Research Open Access Bacterial community establishment in native and non-native soils and the effect of fungal colonization Rashid Nazir 1,2* , Alexander V. Semenov 1 , Nermin Sarigul 1 and Jan Dirk van Elsas 1 *Correspondence: r.nazir@rug.nl 1 Department of Microbial Ecology, University of Groningen Nijenborgh 7, 9747 AG, Groningen, Netherlands. 2 Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan. Abstract Bacterial communities are essential parts of living soils. However, we understand very little of how soil matrices govern the structure of the local microbiota. Here, we report on experiments that address such assembly rules for microbial communities in soil. hus, indigenous soil bacterial communities were extracted from eight diferent soils (denoted V, B, G, WD, L, K, S and WG) and used to inoculate four selected presterilized sandy soils (V, B, G and WD) in microcosms. hen, t hese microcosms were subjected to colonization by the soil saprotrophic fungus Lyophyllum sp. strain Karsten, or were let uncolonized. Fiteen days following introduction, the microcosms were analyzed to enumerate culturable (dilution plating) and total bacteria (quantitative PCR) and bacterial community structures (PCR-DGGE), to assess the abundance and diversity of the bacterial communities. Moreover, fungal-selected culturable bacteria were identiied. In all cases and irrespective of the presence of fungal mycelium, bacterial communities of around 1–5 x 10 8 CFU or 16S rRNA gene copies per g dry soil established. he data furt her clearly showed the inluence of local soil conditions on the establishment of the inoculant bacteria in their native versus non-native soil. hus, cluster analysis of t he PCR-DGGE ingerprints revealed that two soils, i.e., V and B, were strong drivers of the established community structures from the eight source communities, whereas the two remaining soils (G and WD) revealed mixed efects. PCR-DGGE further revealed that the non-native bacterial communities obtained from sandy source soils were more similar to the established native communities than those from clayey soils. Overall, the bacterial communities showed decreased diversities and richness values in the fungal-colonized systems as compared to the non-fungal-afected ones (inoculation and migration sites). In the fungal-afected systems, the recipient soil matrix was of importance, in particular at the inoculation site of the V and B soil matrices and at the migration front of the G matrix. Analysis of the culturable bacterial community across diferent soils revealed that similar bacteria, even originating from diferent sources, were enriched by the colonizing fungus. Particular bacterial types, like Burkholderia and Pseudomonas spp., were found to be selected by the growing fungal hyphae. Further more, an enrichment of type three secretion systems (TTSS) was detected. Keywords: Bacterial community establishment, native and non-native soils, fungal colonization efect, bacterial enrichment, type three secretion system (TTSS) © 2013 Nazir et al; licensee Herbert Publications Ltd. his is an Open Access article distributed under the terms of Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0). his permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Introduction Soil is usually characterized as a complex dynamic system, in which bacteria and fungi live together [12]. These organisms thus occupy the available niche space [9,4] by utilizing the nutrients that are ultimately provided by autotrophic plants or decaying organisms as well as from each other. The microsites in soil where bacteria and fungi meet are called bacterial-fungal interfaces [9]. These are proposed to represent ecological hot spots where the heat of interactions is presumed to occur. A better analysis of such hot spots will enable us to understand the interactions between these two important groups of soil microorganisms. Thus, living together in soil, bacteria and fungi have been hypothesized to exert specific effects on each other [12]. The locally-specific conditions that drive the selective processes in these soil bacterial/fungal hot spots may be quite dependent on soil type. The microbiota of each soil may, thus, be unique for that particular soil, as it has evolved and matured over the time of existence of the soil. Unfortunately, we currently lack detailed knowledge on how indigenous microbial communities are shaped in accordance with the dynamics of the local habitat. Moreover, in the light of the uncertainty on the exact nature of the niche spaces in soil, it is unclear to what extent particular bacterial groups are favored or disfavored in soils. On top of this, an important impact by soil fungi can be expected to occur for soil bacterial communities [19]. Examined bacterial and arbuscular mycorrhizal (AM) fungal assemblages in soil and concluded that fungi are indeed major determinants of the local bacterial assemblages. Early work by Artursson and colleagues [1,2] had already revealed a significant stimulus by the fungus Glomus mosseae on some Paenibacillus spp. as well as particular Gammaproteobacteria in the mycorrhizosphere. Furthermore, they argued that this selective effect was driven by fungal exudates that became available [10]. Investigated the culturable bacterial communities in the mycorrhizosphere of Glomus intraradices and showed that Paenibacillus spp. were specifically selected in this habitat. In another investigation, members of the Oxalobacteriaceae were found to be more abundant in mycorrhizal than in nonmycorrhizal root samples [16]. Previous results by Warmink and van Elsas [21] showed that Microbiology Discovery ISSN 2052-6180