title: Use of DGGE and COMPOCHIP for investigating bacterial communities of various vermicomposts produced from different wastes under dissimilar conditions.
abstract: 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.
authors.affiliation: Department of Environmental Protection, Estación Experimental del Zaidín, Profesor Albareda 1, 18008 Granada, Spain. manuelj.fernandez@eez.csic.es
authors.forename: Manuel J
authors.initials: MJ
authors.lastname: Fernández-Gómez
authors.forename: Rogelio
authors.initials: R
authors.lastname: Nogales
authors.forename: Heribert
authors.initials: H
authors.lastname: Insam
authors.forename: Esperanza
authors.initials: E
authors.lastname: Romero
authors.forename: Marta
authors.initials: M
authors.lastname: Goberna
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D001419:Bacteria / Q000235:genetics*; D002417:Cattle; D016172:DNA Fingerprinting; D017931:DNA Primers / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods*; D004553:Electric Conductivity; D006863:Hydrogen-Ion Concentration; D018551:Solanum lycopersicum; D008372:Manure / Q000032:analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D000069463:Olive Oil; D010938:Plant Oils; D012987:Soil; D012988:Soil Microbiology; D014866:Waste Products / Q000032:analysis
chemical_list: D017931:DNA Primers; D008372:Manure; D000069463:Olive Oil; D010938:Plant Oils; D012987:Soil; D014866:Waste Products