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In the past two decades, great efforts have been made to isolate, characterize or quantify functional microorganisms directly involved in removing nutrients (nitrogen and phosphorus) (Bond et al., 1995; Juretschko et al., 1998; Daims et al., 2006), hydrolyzing and fermenting bacteria (Juretschko et al., 1998; Xia et al., 2008), floc-forming bacteria (Shin et al., 1993; Schmid et al., 2003) and detrimental microorganisms that raise bulking and foaming problems (Wanner, 1994; Guo and Zhang, 2012) in activated sludge. Despite a rapidly increasing knowledge concerning the biochemical and ecological characteristics of these key microbes in wastewater treatment, full-scale activated sludge-based wastewater treatment plants (WWTPs) with nutrient removal still suffer from a series of operational problems, such as process instability (Eikelboom, 2000), sludge settling problems (Jenkins et al., 2004) and poor performance in nutrient removal (Seviour and Nielsen, 2010). Therefore, more fundamental knowledge regarding the microbial structure is essential to elucidate the biological mechanisms behind the problems.
Strikingly, non-random inter-taxa co-occurrence patterns between taxonomically distanced bacteria in activated sludge most likely suggest species interactions, such as mutualism and commensalism. For example, AOB Nitrosomonas co-occurs with NOB Nitrospira (Figure 5) out of a relation of mutualistic symbiosis, in which AOB provides nitrite for NOB, and in return, NOB removes nitrite to prevent its inhibition on AOB. The co-occurrence between the commensal bacteria Flavobacteria and the protein-hydrolyzing bacteria Saprospiraceae (Supplementary Figure S11b) is a typical instance of commensalism, that is, the former cross-feed on amino acids from protein hydrolyzed by the latter, as is often found in biodegradation (Faust and Raes, 2012). On the basis of these meaningful observations, we predict that the deterministic co-occurrence observed between TM7 and Chloroflexi (Anaerolineae; Supplementary Figure S11a) could be derived from a cooperative relation. These two types of bacteria have been detected by FISH to co-occur in filament epiphytic protein-hydrolyzing communities of five full-scale WWTPs (Xia et al., 2007). The recent construction and analysis of TM7 genomes indicate that microaerophilic TM7 often buries its coccus cells deeply in flocs and primarily ferments glucose and other sugars in bioreactors (Albertsen et al., 2013). On the basis of this knowledge, it is speculated that TM7 may colonize to filamentous Chloroflexi in activated sludge bioflocs because of the benefits of minimized oxygen exposure and the easier adsorption of organic molecules (usually in the form of colloids and small particles) caught by the filaments from the bulk wastewater. In return, fermentative TM7 may provide substrates to its filamentous host. Overall, our observation that co-occurring bacteria tend to be taxonomically less related essentially resembles the phylogenetic overdispersion of co-occurring species of plants or animals observed in many studies (Losos, 2008; Bennett et al., 2013), revealing that negative interactions (such as competition) have an important impact on the community assembly of large varieties of biological communities from microorganisms (for example, bacteria) to macroscopic plants and animals. 1e1e36bf2d