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.

Aim  The study of biological invasions has long considered species invasiveness and community invasibility as separate questions. Only recently, there is an increasing recognition that integrating these two questions offers new insights into the mechanisms of biological invasions. This recognition has renewed the interest in two long‐standing and seemingly contradictory hypotheses proposed by Darwin: phylogenetic relatedness of invaders to native communities is predicted to promote naturalization because of appropriate niche‐adaptation but is at the same time predicted to hamper naturalization because of niche overlap with native species. The latter is known as Darwin’s naturalization hypothesis. Location  Global. Methods and Results  We review the studies that have tested these hypotheses and summarize their largely inconsistent outcomes. We argue that most of the inconsistency arises from discrepancies in the applied conceptual frameworks and analytical approaches and not from different model organisms and different ecological contexts. First, observed patterns and results can be seriously flawed by different spatial and phylogenetic scales, which do not equally reveal community assembly mechanisms. Second, different studies have used different metrics, which may test for different specific hypotheses. Thus, we propose a set of metrics derived from the alpha niche concept to measure invaders relatedness to native communities. Finally, approximating species niche differentiation from phylogenetic relatedness is not exempt of assumptions, and invasive species naturalization may result from various ecological mechanisms of biotic resistance that are not necessarily revealed by species phylogeny alone. Main conclusions  The quest for resolving the conundrum of Darwin’s naturalization hypothesis will only be successful if appropriate scales, metrics and analytical tests are thoroughly considered. We give several recommendations and suggest, whenever possible, to use trait‐based measurements of species dissimilarity as the most promising avenue to unravel the mechanisms driving alien species invasions.