Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands)

TY - JOUR

T1 - Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands)

AU - Kowalchuk, G.A.

AU - Stienstra, A.W.

AU - Heilig, G.H.J.

AU - Stephen, J.R.

AU - Woldendorp, J.W.

N1 - Reporting year: 2000 Metis note: 2640; CTE; TME ; ME file:///L:/Endnotedatabases/NIOOPUB/pdfs/Pdfs2000/Kowalchuk_ea_2640.pdf

PY - 2000

Y1 - 2000

N2 - Changes in the community structure of chemolitho-autotrophic ammonia-oxidising bacteria of the beta-subgroup Proteobacteria were monitored during nutrient-impoverishment management of slightly acidic, peaty grassland soils, which decreased in pH with succession. Specific PCR, cloning and sequence analysis. denaturing gradient gel electrophoresis (DGGE) and probe hybridisation were used to analyse rDNA sequences directly recovered from successional soils. Four previously characterised ammonia oxidiser sequence clusters were recovered from each soil, three associated with the genus Nitrosospira and one with the genus Nitrosomonas. All samples were dominated by Nitrosospira-like sequences, Nitrosospira cluster 3 was the most commonly recovered ammonia oxidiser group in all fields, but a greater representation of Nitrosospira clusters 2 and 4 was observed in older fields. Most probable number (MPN) counts were conducted using neutral and slightly acid conditions. Neutral pH (7.5) MPN's suggested a decrease in ammonia oxidiser numbers in later successional fields, but this trend was not observed using slightly acid (pH 5.8) conditions. Analysis of terminal MPN dilutions revealed a distribution of sequence clusters similar to direct soil DNA extractions. However, an increased relative recovery of Nitrosospira cluster 2 was observed for acid pH MPNs compared to neutral pH MPNs from the most acidic soil tested, in agreement with current hypotheses on the relative acid tolerance of this group. [KEYWORDS: beta-subgroup proteobacteria; soil pH; nitrification; DGGE; most probable number (MPN); oligonucleotide hybridisation; Nitrosospira; Nitrosomonas 16s ribosomal-rna; gradient gel-electrophoresis; oxidizing bacteria; nitrosomonas-europaea; gene-sequences; populations; ph; nitrification; diversity; pcr]

AB - Changes in the community structure of chemolitho-autotrophic ammonia-oxidising bacteria of the beta-subgroup Proteobacteria were monitored during nutrient-impoverishment management of slightly acidic, peaty grassland soils, which decreased in pH with succession. Specific PCR, cloning and sequence analysis. denaturing gradient gel electrophoresis (DGGE) and probe hybridisation were used to analyse rDNA sequences directly recovered from successional soils. Four previously characterised ammonia oxidiser sequence clusters were recovered from each soil, three associated with the genus Nitrosospira and one with the genus Nitrosomonas. All samples were dominated by Nitrosospira-like sequences, Nitrosospira cluster 3 was the most commonly recovered ammonia oxidiser group in all fields, but a greater representation of Nitrosospira clusters 2 and 4 was observed in older fields. Most probable number (MPN) counts were conducted using neutral and slightly acid conditions. Neutral pH (7.5) MPN's suggested a decrease in ammonia oxidiser numbers in later successional fields, but this trend was not observed using slightly acid (pH 5.8) conditions. Analysis of terminal MPN dilutions revealed a distribution of sequence clusters similar to direct soil DNA extractions. However, an increased relative recovery of Nitrosospira cluster 2 was observed for acid pH MPNs compared to neutral pH MPNs from the most acidic soil tested, in agreement with current hypotheses on the relative acid tolerance of this group. [KEYWORDS: beta-subgroup proteobacteria; soil pH; nitrification; DGGE; most probable number (MPN); oligonucleotide hybridisation; Nitrosospira; Nitrosomonas 16s ribosomal-rna; gradient gel-electrophoresis; oxidizing bacteria; nitrosomonas-europaea; gene-sequences; populations; ph; nitrification; diversity; pcr]

U2 - 10.1111/j.1574-6941.2000.tb00685.x

DO - 10.1111/j.1574-6941.2000.tb00685.x

M3 - Article

SN - 0168-6496

VL - 31

SP - 207

EP - 215

JO - FEMS Microbiology Ecology

JF - FEMS Microbiology Ecology

IS - 3

ER -