Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake

Abstract

Bacterial diversity in the water column of a freshwater lake in the Netherlands was investigated by analysis of 16S rRNA gene sequences recovered through PCR amplification from total community DNA. Among 23 unique cloned sequences, two appeared to belong to the recently described bacterial division Verrucomicrobiales. One of the two sequences was most similar to a group of environmental clones that form a distinct lineage within the division. The other sequence was divergent (less than 85% similarity) from all 16S rRNA gene sequences, both from cultivated species and from environmental clones, known in this division to date. Analysis by denaturing gradient gel electrophoresis (DGGE) and sequencing of DNA recovered through excision from the DGGE gel showed that the two sequence types were present in the lake throughout the year.

Molecular species discovery in the diatom Sellaphora and its congruence with mating trials.

“…Cells for DNA extraction were harvested from cultures in late exponential growth phase in 90 mm Petri dishes (RBGE) or 50 ml culture flasks (PAE) grown under the conditions detailed above. Cells were harvested by centrifugation and DNA extracted using the Qiagen Plant DNeasy kit (Qiagen, Crawley, UK) (RBGE) or as described in Zwart et al (1998), but without the last purification step (PAE). The partial cox1 gene was amplified using primers GazF2 and KEdtmR (EVans et al 2007).…”

Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia

“…(b) DNA extraction, PCR amplification, amplified ribosomal DNA restriction analysis screening and sequencing DNA was extracted as described in Zwart et al (1998). The 18S rRNA gene was amplified using the primers P2 (5 0 -CTGGTTGATTCTGCCAGT-3 0 ) and P4 (5 0 -TGAT CCTTCYGCAGGTTCAC-3 0 ; Moon-van der Staay et al…”

Invited Review - Fight on Plankton! or, Phytoplankton Shape and Size as Adaptive Tools to Get Ahead in the Struggle for Life

“…Shortly, it consists of lysing the cells by mechanical means (bead beating), nucleic acid extraction (phenol and phenol/chloroform) and nucleic acid purification (Wizard column, Promega, Madison, U.S.A.). After purification, PCR amplifications were performed on the 16S prokaryotic subunit Zwart et al, 1998) and on the 18S eukaryotic subunit of the rRNA gene. Denaturing Gradient Gel Electrophoresis (DGGE) methods were used to investigate and characterise the prokaryotic and the eukaryotic community structures.…”

“…To do this, seston was harvested onto a 0.2 øm nitro-cellulose membrane filter, followed by DNA extraction . After DNA purification, PCR amplifications were performed on both the 16S prokaryotic subunit (Muyzer et al 1998;Zwart et al 1998) and on the 18S eukaryotic subunit ) of the rRNA gene. To investigate and characterise the prokaryotic and eukaryotic community structures, we used Denaturing Gradient Gel Electrophoresis (DGGE) methods .…”