Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession

Abstract

Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

Changes in belowground biodiversity during ecosystem development

“…Moreover, multiple taxa should be considered in concert to achieve a holistic understanding of how belowground biodiversity changes during pedogenesis. Second, most studies reported to date have focused on changes in belowground biodiversity during initial stages of primary succession (i.e., years to centuries) (13,22), with few studies evaluating effects over much longer time scales (i.e., from centuries to thousands or millions of years) (13,15,16). The fate of belowground biodiversity is expected to differ between early and late stages of pedogenesis, because older ecosystems may enter a retrogressive phase (19,(23)(24)(25).…”

Reliability analysis of fish traits reveals discrepancies among databases

“…Trait‐based approaches also enable one to address macroecological questions by potentially reducing species‐specific context dependency and allowing for generalisation across communities and ecosystems (Hortal et al, ; Kunstler et al, ; McGill, Enquist, Weiher, & Westoby, ; Moretti et al, ; Statzner, Bis, Dolédec, & Usseglio‐Polatera, ; Suding et al, ). Trait‐based approaches are employed in many organism groups such as plants (Guittar, Goldberg, Klanderud, Telford, & Vandvik, ; Kergunteuil, Descombes, Glauser, Pellissier, & Rasmann, ), animals (Castro, Dolédec, & Callisto, ; Frimpong & Angermeier, ; Luck, Lavorel, Mcintyre, & Lumb, ; Poff et al, ), phytoplankton (Litchman & Klausmeier, ), and microorganisms (Allison, ; Guittar, Shade, & Litchman, ; Ortiz‐Álvarez, Fierer, Los Ríos, Casamayor, & Barberán, ). However, there is considerable disparity in the methodological advancements among different organism groups.…”

Inference based PICRUSt accuracy varies across sample types and functional categories

“…Microbial community functional profiles are typically of much lower variance compared to their taxonomic profiles likely because of the large proportions of “core” or “housekeeping” functions [18–20]. In this study, we showed that this lack of variance in functional profiles between samples leads to a strong correlation between functional profiles from metagenome sequencing and those estimated from references with PICRUSt, even when the sample labels are randomly shuffled (Fig.…”