A macroecological theory of microbial biodiversity

Abstract

Microorganisms are the most abundant, diverse and functionally important organisms on Earth. Over the past decade, microbial ecologists have produced the largest ever community datasets. However, these data are rarely used to uncover law-like patterns of commonness and rarity, test theories of biodiversity, or explore unifying explanations for the structure of microbial communities. Using a global scale compilation of >20,000 samples from environmental, engineered and host-related ecosystems, we test the power of competing theories to predict distributions of microbial abundance and diversity-abundance scaling laws. We show that these patterns are best explained by the synergistic interaction of stochastic processes that are captured by lognormal dynamics. We demonstrate that lognormal dynamics have predictive power across scales of abundance, a criterion that is essential to biodiversity theory. By understanding the multiplicative and stochastic nature of ecological processes, scientists can better understand the structure and dynamics of Earth's largest and most diverse ecological systems.

Gauging support for macroecological patterns in helminth parasites

“…Gauging support for macroecological hypotheses using these standardized measures of parasite species richness allows for comparison to patterns in free-living species. Similar work for microbial species has suggested that scaling patterns developed for macroscopic free-living species are supported for microbial species richness and evenness (Locey & Lennon, 2016), as well as for microbial diversity-abundance relationships (Shoemaker, Locey, & Lennon, 2017). Investigations of scaling relationships from macroecology may provide further evidence, or interesting counterexamples, of these established scaling relationships.…”

Constant abundances of ubiquitous uncultured protists in the open sea assessed by automated microscopy

“…More recently, lognormal distributions have been fitted to the abundance profiles of widely distributed prokaryotic Operational Taxonomic Units (Niño‐García et al ., ). Our findings show a broader application of the model and suggest that lognormal dynamics underpin the fundamental nature of microbial communities (Prosser et al ., ; Shoemaker et al ., ). Our data highlights the ubiquity and uniformity in the abundance pattern of several protist components in sunlit oceans, indicative of high tolerance to putative environmental changes (Niño‐García et al ., ).…”

“…The abundances of phototrophic and heterotrophic protists and of the MAST taxa were relatively constant along the main oceans investigated, showing a typical unimodal lognormal distribution (i.e., log-transformed abundances normally distributed). This distribution is commonly used to describe taxa/species abundance data, and emerges from the multiplicative interactions of stochastic processes that shape biodiversity (Preston, 1948;McGill et al, 2007;Shoemaker et al, 2017). Specifically, it has been associated to microbial species abundance curves, where many taxa are rare and a few very abundant, and has allowed to provide theoretical diversity estimates (Curtis et al, 2002;Prosser et al, 2007).…”

Toward a methodical framework for comprehensively assessing forest multifunctionality

“…Although the advance in NGS and the possibility to analyze a large number of samples have led to large‐scale and integrated biodiversity studies at the global scale (Shoemaker, Locey, & Lennon, ), standardized soil sampling, storage, and transportation across continents still are a challenge. Accordingly, we developed a soil sampling, freeze‐drying, and preservation protocol that guarantees transportation of soil samples without nucleic acid degradation between laboratories across continents (Weißbecker, Buscot, & Wubet, ).…”

“…They deliver key ecosystem functions and influence important ecosystem processes, including nutrient cycling and nutrient acquisition(Bardgett & van der Putten, 2014). Recent advances in next-generation sequencing (NGS) techniques coupled with meta-barcoding approaches and the associated bioinformatics and statistical analysis tools enabled microbial ecologists to work in large-scale tree diversity experiments to shed light on the poorly understood role of microbial diversity on BEF relationships in forest ecosystems.Although the advance in NGS and the possibility to analyze a large number of samples have led to large-scale and integrated biodiversity studies at the global scale(Shoemaker, Locey, & Lennon, 2017), standardized soil sampling, storage, and transportation across continents still are a challenge. Accordingly, we developed a soil sampling, freeze-drying, and preservation protocol that guarantees transportation of soil samples without nucleic acid degradation between laboratories across continents(Weißbecker, Buscot, & Wubet, 2017).…”