Sugar Beet-Associated Bacterial and Fungal Communities Show a High Indigenous Antagonistic Potential Against Plant Pathogens

Abstract

The aim of this study was to analyze microbial communities in/on sugar beet with special focus on antagonists toward plant pathogens. For this purpose, the composition of microorganisms isolated from the rhizosphere, phyllosphere, endorhiza, and endosphere of field-grown sugar beet plants was analyzed by a multiphasic approach at three different plant development stages at six locations in Europe. The analysis of microbial communities by Single Strand Conformation Polymorphism (SSCP) of 16S/18S rRNA clearly revealed the existence of discrete microenvironment- and site-specific patterns. A total of 1952 bacterial and 1344 fungal isolates screened by dual testing for antagonism toward the pathogens Aphanomyces cochlioides, Phoma betae, Pythium ultimum, and Rhizoctonia solani resulted in 885 bacterial (=45%) and 437 fungal (=33%) antagonists. In general, the indigenous antagonistic potential was very high and influenced by (a) the location, (b) the plant developmental stage, and (3) the microenvironment. Furthermore, we showed for the first time that the antagonistic potential was highly specific for each target pathogen. The majority of antagonistic microorganisms suppressed only one pathogen (bacteria: 664 = 75%; fungi: 256 = 59%), whereas the minority showed a broad host range (bacteria: 4 = 0.5%; fungi: 7 = 1.6%). The bacterial communities harbored the highest antagonistic potential against P. ultimum, whereas the fungal communities contained more antagonists against A. cochlioides and R. solani. In contrast to their high proportion, only a low diversity of antagonists at genotypic and species level was found. Novel antagonistic species, e.g., Subtercola pratensis or Microbacterium testaceum were found in the internal part of the sugar beet body.

Banana-Associated Microbial Communities in Uganda Are Highly Diverse but Dominated by Enterobacteriaceae

“…The microhabitats of plants differ not only in their abiotic parameters but also in their microbial communities (7,49). Due to the fact that plant roots exude an enormous range of potentially valuable small-molecular-weight compounds into the rhizosphere (29,32), this plant-associated microhabitat contains the main microbiome of plants in general.…”

“…Fingerprinting of microbial communities by singlestranded conformational polymorphism (SSCP) was carried out as described by Schwieger and Tebbe (42). Bacterial 16S rRNA gene sequences were amplified by PCR using the bacterial primer pair Unibac-II-515f (5=-GTG CCA GCA GCC GC-3=) and Unibac-II-927r P (5=-CCC GTC AAT TYM TTT GAG TT-3=) according to the method of Zachow et al (49). The PCR was performed by using a total volume of 60 l containing 1ϫ Taq&Go PCR Mastermix (MP Biomedicals, Eschwege, Germany), 1.5 mM MgCl 2 , 0.2 M concentrations of each primer, and 1 l of template DNA (95°C for 5 min, followed by 32 cycles of 95°C for 20 s, 54°C for 15 s, and 72°C for 30 s, with a final elongation at 72°C for 10 min).…”

The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

“…Organotrophic fungi, better known as saprotrophic fungi, occur in the rhizosphere as has been shown by both cultivable-, biochemical-and PCR-based techniques (Smit et al 1999;Viebahn et al 2005;Berg et al 2005;Baum and Hrynkiewicz 2006;De Boer et al 2008;Zachow et al 2008). The rhizosphere saprotrophic fungal community appears to consist of both yeasts and filamentous fungi with representatives of all major terrestrial phyla (Ascomycota and Basidiomycota) and sub-phyla (Mucoromycotina; Marcial Gomes et al 2003;Renker et al 2004;Berg et al 2005;Vujanovic et al 2007).…”

Plant host habitat and root exudates shape soil bacterial community structure

“…Certain bacteria are considered as beneficial, because they produce phytohormones (Azospirillum and Pseudomonas) (Mantelin and Touraine, 2004;Preston, 2004) and antifungal compounds (Stenotrophomonas, Pseudomonas and Microbacterium) (Preston, 2004;Kai et al, 2007;Zachow et al, 2008) or contribute to biogeochemical cycling of sulphur (Acidovorax) (Schmalenberger and Kertesz, 2007) or nitrogen, as diazotrophs and denitrifiers (Azospirillum) (Costacurta and Vanderleyden, 1995). Bacteria considered as human opportunistic pathogens, such as Stenotrophomonas maltophilia, Enterobacter cloacae (Berg et al, 2005) or vine phytopathogenic bacteria, such as Xylophilus ampelinus (Grall and Manceau, 2003), were able to assimilate root exudates and to proliferate in the rhizosphere of different plant species.…”