IncP-1 and PromA Group Plasmids Are Major Providers of Horizontal Gene Transfer Capacities Across Bacteria in the Mycosphere of Different Soil Fungi

Abstract

Plasmids of the IncP-1β group have been found to be important carriers of accessory genes that enhance the ecological fitness of bacteria, whereas plasmids of the PromA group are key agents of horizontal gene transfer in particular soil settings. However, there is still a paucity of knowledge with respect to the diversity, abundance, and involvement in horizontal gene transfer of plasmids of both groups in the mycosphere. Using triparental exogenous isolation based on the IncQ tracer plasmid pSUP104 as well as direct molecular detection, we analyzed the pool of mobilizer and self-transferable plasmids in mycosphere soil. Replicate mushroom types that were related to Russula, Inocybe, Ampulloclitocybe, and Galerina spp. were sampled from a forest soil area, and bulk soil was used as the control. The data showed that the levels of IncP-1β plasmids are significantly raised across several of the mycospheres analyzed, whereas those of PromA group plasmids were similar across the mycospheres and corresponding bulk soil. Moreover, the frequencies of triparental exogenous isolation of mobilizer plasmids into a Pseudomonas fluorescens recipient strain were significantly elevated in communities from several mycospheres as compared with those from bulk soil. Molecular analysis of selected transconjugants, as well as from directly isolated strains, revealed the presence of plasmids of three size groups, i.e., (1) 40-45, (2) 50-60, and (3) ≥60 kb, across all isolations. Replicon typing using IncN, IncW and IncA/C proxies revealed no positive signals. In contrast, a suite of plasmids produced signals with IncP-1β as well as PromA type replicon typing systems. Moreover, a selected subset of plasmids, obtained from the Inocybe and Galerina isolates, was transferred out further, revealing their capacities to transfer and mobilize across a broad host range.

The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions

“…1). In addition, direct evidence from triparental exogenous isolation experiments has revealed that plasmid transfer frequencies were significantly increased from communities from the mycospheres of several fungi in a forest soil as compared to those from bulk soil (Zhang et al, 2014). What evidence do we have for HGT-driven adaptive processes in the mycosphere?…”

“…In this respect, plasmid pTer331 was detected in a mycosphere-isolated Collimonas fungivorans strain (Mela et al, 2008), whereas plasmid pIPO2 was obtained from a rhizosphere in which fungi possibly played a role (Van Elsas et al, 1998;Tauch et al, 2002). We recently obtained evidence for the presence of PromA group plasmids in mycospheres of several ectomycorrhizal fungi in a forest soil (Zhang et al, 2014). Such cryptic plasmids might be considered a pool to create standing genetic variation within a population, allowing bacterial communities to gain robustness in the uncertainty of environmental changes (Jain et al, 2003;Hermisson & Pennings, 2005).…”

“…Thus, the mycosphere, with its ability to generate abundant surface areas and increased nutrient availability to its associates, can be thought of an excellent provider of opportunities for HGT. Indeed, Zhang et al (2014) have shown that transfer frequencies within bacterial communities from the mycosphere of Russula, Ampulloclitocybe and Inocybe were significantly higher than with those from the corresponding bulk soils, ranging from 10 À8 to 10 À6 per recipient. The cellular partners that are present, that is bacteria of different types and fungi, are probably in a continuous quest for available substrate, for which they compete, but occasionally they may also cooperate.…”

Proma Plasmids are Instrumental in the Dissemination of Linuron Catabolic Genes between Different Genera

“…With the exception of SFA231 (Li et al, 2014), pMOL98 (Van der Auwera et al, 2009) and pSB102 (Schneiker et al, 2001) which carry heavy metal resistance-related genes, all 12 completely sequenced PromA plasmids identified to date are cryptic plasmids with no clear indication of their ecological or possible benefit for the host organism. It was hypothesized that the main role of these plasmids is to mobilize other plasmids (Zhang et al, 2015).…”

Mycelia as a focal point for horizontal gene transfer among soil bacteria

“…Mycelial organisms like fungi establish a dense network of thread-like hyphae, which provides ample amounts of nutrients and colonisable surfaces that both are prerequisites for bacterial HGT14. Plasmids of ecological relevance have been discovered in the vicinity of hyphae, such as plasmid-encoded genes for monoaromatics degradation in Pseudomonas fluorescens 15 or elevated levels of IncP-1β plasmids, known to encode a variety of ecological traits1617. Starting out from these observations, we hypothesized that mycelia promote bacterial conjugation by acting as transport networks for bacteria, a concept described as the ‘ fungal highway ’181920.…”