Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation

Abstract

Discerning network interactions among different species/populations in microbial communities has evoked substantial interests in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. Here, we modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140-269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. Particularly, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.

Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake

“…The RMT-based approach is a widely used and robust tool for network construction and has been successfully used to construct various networks, including gene regulatory networks (Zhou et al, 2010; Lin et al, 2011, 2013), functional molecular ecological networks (Zhou et al, 2010) and phylogenetic molecular ecological networks (Zhou et al, 2011; Tu et al, 2016). To construct reliable co-occurrence ecological networks, the RMT-based network method was used (Deng et al, 2015), and only OTUs observed in at least 8 of the 12 samples were used for subsequent network analyses. Specifically, the validated pairwise correlations between OTUs were determined based on a Pearson correlation coefficient cutoff of 0.9 and 0.89 that was automatically identified based on RMT for PAB and FLB, respectively, and then was used for network construction.…”

“…PAB are usually associated with colloids and algae (Shao et al, 2014) and are considered algae-associated microbes, particularly during algal blooms (Riemann and Winding, 2001; Cai et al, 2013b), that were shown to have positive or negative effects on algal growth (e.g., algicidal bacteria) in a previous study (Berg et al, 2009). Microbes do not live separately but rather interact with each other to form ecological networks and accomplish ecosystem functions (e.g., material and energy flows, ecosystem stability) (Deng et al, 2015; Shi et al, 2016). Therefore, explaining and predicting the variation in network structure are essential parts of microbial ecology (Zhou et al, 2010) and are useful for guiding practical applications, including biodiversity preservation and ecosystem management.…”

“…Culture-independent molecular technology has developed rapidly in recent years and has been acknowledged as a feasible approach to study complex microbial communities. Emerging high-throughput sequencing technologies can provide a comprehensive understanding of the specific microbial species that live and thrive in various environments (Logares et al, 2014), and network-based approaches have been successfully used to evaluate the influence of environmental disturbances on the whole community (Raes and Bork, 2008; Zhou et al, 2010) and analyze microbial interactions in diverse habitats, including marine (Wang Y. et al, 2015), soil (Tu et al, 2015), acid mine drainage (Kuang et al, 2016) and groundwater environments (Deng et al, 2015). However, relevant research on microbial interactions during algal blooms is still limited, especially for the relationship between algae and associated bacteria.…”

Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

“…Thereafter, a series of thresholds from 0.30 to 1.00 with 0.01 intervals were applied to the matrix, and only the similarity values above a certain threshold were kept for calculating matrix eigenvalues. The finest threshold was chosen when the nearest neighbour spacing distribution of eigenvalues followed Poisson distribution, which represents specific and nonrandom properties of complex systems (Deng et al, 2012), and meanwhile the threshold should be as low as possible (Deng et al, 2016). Network analyses were performed using an online analysis pipeline at http://ieg2.ou.edu/MENA.…”

Relationships between microbial communities and groundwater chemistry in two pristine confined groundwater aquifers in central China

“…Previous reports indicated that the presence of SO 4 2− in groundwater significantly influenced the diversity of subterranean microbial communities (Pedersen, Bengtsson, Edlund, & Eriksson, ). Particularly, several sulphate‐reducing bacteria had strong negative interactions with other microorganisms (Deng et al, ). Our results further confirm the effect of SO 4 2− and sulphate‐reducing bacteria on the microbial community.…”