Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation.

Anna Christine Trego,Umer Zeeshan Ijaz,Florence Abram,Paul G Mcateer,Corine Nzeteu,Therese Mahony,Vincent O’Flaherty

doi:10.3389/fmicb.2021.666584

Abstract

Advances in null-model approaches have resulted in a deeper understanding of community assembly mechanisms for a variety of complex microbiomes. One under-explored application is assembly of communities from the built-environment, especially during process disturbances. Anaerobic digestion for biological wastewater treatment is often underpinned by retaining millions of active granular biofilm aggregates. Flotation of granules is a major problem, resulting in process failure. Anaerobic aggregates were sampled from three identical bioreactors treating dairy wastewater. Microbiome structure was analysed using qPCR and 16S rRNA gene amplicon sequencing from DNA and cDNA. A comprehensive null-model approach quantified assembly mechanisms of floating and settled communities. Significant differences in diversity were observed between floating and settled granules, in particular, we highlight the changing abundances of Methanosaeta and Lactococcus. Both stochastic and deterministic processes were important for community assembly. Homogeneous selection was the primary mechanism for all categories, but dispersal processes also contributed. The lottery model was used to identify clade-level competition driving community assembly. Lottery “winners” were identified with different winners between floating and settled groups. Some groups changed their winner status when flotation occurred. Spirochaetaceae, for example, was only a winner in settled biomass (cDNA-level) and lost its winner status during flotation. Alternatively, Arcobacter butzerli gained winner status during flotation. This analysis provides a deeper understanding of changes that occur during process instabilities and identified groups which may be washed out—an important consideration for process control.

Highlights

Even Earth’s most extreme environments are teeming with complex microbial communities, performing vital eco-system functions
The combination of null models used in this study revealed that both stochastic and deterministic processes simultaneously drive community assembly—an idea that could reconcile conflicting reports from built environments (Ofiteru et al, 2010; Zhou et al, 2013; Vanwonterghem et al, 2014; Leventhal et al, 2018; Ali et al, 2019)
The lottery model suggested that these selection processes may have been governed by intense competition between species

Summary

Introduction

Even Earth’s most extreme environments are teeming with complex microbial communities, performing vital eco-system functions. Understanding and measuring biodiversity and the way these complex communities assemble and continue to develop has intrigued ecologists for decades (Gaston, 2000). The use of null-models for identifying and quantifying community assembly has continued to gain traction with several advances in both methodology and interpretation (Presley et al, 2010; Chase et al, 2011; Stegen et al, 2012; Tucker et al, 2016; Zhou and Ning, 2017; Verster and Borenstein, 2018; Ning et al, 2019; Vass et al, 2020). A lottery-based approach was implemented to explore clade-based assembly in the human gut microbiome by identifying lottery “winners” which were out-competing other closely related taxa (Verster and Borenstein, 2018)

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Conclusion