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Molecular Analysis of Bacterial Community Succession During Prolonged Compost Curing

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Molecular Analysis of Bacterial Community Succession During Prolonged Compost Curing RESEARCH ARTICLE Molecularanalysis of bacterial community succession during prolonged compost curing Michael Danon1, Ingrid H. Franke-Whittle2, Heribert Insam2, Yona Chen1 & Yitzhak Hadar1 1Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel; and 2Institute for Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria Downloaded from https://academic.oup.com/femsec/article/65/1/133/620549 by guest on 30 September 2021 Correspondence: Yitzhak Hadar, Abstract Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food The compost environment consists of complex organic materials that form a and Environmental Quality Sciences, The habitat for a rich and diverse microbial community. The aim of this research was to Hebrew University of Jerusalem, PO Box 12, study the dynamics of microbial communities during the compost-curing phase. Rehovot 76100, Israel. Tel.: 1972 8 9489935; Three different methods based on 16S rRNA gene sequence were applied to fax: 1972 8 9468785; e-mail: monitor changes in the microbial communities: (1) denaturing gradient gel [email protected] electrophoresis of PCR-generated rRNA gene fragments; (2) partial rRNA gene clone libraries; and (3) a microarray of oligonucleotide probes targeting rRNA Received 20 December 2007; revised 11 March gene sequences. All three methods indicated distinctive community shifts during 2008; accepted 10 April 2008. First published online 4 June 2008. curing and the dominant species prevailing during the different curing stages were identified. We found a successional transition of different bacterial phylogenetic DOI:10.1111/j.1574-6941.2008.00506.x groups during compost curing. The Proteobacteria were the most abundant phylum in all cases. The Bacteroidetes and the Gammaproteobacteria were Editor: Alfons Stams ubiquitous. During the midcuring stage, Actinobacteria were dominant. Different members of nitrifying bacteria and cellulose and macromolecule-degrading Keywords bacteria were found throughout the curing process. In contrast, pathogens were biosolids compost; clone library; community not detected. In the cured compost, bacterial population shifts were still observed composition; oligonucleotide microarray; after the compost organic matter and other biochemical properties had seemingly organic matter degradation; PCR-DGGE. stabilized. toward Sclerotium rolfsii has been demonstrated during Introduction prolonged curing time (Danon et al., 2007). Compost of an Composting is an aerobic process by which organic materi- appropriate age should therefore be used to control disease als are degraded through the activities of successive groups in infested soils before sowing. The successful application of of microorganisms. Soil amendment with composted or- compost is considerably dependent on the selection of an ganic material is an ancient practice that is applied through- appropriate curing period. out the world, and the long-term benefits of compost The biochemistry of the compost-curing process has been application to fields are well documented (Ros et al., 2006). studied extensively. Chen et al. (1989) found that the Previous studies have emphasized the importance of achiev- original cellulose and hemicellulose contents of cattle man- ing compost maturity to ensure balanced plant nutrition ure were reduced by one-third during a 5-month compost- and for the biological control of soil-borne plant disease ing and maturing process. Hemicellulose and cellulose may (Fuchs, 2002; Noble & Coventry, 2005). Compost maturity be the main substrates for microorganisms during the is achieved during the curing process. The duration of maturation process because these components are present curing in the industry varies according to a number of in large quantities in cattle manure and the less complex factors, including source materials, composting process and carbon sources are consumed early on in the process (Chen facility, climate, and planned utilization of the final product. et al., 1989). Recently, Tang et al. (2006) reported that Noncured composts may be phytotoxic, whereas extensively organic matter decomposition during the maturation of cured composts may lose their plant-disease-suppressive cattle-manure compost resulted in decreased C/N ratios, properties. For instance, loss of compost suppressiveness microbial biomass, and microbial diversity. The C/N ratio in FEMS Microbiol Ecol 65 (2008) 133–144 c 2008 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved 134 M. Danon et al. the compost may level off much before the compost vation-independent techniques based on 16S rRNA gene stabilizes (Chefetz et al., 1996) and although the concentra- sequences: PCR-denaturing gradient gel electrophoresis tion of the dissolved organic carbon (DOC) of municipal (DGGE), clone libraries, and an oligonucleotide microarray solid-waste compost did not change at maturation, the (COMPOCHIP). Molecular techniques are becoming in- relative concentrations of different hydrophilic and hydro- creasingly useful for the detection of different microorgan- phobic fractions in the dissolved organic matter continued isms without first having to isolate and cultivate them (Dees to change concomitant with the decrease in phytotoxicity & Ghiorse, 2001; Green et al., 2004; Franke-Whittle et al., (Chefetz et al., 1998). Tang et al. (2006) showed that during 2005; Kelly et al., 2005). Although they share the same basis, the maturation period, the proportion of Actinobacteria i.e. exploiting conserved and variable regions in the riboso- increases slightly, and this was associated with the disap- mal small subunit sequence, each of the techniques used in pearance of phytotoxicity. our study has its inherent advantages and disadvantages. A Downloaded from https://academic.oup.com/femsec/article/65/1/133/620549 by guest on 30 September 2021 Considerable effort and a variety of techniques have been combined analysis was therefore expected to produce more applied to the study of compost microbial populations reliable information on the qualitative and quantitative (Cahyani et al., 2003; Schloss et al., 2003; Ryckeboer et al., succession of bacterial populations during compost curing. 2003b). The initial phase of composting is thought to be the most dynamic part of the process and is characterized by rapid increases in temperature, large changes in pH, and the Materials and methods degradation of simple organic compounds. Schloss et al. Prolonged compost-curing process and compost (2003) reported two significant shifts in the composition of sampling the microbial community: one occurring between 12 and 24 h and the other between 60 and 72 h into the process. Compost samples were obtained from a commercial com- Ryckeboer et al. (2003b) attempted to determine the micro- posting facility (Shacham, Givaat Ada, Dlila Facility, Israel) bial succession of the dominating taxa and functional that prepared compost from a mixture of sewage sludge and groups of microorganisms, as well as the total microbial yard waste (1 : 1, v/v) in windrows (2.5 m wide and 2 m activity during composting of biowaste, using incubation, high). Aeration was achieved by bi-weekly turning for the isolation, and enumeration techniques. They reported that entire 12-week composting process. The biosolids compost, bacteria dominated during the thermophilic phase while considered to be mature by the producers, i.e. appropriate fungi, Streptomycetes, and yeasts were below detection for field application, was sampled and further treated as limits. Different bacterial populations were found in the follows: c. 700 L of bulk compost was collected and placed in thermophilic and mesophilic composting phases. During a cubic, 700-L bin, rewetted and turned every 2 weeks for the the peak-heating phase of fresh wastes, the only bacteria first month, then every month for the next 4 months. The isolated were bacilli; however, during the cooling and resultant compost pile was then left unturned for seven maturation phases, the bacterial diversity of both Gram- additional months (in total, 1 year of prolonged curing). positive and Gram-negative bacteria increased (Ryckeboer Compost temperature in the container increased after et al., 2003b). Using cultivation-independent methods, rewetting to 42 1C in the first week, and then decreased over Cahyani et al. (2003) studied the bacterial communities in the next 2 weeks to 32 1C(c.51C above ambient). Approxi- composting of rice straw. They reported a successional mately 20 L of compost was sampled from the bin at time 0 transition of bacterial community members: Alphaproteo- (beginning of prolonged curing), then after each turning, bacteria in the raw materials, Bacillus and Actinomycetes at and stored at 4 1C until analysis. the thermophilic stage, and Cytophaga and clostridial mem- bers at the middle and curing stages. These authors reported DNA extraction, general molecular procedures, that the microbial community remained stable during the and replications curing phase. In contrast, Steger et al. (2007) revealed compositional changes within the Actinobacteria commu- DNA from 0.25 g of compost subsamples was extracted nity in a full-scale composting process of organic household using a ‘PowerSoil’ kit (Mobio, Solana Beach, CA). The waste over a period of 57 weeks. DNA extracts were used as templates for PCR amplification Despite the important role of microbial
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