Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil Samiran Banerjee * , Clive A. Kirkby, Dione Schmutter, Andrew Bissett, John A. Kirkegaard, Alan E. Richardson CSIRO Agriculture, ACT 2601, Australia article info Article history: Received 9 February 2016 Received in revised form 23 March 2016 Accepted 28 March 2016 Available online 3 April 2016 Keywords: Organic matter Decomposition Network analysis Co-occurrence Keystone taxa abstract Organic matter (OM) decomposition and breakdown of crop residues are directly linked to carbon (C) sequestration in agricultural soils as a portion of the decomposed C becomes assimilated into stable microbial biomass. Microbial decomposition of OM may vary with quality of OM, addition of nutrients and functional types of microbes. While the role of fungi and bacteria in OM decomposition has received considerable attention, the succession and co-occurrence patterns of these communities during decomposition remain unexplored. Using 454 pyrosequencing and network analysis of bacterial 16S rRNA and fungal ITS genes in a time-course microcosm experiment, this study shows a positive effect of nutrient addition on overall microbial biomass and abundance of bacteria and fungi. Abundance of different bacterial and fungal groups changed up to 300-folds under straw- and nutrient amended treatments while the rate of decomposition remained similar, indicating a possible functional redun- dancy. Moreover, addition of nutrients significantly altered the co-occurrence patterns of fungal and bacterial communities, and these patterns were resource-driven and not phylogeny-driven. Richness, evenness and diversity decreased and were negatively associated with decomposition rate. Acidobacteria, Frateuria and Gemmatimonas in bacteria and Chaetomium, Cephalotheca and Fusarium in fungi were found as the keystone taxa. These taxa showed strong positive associations with decomposition, indicating their importance in C turnover. Overall, we show that addition of nutrients reduces diversity but favours the keystone taxa, and thereby increases microbial biomass. © 2016 Elsevier Ltd. All rights reserved. 1. Introduction Soils comprise the largest sink of terrestrial C, 2500 Gt at 1 m depth, and approximately 25% of the soil C has been lost to the atmosphere due to intensive agricultural production (Lal, 2004). Enhancing the potential of agricultural soils to sequester C has significant implications for reducing atmospheric CO 2 and also for alleviating soil degradation and nutrient depletion. The pivotal role of soil microbiota in C sequestration is now well-acknowledged (Dungait et al., 2012; Schimel and Schaeffer, 2012; Trivedi et al., 2013; Wieder et al., 2013) with recent studies reporting that fine- fraction C, i.e., stable OM, is likely of microbial origin (Liang and Balser, 2011; Schmidt et al., 2011). The amount of microbially derived organic C in soil is determined by this balance of miner- alization and assimilation i.e. microbial carbon use efficiency (Allison et al., 2010; Wieder et al., 2013), which may depend on community structure and composition and/or organic matter quality (Fontaine et al., 2003; Six et al., 2006). The quality of straw-stubble is a very relevant issue for stubble management in agricultural soils as it can affect the rate of its decomposition (Blagodatskaya and Kuzyakov, 2008; Fontaine et al., 2003). For example, the energy content of straw-stubble may change with straw-age (i.e. with time from harvest), which may determine its breakdown and further incorporation into soils organic matter. This is particularly important because for soil mi- croorganisms, the ability to breakdown ‘fresh’ organic matter compared to ‘old’ organic matter may change with functional types (Fontaine et al., 2003). For example, it has been suggested that residue decomposition may be initially dominated by r -strategists (copiotrophs, preferring fresh organic matter and higher nutrient * Corresponding author. E-mail address: samiran.banerjee@csiro.au (S. Banerjee). Contents lists available at ScienceDirect Soil Biology & Biochemistry journal homepage: www.elsevier.com/locate/soilbio http://dx.doi.org/10.1016/j.soilbio.2016.03.017 0038-0717/© 2016 Elsevier Ltd. All rights reserved. Soil Biology & Biochemistry 97 (2016) 188e198