Vast (but avoidable) underestimation of global biodiversity

Enumerating soil biodiversity

Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.

Macroevolutionary constraints on global microbial diversity

Biologists have long sought to quantify the number of species on Earth. Often missing from these efforts is the contribution of microorganisms, the smallest but most abundant form of life on the planet. Despite recent large-scale sampling efforts, estimates of global microbial diversity span many orders of magnitude. It is important to consider how speciation and extinction over the last 4 billion years constrain inventories of biodiversity. We parameterized macroevolutionary models based on birth-death processes that assume constant and universal speciation and extinction rates. The models reveal that richness beyond 1012 species is feasible and in agreement with empirical predictions. Additional simulations suggest that mass extinction events do not place hard limits on modern-day microbial diversity. Together, our study provides independent support for a massive global-scale microbiome while shedding light on the upper limits of life on Earth.

Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks

Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the database, since representative relatives must be present. Many genomic sequences cannot be classified at all or only with a high misclassification rate. Here we present BERTax, a deep neural network program based on natural language processing to precisely classify the superkingdom and phylum of DNA sequences taxonomically without the need for a known representative relative from a database. We show BERTax to be at least on par with the state-of-the-art approaches when taxonomically similar species are part of the training data. For novel organisms, however, BERTax clearly outperforms any existing approach. Finally, we show that BERTax can also be combined with database approaches to further increase the prediction quality in almost all cases. Since BERTax is not based on similar entries in databases, it allows precise taxonomic classification of a broader range of genomic sequences, thus increasing the overall information gain.

The Relevance of the Bacterial Microbiome, Archaeome and Mycobiome in Pediatric Asthma and Respiratory Disorders

Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential role of archaea remains poorly understood. In this review, we discuss the contribution of all three domains of cellular life to human naso- and oropharyngeal microbiomes, i.e., bacterial microbiota, eukaryotes (mostly fungi), as well as the archaeome and their relation to respiratory and atopic disorders in infancy and adolescence. With this review, we aim to summarize state-of-the-art contributions to the field published in the last decade. In particular, we intend to build bridges between basic and clinical science.

Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species

There are fewer than 20,000 prokaryotic species with validly published names, meaning >99% of a reasonable estimate of microbial diversity remains formally unnamed. Here we explore the damaging consequences of the current practice in which each new species is described in a standardized publication, most typically a 'single strain species description'. This approach is both an impediment to scaling up progress in naming the microbial world and also a significant factor in the poor reputation of the discipline of microbial taxonomy. We conclude that significant changes in author habits are needed and make constructive suggestions as to how author practice should adapt.