Ecological Indicators 18 (2012) 218–226 Contents lists available at SciVerse ScienceDirect Ecological Indicators journal homepage: www.elsevier.com/locate/ecolind Soil quality indicators for intensive vegetable production systems in Java, Indonesia Bram Moeskops a,∗ , David Buchan a , Sukristiyonubowo b , Stefaan De Neve a , Bart De Gusseme c , Ladiyani Retno Widowati b , Diah Setyorini b , Steven Sleutel a a Department of Soil Management, Ghent University, Coupure Links 653, 9000 Gent, Belgium b Indonesian Soil Research Institute, Bogor 16123, Indonesia c Department of Biochemical and Microbial Technology, Ghent University, 9000 Gent, Belgium article info Article history: Received 17 December 2010 Received in revised form 8 November 2011 Accepted 12 November 2011 Keywords: Organic farming Soil quality Ergosterol PLFA Enzyme activity Indonesia abstract We explored the value of ergosterol, phospholipid fatty acid (PLFA) profiles and neutral lipid fatty acid (NLFA) 16:15c as soil quality indicators for the intensive systems of vegetable production in the humid tropical climate of West Java, by comparing organic and conventional management. Additionally, we measured dehydrogenase and -glucosidase activity. A secondary forest was included to obtain reference values under undisturbed conditions. Organic and conventional agriculture, and secondary forest each differed in the composition of the microbial community measured by PLFA profiles. Ergosterol appeared not to be universally applicable as a fungal biomarker and in this respect seemed to be inferior compared to PLFA fungal markers. NLFA 16:15c may provide additional information as an indicator of arbuscular mycorrhizal fungi, but its high variability complicated the interpretation of data. The ratio of cy17:0 to 16:17c was effectively applied as an indicator of physiological stress experienced by the bacterial community. Conventional vegetable production resulted in higher cy17:0/16:17c ratios. Finally, a soil quality index, developed by stepwise canonical discriminant analysis and based on the absolute amount of PLFA 16:0, the relative amount of PLFAs 10Me16:0 and 10Me18:0, and dehydrogenase activity, was successfully validated. © 2011 Elsevier Ltd. All rights reserved. 1. Introduction Numerous reports warn for the overuse of fertilizer and pesti- cides in vegetable production in Southeast Asia (see Moeskops et al., 2010 for a discussion of Mazlan and Mumford, 2005; Phupaibul et al., 2002; Poudel et al., 1998; Rerkasem, 2005; Schroer et al., 2005). The intensive character of vegetable production in Southeast Asia and Indonesia is further enhanced by continuous cultivation, made possible by the constantly high temperatures which pre- vail year-round. In the highlands of West Java, fallow periods are restricted to a few weeks only and cultivation of 4–6 crops per year on the same field is not uncommon. When monitoring the on-going land degradation in the trop- ics, sensitive soil quality indicators are to be identified. Because ∗ Corresponding author. Tel.: +32 9 264 60 61; fax: +32 9 264 62 47. E-mail addresses: Bram.Moeskops@gmail.com (B. Moeskops), David.Buchan@UGent.be (D. Buchan), sukristiyonubowo@yahoo.com (Sukristiyonubowo), Stefaan.DeNeve@UGent.be (S. De Neve), Bart.DeGusseme@UGent.be (B. De Gusseme), ladiyaniw@yahoo.com (L.R. Widowati), dsh@indo.net.id (D. Setyorini), Steven.Sleutel@UGent.be (S. Sleutel). of the role of the microbial community in maintaining soil fer- tility (Giller et al., 1997) and the suppression of diseases (Janvier et al., 2007), and due to its rapid response to changes in man- agement, microbial indicators seem to be particularly useful for the assessment of soil quality. Phospholipid and neutral fatty acids (PLFAs and NLFAs) and ergosterol are membrane bound cell com- ponents that are increasingly used to study the composition of the microbial community in soil. Ergosterol is the predominant sterol in fungal cell membranes. It is specific to higher fungal phyla, but does not occur in arbuscular mycorrhizal fungi (AMF) (Joergensen and Wichern, 2008; West et al., 1987). Due to their specificity and rapid degradation after cell death, PLFAs are reliable measures of the viable cell biomass of specific groups of microorganisms (Zelles, 1999). While PCR-based methods offer more insight into changes in specific microbial populations, PLFA analysis is the most power- ful approach to demonstrate change in total microbial community structure (Ramsey et al., 2006). In this study, we will pay particular attention to the ratio of PLFA cy17:0 to PLFA 16:17c. As (Gram- negative) bacteria enter the stationary growth phase, monoenoic 7 PLFAs are transformed into cyclopropyl fatty acids and hence the ratio of cy17:0 to 16:17c has been proposed as an indicator of stress in the bacterial community (Bossio and Scow, 1998; Petersen and Klug, 1994). Bossio and Scow (1998) and Petersen and Klug 1470-160X/$ – see front matter © 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.ecolind.2011.11.011