Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors

Abstract

Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance. IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.

The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance

“…Changes in microbiome structure do not always translate to change in community function, possibly due to functional redundancy among taxa. In addition, functional recovery may proceed at a different rate from taxonomic recovery [ 69 ]. Furthermore, disturbance to the microbial community does not necessarily translate to a detriment for the host: change to the microbiota following disease may erode function, but alternatively may indicate selective change toward a microbial community that is more resistant to Bd invasion (i.e., community adaptation to Bd).…”

Microbiome assembly predictably shapes diversity across a range of disturbance frequencies

“…Indeed, microbial seed-banks are thought to contribute to the maintenance of microbial diversity 47 and have been described as essential for understanding temporal community changes 48 . Further, stochastic assembly processes were shown to be more preponderant within the rare fraction of the microbial community 22 . Nonetheless, other processes might also be promoting stochastic assembly at intermediate disturbance frequencies, like ecological drift 36 and feedback mechanisms linked to density dependence and species interactions 49 .…”

“…The idea of community assembly processes underlying the observed patterns of diversity is reasonable, as such processes are believed to shape community structure 18 , which also links them to ecosystem function. These processes, either deterministic or stochastic, are known to act in combination to form community assembly [19][20][21][22] and can cause replicate communities to reach a similar or variable structure and function 17,23 . Further, while recent studies have reported positive correlations of strength of stochasticity with α-diversity in bacterial 24 and fungal 25 communities, the role of assembly processes behind diversity patterns under fluctuating disturbances is still unclear.…”

Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers

“…The focus of this work was on the stability of the nitrite oxidation function and the nitrifying microbial community, with overall community dynamics described in detail elsewhere 34 . Understanding community and activity dynamics of nitrifying bacteria is essential for improving design and operation of wastewater treatment biological processes 35 .…”