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Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA. 

Jatropha curcas seeds, as an abundant lignocellulosic biomass, offer a highly promising and ideal alternative for producing energy in the form of methane. Use of J. curcas seeds has the potential to significantly bolster the biofuel sector, fostering a more sustainable circular economy. In the current study, different fractions of processed J. curcas seeds were investigated for biogas production. J. curcas seed pressed cake, a by-product of biodiesel production, was subjected to methanolic extraction. The remaining solids, referred to as methanolic residues, yielded more biogas in batch experiments than pressed cake and residues from aqueous and n-hexane extractions. The compounds extracted with methanol inhibited hydrolysis and reduced biogas production by 35.5% compared to the same setup without extracts. In continuous reactors fed with methanolic residues, the highest biogas yield occurred at an organic loading rate (OLR) of 1 g VS L−1 day−1 and a hydraulic retention time (HRT) of 20 days. The relative abundance of acetogenic bacteria was higher in reactors fed with methanolic residues than in those fed with seed pressed cake, seed oil, and whole seed. Jatropha seed oil and whole seed did not inhibit methanogens. A higher relative abundance of methanogenic communities was observed in all reactors at HRT of 20 days compared to those at HRTs at 15 and 10 days. These findings can be used to increase biogas production during anaerobic digestion of J. curcas seed components and suggests a zero-waste biorefinery production route for value added compounds derived from the removal of biogas-inhibiting components. 

Both deterministic and stochastic forces shape biofilm communities, but the balance between those forces is variable. Quantifying the balance is both desirable and challenging. For example, drift-driven failure, a stochastic force, can be thought of as an organism experiencing ‘bad luck’ and manipulating ‘luck’ as a factor in real-world systems is difficult. We used an agent-based model to manipulate luck by controlling seed cevalues governing random number generation. We determined which organism among identical competitors experienced the greatest drift-driven failure, gave it a deterministic growth advantage and re-ran the simulation with the same seed. This enabled quantifying the growth advantage required to overcome drift, e.g. a 50% chance to thrive may require a 10–20% improved growth rate. Further, we found that crowding intensity affected that balance. At moderate spacings, there were wide ranges where neither drift nor selection dominated. Those ranges shrank at extreme spacings; close and loose crowding, respectively, favoured drift and selection. We explain how these results may partially illuminate two conundrums: the fact that a stably operating wastewater treatment plant's microbial community can vary greatly over time and the difference between equivalent and total community size in neutral community assembly models.