Pest Management Science Pest Manag Sci 63:269–275 (2007) Impact of a new biopesticide produced by Paenibacillus sp. strain B2 on the genetic structure and density of soil bacterial communities Sameh Selim, 1 Fabrice Martin-Laurent, 2 Nadine Rouard, 2 Silvio Gianinazzi 1 and Diederik van Tuinen 1∗ 1 UMR INRA 1088/CNRS 5184/Universit ´ e de Bourgogne, Plante-Microbe-Environnement CMSE-INRA, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France 2 CMSE, UMR 1229 INRA/Universit ´ e de Bourgogne, Microbiologie et G ´ eochimie des Sols, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France Abstract: The effect of paenimyxin, a new biopesticide produced by Paenibacillus sp. strain B2, on the density of soil bacterial communities was assessed by colony counting and by 16S rDNA and nirK quantitative polymerase chain reaction (PCR). Paenimyxin had a negative effect on the bacterial colony-forming unit (CFU) number, which was significantly reduced 2 and 4 days after treatment. The effect of paenimyxin on cultivatable bacteria was negligible 7 days after treatment. Approximately 10 7 16S rDNA sequences per gram of soil (dry weight) were detected by quantitative PCR in all samples. Paenimyxin did not affect the quantification of 16S rDNA or of the denitrifying bacterial community. In addition, RISA fingerprinting showed that the genetic structure of the bacterial communities was significantly modified 2 days after paenimyxin application at 50 μM and 4 days after treatment at lower concentrations (0.5 and 5 μM). The impact of paenimyxin treatment on the genetic structure of soil bacterial communities was transient, as no effect could be observed after 7, 14 and 28 days when compared with the untreated control.  2007 Society of Chemical Industry Keywords: biopesticide; paenimyxin; soil DNA; quantitative PCR 1 INTRODUCTION Soil health refers to the biological, chemical and physical features of soil that are essential to long-term, sustainable agricultural productivity with minimal environmental impact. 1 The average losses in crop productivity owing to biotic agents (pests, diseases, weeds) is about 40%. 2 The control of plant pests, diseases and weeds is achieved mainly by spraying crops with synthetic chemical pesticides. 2,3 Although pesticide use permits a certain quality of agricultural production, intense use is known to contribute to the contamination of soil and water resources at concentrations often exceeding the European limit of 0.1 μgL −1 in drinking water. 4 In addition, the heavy use of chemicals in agriculture reduces soil biodiversity, leading to soil compaction and other disturbances. This in turn leads to adverse ecological alterations, resulting in a loss of agricultural productivity. 1 The development of new practices will improve agricultural sustainability. An alternative option for maintaining crop health and yields is to develop biological products based on beneficial microorganisms. 5 Microbial pesticides are being introduced as part of this new scenario of crop protection. Currently, several beneficial microorganisms are the active ingredients of a new generation of microbial pesticides or the basis of many natural antagonistic products of microbial origin. 6 Although more than 500 antimicrobial peptides have been described, 7 and a relatively high number patented as biopesticides, only a few have been registered for agricultural use. The excessive specificity of most biopesticides and their biosafety in terms of impact on the soil microflora and environment are major factors limiting their use in agriculture. 6 Notably, the impact of biopesticide application on the environment needs to be evaluated, and, more particularly, the effect on soil microorganisms, which are among the most diverse components of terrestrial ecosystems, responsible for organic matter transformation and contributing to the C and N ratio. No studies of the impact of purified antimicrobial compounds on soil microbial diversity on the basis of a culture-independent approach have been reported to date. The present authors recently identified a ∗ Correspondence to: Diederik van Tuinen, UMR INRA 1088/CNRS 5184/Universit ´ e de Bourgogne, Plante-Microbe-Environnement CMSE-INRA, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France E-mail: tuinen@epoisses.inra.fr (Received 15 March 2006; revised version received 29 August 2006; accepted 12 October 2006) Published online 23 January 2007; DOI: 10.1002/ps.1335  2007 Society of Chemical Industry. Pest Manag Sci 1526–498X/2007/$30.00