Massilia brevitalea sp. nov., a novel betaproteobacterium isolated from lysimeter soil.

A Gram-negative, strictly aerobic bacterium, designated strain byr23-80T, was isolated from lysimeter soil by using a high-throughput cultivation technique. Cells of strain byr23-80T were found to be short rods that multiplied by binary fission and were motile by means of a single polar flagellum. Occasionally, two to three polar or lateral flagella were observed. The optimum growth temperature was 15 degrees C and the pH optimum was 7.0-7.5. The predominant cellular fatty acids were C16 : 1omega7c (54.7 %) and C16 : 0 (21.4 %). In addition, the diagnostic fatty acids C10 : 0 3-OH and C12 : 0 2-OH were detected. Q-8 was the predominant respiratory quinone. The isolate was physiologically very versatile, using a wide range of sugars, organic acids and amino acids as single carbon and energy sources for growth. The G+C content of the genomic DNA was 65.3 mol%. Phylogenetic analyses supported the assignment of strain byr23-80T to the genus Massilia within the family Oxalobacteraceae of the class Betaproteobacteria. Within the genus, strain byr23-80T was most closely related to Massilia aurea DSM 18055T, with a 16S rRNA gene sequence similarity of 98.3 %. However, DNA-DNA hybridization revealed a pairwise similarity for the genomic DNA of only 20.1 % between strain byr23-80T and strain DSM 18055T. The novel isolate could be distinguished from the existing species Massilia timonae, Massilia dura, Massilia albidiflava, Massilia plicata, Massilia lutea and M. aurea by its significantly lower temperature optimum for growth and by the absence of gelatinase, alpha-galactosidase and beta-galactosidase activities. On the basis of these characteristics, strain byr23-80T constitutes a novel species of the genus Massilia, for which the name Massilia brevitalea sp. nov. is proposed. The type strain is byr23-80T (=DSM 18925T=ATCC BAA-1465T).

Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity.

Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Verrucomicrobia populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the Betaproteobacteria species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.