Abundance, composition, diversity and novelty of soil Proteobacteria

Abstract

Small subunit (16S) rRNA gene surveys generating near full-length 16S rRNA clones offer a unique opportunity for in-depth phylogenetic analysis to highlight the breadth of diversity within various major bacterial phyla encountered in soil. This study offers a detailed phylogenetic analysis of the Proteobacteria-affiliated clones identified from 13 001 nearly full-length 16S rRNA gene clones derived from Oklahoma tall-grass prairie soil. Proteobacteria was the most abundant phylum in the community, and comprised 25% of the total clones. The most abundant and diverse class within the Proteobacteria was Alphaproteobacteria, followed by the Delta-, Beta-and Gammaproteobacteria. Members of the Epsilon-and Zetaproteobacteria were not detected in the dataset. Our analysis identified 15 novel order-level and 48 novel family-level Proteobacteria lineages. In addition, we show that the majority of Proteobacteria clones in the dataset belong to orders and families containing no described cultivated representatives (50% and 65%, respectively). An examination of the ecological distribution of the six most abundant Proteobacteria lineages in this dataset with no characterized pure culture representatives provided important information regarding their global distribution and environmental preferences. This level of novel phylogenetic diversity indicates that our understanding of the functions of soil microorganisms, even those belonging to phyla with numerous and diverse well-characterized cultured representatives such as the Proteobacteria, remains far from adequate.

Changes in the abundance and structure of bacterial communities under long-term fertilization treatments in a peanut monocropping system

“…The most dominant bacterial group in this soil was the Proteobacteria, similar to a report for several soils, which has great importance to global carbon, nitrogen and sulfur cycling (Spain et al 2009). Actinobacteria was the second most abundant phylum and on average proportion abundance across the treatments was found to be S-CF > L-OM > L-CF (Fig.…”

Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica

“…The high number of Clostridia suggests that anaerobic bacteria are abundant in Antarctic maritime vascular plant rhizospheres, which is the usual pattern found in temperate and tropical soils. However, the most common phylum in soils worldwide is Proteobacteria, even when the diversity is analyzed by a wide range of techniques (clone libraries, pyrosequencing and microarrays) (Janssen, 2006;Spain et al, 2009). Despite the fact that we also found a great abundance of Proteobacteria sequences, which represented 24.8% to almost 40% of all sequences found in the Antarctic rhizosphere samples (depending on the sample), this was not the dominant phylum.…”

Effects of Plant Genotype and Growth Stage on the Betaproteobacterial Communities Associated with Different Potato Cultivars in Two Fields

“…The less dominant groups might become apparent in PCR-DGGE analysis only if specific primers are used to reduce the complexity, which improves resolution of the rarer types. The analysis of the betaproteobacteria allowed us to examine such a less dominant group, which has previously been shown to account for around 4 to 16% of a soil bacterial community (50). Interestingly, the observed cultivar effect, which correlated with the tuber starch content and root development, also correlated with growth stage; this effect was absent at the young-plant stage and was more evident at the flowering stage.…”