Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla Harald Cederlund a , Ella Wessén a , Karin Enwall a , Christopher M. Jones a , Jaanis Juhanson a , Mikael Pell a , Laurent Philippot b, c , Sara Hallin a, * a Swedish University of Agricultural Science, Department of Microbiology, Box 7025, 75007 Uppsala, Sweden b INRA, UMR1347 Agroecologie, 2100 Dijon, France c Université de Bourgogne, UMR 1229, F-21000 Dijon, France A R T I C L E I N F O Article history: Received 28 March 2014 Received in revised form 1 June 2014 Accepted 18 June 2014 Available online xxx Keywords: Biological indicators Long-term experiment Microbial community Nitrogen fertilization Organic amendment Soil status A B S T R A C T Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatments. We hypothesized that the long-term treatments had created distinctly different ecological niches for soil bacteria, suitable for either fast-growing copiotrophic bacteria, or slow-growing oligotrophic bacteria. Based on terminal-restriction fragment length polymorphism of the 16S rRNA genes from the total soil bacterial community and taxa-specific quantitative real-time PCR of seven different groups, all treatments significantly affected the community structure, but nitrogen fertilization was the most important driver for changes in the relative abundances of the studied taxa. According to an indicator species analysis, the changes were largely explained by the decline in the relative abundances of Acidobacteria, Gemmatimonadetes and Verrucomicrobia with nitrogen fertilization. Conditions more favourable for copiotrophic life strategies were indicated in these plots by the decreased metabolic quotient, i.e. the ratio between basal respiration rate and soil biomass. Apart from the Alphaproteobac- teria that were significantly associated with peat, no taxa were indicative of organic amendment in general. However, several significant indicators of both peat and straw were identified among the terminal restriction fragments suggesting that changes induced by the organic amendments were mainly manifested at a lower taxonomical level. Our findings strengthen the proposition that certain higher bacterial taxa adapt in an ecologically coherent way in response to changes induced by fertilization. ã 2014 Elsevier B.V. All rights reserved. 1. Introduction Agricultural soils are managed with the aim to maintain or increase productivity, which is typically achieved by sustaining a high soil organic matter (SOM) content and applying nitrogen (N) fertilizers. Both mineral nitrogen and organic amendments affect the size and composition of soil bacterial communities, as well as the ecosystem processes and services they mediate, e.g. soil organic matter decomposition, nutrient cycling and carbon sequestration. Agricultural practices that impact SOM can signifi- cantly alter the indigenous soil microbial community structure (Enwall et al., 2007; Peacock et al., 2001; Stark et al., 2008), and it has been suggested that the bacterial community structure is more affected than the fungal community by organic fertilizers (Lejon et al., 2007; Marschner et al., 2003). In addition, several recent studies have shown that N-fertilization leads to changes in the relative abundances of specific bacterial phyla (Nemergut et al., 2008; Turlapati et al., 2013; Wessén et al., 2010). Ramirez et al. (2012) demonstrated that some of these changes appear to be consistent across a broad range of soil types and that Actino- bacteria and Firmicutes were consistently favoured by N-fertiliza- tion, whereas the relative abundance of Acidobacteria and Verrucomicrobia decreased. Philippot et al. (2009, 2010) argued that high bacterial taxa display properties of ecological coherence since they respond predictably to environmental factors, although ecological traits that characterize bacterial taxa defined at higher taxonomic ranks may be more unifying than universal. Earlier, Fierer et al. (2007) * Corresponding author. Tel.: +46 18 67 32 09; fax: +46 18 67 33 92. E-mail address: sara.hallin@slu.se (S. Hallin). http://dx.doi.org/10.1016/j.apsoil.2014.06.003 0929-1393/ ã 2014 Elsevier B.V. All rights reserved. Applied Soil Ecology 84 (2014) 62–68 Contents lists available at ScienceDirect Applied Soil Ecology journal homepage: www.else vie r.com/locate /apsoil