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.
Highlights
IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales
Community assembly mechanisms are inherently linked with ecosystem function, as they play an important role in shaping community structure [12]
Microbial communities can be assessed in terms of their functional gene structure [42], and while functional gene assembly can be assessed via microarray [22, 43] or clone library [44] approaches, a more complete view of the functional gene structure of the microbial community can be obtained through shotgun metagenomics
Summary
IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. Press disturbances that impose a long-term continuous change of species abundances by altering the environment [8] are of interest in microbial ecology, as they can drive systems to alternative stable states with different community function and structure [9]. An assessment of community assembly mechanisms combining both 16S rRNA gene amplicon and shotgun metagenomics sequencing would provide important insights toward a better understanding of the effect of disturbance in community assembly, structure, and function, while still allowing a comparison with prior findings. Such evaluation is seldom carried out in complex and engineered microbial systems like bioreactors for wastewater treatment
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