Significance: Across ecology, and particularly within microbial ecology, there is limited understanding of the mechanisms governing the relative influences of stochastic and deterministic processes. Filling this knowledge gap is a major challenge that requires the development of novel conceptual paradigms, experiments, and ecological models. Here we ( i ) present a conceptual model that couples the stochastic/deterministic balance to primary and secondary ecological succession, thereby integrating previously isolated conceptual domains; ( ii ) evaluate this model over 105 years of ecosystem development, revealing a systematic shift in the type and strength of ecological selection; and ( iii ) couple empirical data with a new simulation model to elucidate underlying mechanisms and characterize their scale dependency. The insights and conceptual framework provided here represent a nexus for cross-system integration.

Rare species are increasingly recognized as crucial, yet vulnerable components of Earth’s ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity–function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of ( i ) differentially constructed culturable bacterial communities, and ( ii ) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJN^T, was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJN^T and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98·7 %) and Burkholderia phenazinium (98·5 %). Analysis of whole-cell protein profiles and DNA–DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJN^T had a DNA G+C content of 61·0 mol%. Only low levels of DNA–DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJN^T and closely related species were identified. The predominant fatty acids in strain PsJN^T were 16 : 0, 18 : 1ω7c and summed feature 3 (comprising 16 : 1ω7c and/or iso-15 : 0 2-OH). Isolate PsJN^T showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJN^T and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJN^T (=LMG 22146^T=CCUG 49060^T).