692, FJ004693, FJ004694, FJ004695, FJ004696, FJ004697, FJ004698, FJ004699, FJ004700, FJ004701, FJ004702, FJ004703, FJ004704, FJ004705, FJ004706, FJ004707, FJ004708, FJ004709, FJ004710, FJ004711, FJ004712, FJ004713, FJ004714, FJ004715, FJ004716, FJ004717, FJ004718, FJ004719, FJ004720, FJ004721, FJ004722, FJ004723, FJ004724, FJ004725, FJ004726, FJ004727, FJ004728, FJ004729, FJ004730, FJ004731, FJ004732, FJ004733, FJ004734, FJ004735, FJ004736, FJ004737, FJ004738, FJ004739, FJ004740, FJ004741, FJ004742, FJ004743, FJ004744, FJ004745, FJ004746, FJ004747, FJ004748, FJ004749, FJ004750, FJ004751, FJ004752, FJ004753, FJ004754, FJ004755, FJ004756, FJ004757, FJ004758, FJ004759, FJ004760, FJ004761, FJ004762, FJ004763, FJ004764, FJ004765, FJ004766, FJ004767, FJ004768, FJ004769, FJ004770, FJ004771, FJ004772, FJ004773, FJ004774, FJ004775, FJ004776, FJ004777, FJ004778, FJ004779, FJ004780, FJ004781, FJ004782, FJ004783, FJ004784, FJ004785, FJ004786, FJ004787, FJ004788, FJ004789, FJ004790, FJ004791, FJ004792, FJ004793, FJ004794, FJ004795, FJ004796, FJ004797, FJ004798

External Links

PubMed source DOI: 10.1038/ismej.2008.113 View journal details

Analysis Services

Phylogenetic diversity of Acidobacteria in a former agricultural soil.

Contact

WeChat Official Account