Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils

Abstract

An uncultured bacterium of the Verrucomicrobiales cluster was identified by its 16S rDNA sequence as a major bacterium in Dutch Drentse A grassland soils. Potential metabolic activity of the according organism was estimated by applying direct ribosome isolation from soil and partial amplification of the 16S rRNA via RT-PCR using bacteria-specific primers. Temperature gradient gel electrophoresis separated the amplicons sequence specifically into reproducible fingerprints. One of the fingerprint bands matched with the signal of clone DA101. Southern blot hybridization with a DA101-specific V6 probe confirmed sequence identity. It is the first time that an organism of the Verrucomicrobiales cluster has been indicated as a potential major metabolizer in environmental microbial communities.

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…One phylotype from this group of Spartobacteria represented up to 31% of total 16S rRNA gene sequences recovered from prairie soils 10 . This phylotype shares 99% 16S rRNA gene sequence identity with a ribosomal clone named 'DA101', first described in 1998 as a particularly abundant 16S rRNA sequence recovered from grassland soils in the Netherlands 15 . To determine if the DA101 phylotype (termed 'DA101' herein) is abundant in other soils, we re-analysed amplicon 16S rRNA gene sequence data obtained from >1,000 soils representing a wide range of soil and site characteristics (Supplementary Table 1).…”

“…Five abundant Verrucomicrobia phylotypes were described in Fierer et al 10 , but a single phylotype with 99% identity to the clone DA101 (ref. 15) was clearly dominant. We searched previously published soil data sets for representative sequences with 100% identity to this DA101 phylotype, including 31 soils from US native tallgrass prairies 10 , 64 soils from matched forest and grassland sites across North America 51 , 595 soils collected from Central Park in New York City 1 , 367 grassland soils collected from North America, Europe, Australia and Africa 17 , and a cross-biome collection of 15 desert and non-desert soils from across the globe 18 .…”

Bacterial Communities Involved in Soil Formation and Plant Establishment Triggered by Pyrite Bioweathering on Arctic Moraines

“…Nemergut et al [9] hypothesized that Comamonadaceae are typical populations of ice environment, that during deglaciation are seeded in the developing soil, decreasing in relative abundance along with soil age. Only in the vegetated area, we detected also the occurrence of Actinomycetales and Verrucomicrobiae, known as typical soil microbiota [33,34]. Verrucomicrobia, Bacteroidetes, and Acidobacteria were found in late successional stages of ecosystem development on the foreland of Puca glacier (Peruvian Andes) and were considered proxy of old soil microbiota [9].…”

Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia

“…16S rRNA genes originating from representatives of subdivision 2 make up most to all of the verrucomicrobial 16S rRNA genes detected in PCR-based surveys of soil bacterial communities (1,2,8,10,12,15,22,30,34,36,37,39,53; L. Schoenborn and P. H. Janssen, unpublished data). One such 16S rRNA gene, designated EA25, was estimated to originate from a species with a population size of up to 2 ϫ 10 8 cells per g of soil (33) and therefore could represent 1 to 10% of all of the bacteria in that soil.…”

“…16S rRNA genes derived from members of this phylum have been detected in soils around the world. Members of the Verrucomicrobia are estimated to comprise between 1.2 and 10.9% of the total bacteria in soil and on average represent 5.0% of all surveyed 16S rRNA genes (1,2,8,10,12,15,22,30,34,36,37,39; L. Schoenborn and P. H. Janssen, unpublished data). Some libraries prepared from soil DNA lack genes indicative of members of the phylum Verrucomicrobia, but these are generally from studies with fewer than 70 analyzed sequences (e.g., references 11 and 38) so that smaller populations of verrucomicrobia, at the lower end of the abundance range, may not have been detected.…”