Use of DGGE and COMPOCHIP for investigating bacterial communities of various vermicomposts produced from different wastes under dissimilar conditions.

This study describes the use of denaturing gradient gel electrophoresis (DGGE) and COMPOCHIP (i.e. a microarray targeting typical bacteria of stabilized organic materials and pathogenic bacteria) for investigating the bacterial communities of four different vermicomposts. These included a commercial vermicompost produced from cattle manure (CM) and three vermicomposts produced at pilot-scale by recycling: damaged tomato fruits (DT); olive-mill waste mixed with biosolids (OB); and winery wastes (WW). DGGE provided distinctive fingerprints of each vermicompost, which were statistically related to their particular chemical features. The comparison of the various vermicompost fingerprints showed that they contained bacterial communities with an average similarity coefficient of close to 80%. COMPOCHIP detected the presence of Sphingobacterium, Streptomyces, Alpha-Proteobacteria, Delta-Proteobacteria, and Firmicutes in all the vermicomposts. COMPOCHIP showed differences in the abundance of particular bacterial taxa among the vermicomposts, giving an idea about the usefulness of each vermicompost in the search for bacteria valuable to biotechnology. The joint use of DGGE and COMPOCHIP is a useful tool to compare vermicompost bacterial communities and to assess the potential of different vermicomposts as bioactive organic materials.

[1]  D. Lane.  16S/23S rRNA sequencing , 1991 .

[2]  R. B. Jackson,et al.  The diversity and biogeography of soil bacterial communities. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[3]  R. Nogales,et al.  Feasibility of vermicomposting for vegetable greenhouse waste recycling. , 2010, Bioresource technology.

[4]  Yuming Fu,et al.  Ethylene removal evaluation and bacterial community analysis of vermicompost as biofilter material. , 2011, Journal of hazardous materials.

[5]  J. Fernández-Bayo,et al.  Improved retention of imidacloprid (Confidor) in soils by adding vermicompost from spent grape marc. , 2007, The Science of the total environment.

[6]  H. Heuer,et al.  Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients , 1997, Applied and environmental microbiology.

[7]  C. Edwards,et al.  Effects of vermicomposts produced from cattle manure, food waste and paper waste on the growth and yield of peppers in the field , 2005 .

[8]  Diet-related composition of the gut microbiota of Lumbricus rubellus as revealed by a molecular fingerprinting technique and cloning , 2009 .

[9]  A. Mukherjee,et al.  Crude petroleum-oil biodegradation efficiency of Bacillus subtilis and Pseudomonas aeruginosa strains isolated from a petroleum-oil contaminated soil from North-East India. , 2007, Bioresource technology.

[10]  Zubair Aslam,et al.  Bacterial community composition and chitinase gene diversity of vermicompost with antifungal activity. , 2009, Bioresource technology.

[11]  Subramaniam Gopalakrishnan,et al.  Evaluation of actinomycete isolates obtained from herbal vermicompost for the biological control of Fusarium wilt of chickpea , 2011 .

[12]  Michael Wagner,et al.  Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions , 2007, Microbial Ecology.

[13]  M. M. Szczech,et al.  Suppressiveness of Vermicompost against Fusarium Wilt of Tomato , 1999 .

[14]  C. Tebbe,et al.  Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes , 2000, Applied and Environmental Microbiology.

[15]  P. Kanekar,et al.  A novel extracellular protease from Pseudomonas aeruginosa MCM B-327: enzyme production and its partial characterization. , 2011, New biotechnology.

[16]  A. Vivas,et al.  Restoring biochemical activity and bacterial diversity in a trichloroethylene-contaminated soil: the reclamation effect of vermicomposted olive wastes , 2009, Environmental science and pollution research international.

[17]  Dittmar Hahn,et al.  Automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of Lumbricus terrestris L. , 2002, Journal of microbiological methods.

[18]  H. Insam,et al.  Molecular analysis of bacterial community succession during prolonged compost curing. , 2008, FEMS microbiology ecology.

[19]  L. Dendooven,et al.  Vermicompost as a soil supplement to improve growth, yield and fruit quality of tomato (Lycopersicum esculentum). , 2007, Bioresource technology.

[20]  Kyung-Suk Cho,et al.  Earthworm cast as a promising filter bed material and its methanotrophic contribution to methane removal. , 2010, Journal of hazardous materials.

[21]  L. Delgado-Moreno,et al.  Compost and vermicompost of olive cake to bioremediate triazines-contaminated soil. , 2009, The Science of the total environment.

[22]  J. Domínguez,et al.  Reduction of total coliform numbers during vermicomposting is caused by short-term direct effects of earthworms on microorganisms and depends on the dose of application of pig slurry. , 2009, The Science of the total environment.

[23]  D. Bagyaraj,et al.  Influence of vermicompost application on the available macronutrients and selected microbial populations in a paddy field , 1992 .

[24]  Heribert Insam,et al.  Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. , 2005, Journal of microbiological methods.

[25]  T. Nechitaylo,et al.  Culturable microorganisms from the earthworm digestive tract , 2009, Microbiology.

[26]  Sidney A. Williams,et al.  Official Methods of Analysis of the Association of Official Analytical Chemists , 1971, Soil Science Society of America Journal.

[27]  T. Chandra,et al.  Do earthworms affect dynamics of functional response and genetic structure of microbial community in a lab-scale composting system? , 2009, Bioresource technology.

[28]  C. Tebbe,et al.  Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes , 2006, Applied Microbiology and Biotechnology.

[29]  C. Edwards,et al.  Vermiculture Technology : Earthworms, Organic Wastes, and Environmental Management , 2010 .

[30]  G. Osipov,et al.  Comparative Investigation of Vermicompost Microbial Communities , 2002 .

[31]  Heribert Insam,et al.  Continuous-feeding vermicomposting as a recycling management method to revalue tomato-fruit wastes from greenhouse crops. , 2010, Waste management.

[32]  C. Manaia,et al.  Diversity of Bacterial Isolates from Commercial and Homemade Composts , 2008, Microbial Ecology.

[33]  J. Domínguez,et al.  Vermicomposting: Earthworms Enhance the Work of Microbes , 2010 .

[34]  Jérôme Harmand,et al.  Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. , 2006, Environmental microbiology.

[35]  H. Insam,et al.  Bacterial community patterns and thermal analyses of composts of various origins , 2008, Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA.

[36]  C. Edwards,et al.  Suppression of insect pest populations and damage to plants by vermicomposts. , 2005, Bioresource technology.

[37]  C. Edwards,et al.  Interactions between earthworms and microorganisms in organic-matter breakdown , 1988 .