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

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.

Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors

“…Recent studies suggest that both contribute to the assembly of microbial communities in WWTPs. However, there is no agreement about the importance of deterministic and stochastic processes in this system 12 , 13 .…”

Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

“…The choice between WGS and short-read amplicons also comes down to the aim of the proposed study, whether the goal is to explore microbial ecology [ 17 , 18 , 19 ], or to discover novel genomes [ 20 ]. Not only is sequencing short-read amplicons cheaper [ 21 ], but the downstream analysis is more accessible, faster and can access ever-improving reference databases [ 22 , 23 , 24 , 25 ].…”

“…This will allow for basic diversity statistics, the identification of discriminant taxa and a core microbiome (e.g., [ 43 ]). However, for more advanced ecological modelling to be applied, usually a minimum of five to six replicates are required; this will usually satisfy criteria for the null models which often underpin community assembly analysis (e.g., [ 18 , 44 , 45 ]). Finally, for even more involved methods such as network inferences, upwards of 35 samples per category are often necessary to obtain reliable results (e.g., [ 46 , 47 ]).…”

“…Notably, Quantitative Process Estimates (QPE) uses null modelling to quantify assembly within an ecological framework based on selection and dispersal mechanisms [ 94 ]. Specifically, it classifies assembly mechanisms as (i) variable selection , when selective environmental conditions result in high compositional turnover; (ii) homogenous selection , when static environmental conditions result in consistent selective pressure; (iii) dispersal limitation , when low rates of dispersal (movement of microorganisms in space) result in high community turnover (this drives ecological drift); (iv) homogenizing dispersal , when high compositional turnover is fueled by high dispersal rates; or (v) “ undominated ”, when compositional turnover is neither the result of selection nor dispersal [ 18 , 95 ]. QPE holds several advantages over other types of assembly quantification tools: (i) it incorporates both phylogenetically informed, and phylogenetically uninformed data making it better suited for understanding ecological phenomena—whereas several other available methods do not take phylogeny into account (such as the stochasticity ratio (SR), discussed next); (ii) with QPE we can measure the relative contribution of different processes acting simultaneously upon a community; and (iii) QPE allows for the identification and comparison of dominant assembly mechanisms under different conditions.…”

Autotrophic Denitrification of Nitrate Rich Wastewater in Fluidized Bed Reactors Using Pyrite and Elemental Sulfur as Electron Donors

“…Amplicon Sequencing Variants (ASVs) were constructed using Qiime2 workflow according to Trego et al (2021). All code for sequence processing can be found at (https://github.com/umerijaz/tutorials/blob/master/qiime2_tutorial.md).…”