Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies

Abstract

The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the Sphingomonadaceae family at the bases of the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans in comparison to the adjacent bulk soil. To do so, we used a previously designed Sphingomonadaceae-specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a Sphingomonadaceae-specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the Sphingomonadaceae community structures. The effect was especially prevalent with R. exalbicans. Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of L. proxima and R. exalbicans still revealed divergent community structures, indicating that different fungi select for different members of the Sphingomonadaceae family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific Sphingomonadaceae types. It further showed that major groups from the mycospheres of R. exalbicans and L. proxima did not cluster with known bacteria from the database, indicating new groups within the family of Sphingomonadaceae present in these environments.

Bacterial community establishment in native and non-native soils and the effect of fungal colonization

“…Major Sphingomonas groups from the examined mycospheres did not cluster with Sphingomonadaceae in public databases, which indicate that novel groups of this family were present. Interestingly, similar bacterial community structures were observed for the same fungal species from different sampling sites, whereas the corresponding bulk soil communities differed from each other [3]. This indicates a strong selective effect on similar groups of soil bacteria.…”

“…One other Burkholderia strain, i.e., BS407, was remotely related to any other described species. The strains affiliated with Pseudomonas were further identified as P. putida (6) and P. fluorescens (3). Except for two Burkholderia sp.…”

“…For instance, clear selective effects were found to be exerted by the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans growing in forest soil on members of the Sphingomonadaceae [3]. Major Sphingomonas groups from the examined mycospheres did not cluster with Sphingomonadaceae in public databases, which indicate that novel groups of this family were present.…”

Different Selective Effects on Rhizosphere Bacteria Exerted by Genetically Modified versus Conventional Potato Lines

“…were recently obtained from DGGE bands in long-term in vitro cultivated plants [63], possibly indicating their role as endophytes. Sphingomonas has been described in association with soil affected by the release of carbonaceous compounds originating from plant roots [64] or from fungal hyphae, being an active member of the mycosphere [65]. This clearly indicates that such organisms may represent sensors of variation in the chemical profile of root exudates due to modifications in plant metabolism.…”

Diversity of endophytic bacteria in Caragana microphylla grown in the desert grassland of the Ningxia Hui Autonomous Region of China

“…Similarly, members of the Sphingomonadaceae family are widespread in different types of soils, sediments, and pelagic aquatic environments, and are known for their ability to utilize a wide variety of carbon sources; several are in fact renowned degraders of recalcitrant (xenobiotic) molecules (Leys et al, 2004). Additionally, some sphingomonads were also found to play important roles in the mycorrhizosphere (Boersma et al, 2009).…”