State-Space-Based Framework for Predicting Microbial Interaction Variability in Wastewater Treatment Plants

Abstract

Substantial attempts have been made to control microbial communities for environmental integrity, biosystem performance, and human health. However, it is difficult to manipulate microbial communities in practice due to the varying and nonlinear nature of interspecific interaction networks. Here, we develop a manifoldbased framework to investigate the patterns of microbial interaction variability in wastewater treatment plants using manifold geometric properties and design a simple control strategy to manipulate the microbes in nonlinear communities. We validate our framework using the readily available and nonsequential microbiome profiles of wastewater treatment plants. Our results show that some microbes in the activated sludge and anammox communities display deterministic rival or cooperative relationships and constitute a stable subnetwork within the whole nonlinear community network. We further use a simulation to demonstrate that these microbes can be used to drive a microbe in a target direction regardless of the community dynamics. Overall, our framework can provide a time-efficient solution to select effective control inputs for reliable manipulation in varying microbial networks, opening up new possibilities across a range of biological fields, including wastewater treatment plants.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

“…We found that several core denitrifying bacteria lack key NO reduction genes, such as the strict core genus Desulfobacillus, revealing an overlooked synergy between anammox and denitrifying bacteria using NO as an intermediate. Additionally, our ndings revealed that the strong correlation between the genera Denitratisoma and anammox bacteria [23,76] was probably due to the key role of the phylogenetically similar genus Desulfobacillus in anammox microbiota. This interspecies interaction is more likely to depend on NO instead of nitrite, which warrants veri cation in future studies [86].…”

“…Moreover, with the discovery of novel species, including anammox bacteria, the study of species diversity has become highly important in anammox systems [19,20]. However, a large proportion of microorganisms and their functional potential in anammox systems are overlooked [21][22][23], largely due to the low taxonomic resolution of genomes [24,25].…”

Multipathway of Nitrogen Metabolism Revealed by Genome-Centered Metatranscriptomics from Pyrite-Guided Mixotrophic Partial Denitrification/Anammox Installations

“…Additionally, multitype electron-capturing coupled NO 3 – -N reduction metabolic pathways were also identified in the PRO3 ( Denitratisoma ) genome, including the TCA cycle, rASR pathway, and denitrification-related gene clusters assigned to this bin. Generally, Denitratisoma is classified as a heterotrophic denitrifying organism . Under C-org feeding, Denitratisoma expressed respiratory nitrate reductase genes ( narGH / napAD ), which reduce NO 3 – -N to NO 2 – -N and require the transport of NO 3 – -N into the cell inner membrane and cytoplasm .…”

“…Generally, Denitratisoma is classified as a heterotrophic denitrifying organism. 23 Under C-org feeding, Denitratisoma expressed respiratory nitrate reductase genes (narGH/napAD), which reduce NO 3 − -N to NO 2 − -N and require the transport of NO 3 − -N into the cell inner membrane and cytoplasm. 21 However, when pyrites were injected, PRO3 developed the rASR pathway (working principle refers to PRO2) in parallel to sharing the C-org metabolic load.…”