Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.

The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.

Vocal convergence and social proximity shape the calls of the most basal Passeriformes, New Zealand Wrens.

Despite extensive research on avian vocal learning, we still lack a general understanding of how and when this ability evolved in birds. As the closest living relatives of the earliest Passeriformes, the New Zealand wrens (Acanthisitti) hold a key phylogenetic position for furthering our understanding of the evolution of vocal learning because they share a common ancestor with two vocal learners: oscines and parrots. However, the vocal learning abilities of New Zealand wrens remain unexplored.

Microbiology of Big Soda Lake, a multi-extreme meromictic volcanic crater lake in the Nevada desert.

Big Soda Lake, Nevada, is a multi-extreme meromictic lake, whose hypersaline hyperalkaline bottom waters feature permanent anoxia and high concentrations of arsenic, sulphide and ammonia. These properties make Big Soda Lake-and the adjacent Little Soda Lake-a fascinating system for exploring life's boundaries, discovering novel microbial taxa and identifying biotechnologically useful strains. To date, the taxonomic diversity and metabolic capabilities of microorganisms in this system remain largely unknown.

Trait biases in microbial reference genomes.

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures.

Transport-limited reactions in microbial systems.

Predicting microbial metabolic rates and emergent biogeochemical fluxes remains challenging due to the many unknown population dynamical, physiological and reaction-kinetic parameters and uncertainties in species composition. Here, we show that the need for these parameters can be eliminated when population dynamics and reaction kinetics operate at much shorter time scales than physical mixing processes. Such scenarios are widespread in poorly mixed water columns and sediments.

The scaling of diversification rates with age is likely explained by sampling bias.

Numerous phylogenetic studies reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates. The causes of this age-rate-scaling (ARS), whether biological and/or artifactual, remain unresolved. Here we fit diversification models to thousands of eukaryotic time-calibrated phylogenies to explore multiple potential causes of the ARS including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and an important and ubiquitous form of sampling bias-preferentially analyzing larger extant clades.

SARS-CoV-2 infections in 165 countries over time.

Background: Understanding the dynamics of the COVID-19 pandemic and evaluating the efficacy of control measures requires knowledge of the number of infections over time. This number, however, often differs from the number of confirmed cases because of a large fraction of asymptomatic infections and different testing strategies.

Methods: This study uses death count statistics, age-dependent infection fatality risks, and stochastic modeling to estimate the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections among adults (aged 20 years or older) in 165 countries over time, from early 2020 until June 25, 2021.

Solutions in microbiome engineering: prioritizing barriers to organism establishment.

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function.

Response to "Vast (but avoidable) underestimation of global biodiversity".

This Formal Comment provides clarifications on the authors' recent estimates of global bacterial diversity and the current status of the field, and responds to a Formal Comment from John Wiens regarding their prior work.

The rates of global bacterial and archaeal dispersal.

The phylogenetic resolution at which microorganisms display geographic endemism, the rates at which they disperse at global scales, and the role of humans on global microbial dispersal are largely unknown. Answering these questions is necessary for interpreting microbial biogeography, ecology, and macroevolution and for predicting the spread of emerging pathogenic strains. To resolve these questions, I analyzed the geographic and evolutionary relationships between 36,795 bacterial and archaeal ("prokaryotic") genomes from ∼7000 locations around the world.

Unifying Phylogenetic Birth-Death Models in Epidemiology and Macroevolution.

Birth-death stochastic processes are the foundations of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth-death model variants that have been developed; these impose different assumptions about the temporal dynamics of the parameters and about the sampling process. As each of these variants was individually derived, it has been difficult to understand the relationships between them as well as their precise biological and mathematical assumptions.

Why extinction estimates from extant phylogenies are so often zero.

Time-calibrated phylogenies of extant species ("extant timetrees") are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models. These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the fossil record and the fact that the majority of species ever to have existed are now extinct. To date, the causes of this discrepancy remain unresolved.

Fundamental Identifiability Limits in Molecular Epidemiology.

Viral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data to estimate epidemiological parameters such as the effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particularly when sampling is poor or delayed. It remains generally unknown, however, how robust phylodynamic epidemiological inferences are, especially when there is uncertainty regarding pathogen prevalence and sampling intensity.

Phylogeographic Estimation and Simulation of Global Diffusive Dispersal.

The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example, for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2D plane; however, the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because spherical Brownian motion (SBM) differs from planar Brownian motion. No statistical method exists for estimating SBM diffusion coefficients from a given timetree and tip coordinates, and no method exists for simulating SBM along a given timetree.

Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms.

Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions.

Extant timetrees are consistent with a myriad of diversification histories.

Time-calibrated phylogenies of extant species (referred to here as 'extant timetrees') are widely used for estimating diversification dynamics. However, there has been considerable debate surrounding the reliability of these inferences and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth-death model, which underlies most existing methods of estimation.

Simulating trees with millions of species.

Motivation: The birth-death (BD) model constitutes the theoretical backbone of most phylogenetic tools for reconstructing speciation/extinction dynamics over time. Performing simulations of reconstructed trees (linking extant taxa) under the BD model in backward time, conditioned on the number of species sampled at present day and, in some cases, a specific time interval since the most recent common ancestor (MRCA), is needed for assessing the performance of reconstruction tools, for parametric bootstrapping and for detecting data outliers. The few simulation tools that exist scale poorly to large modern phylogenies, which can comprise thousands or even millions of tips (and rising).

Microbial metabolite fluxes in a model marine anoxic ecosystem.

Permanently anoxic regions in the ocean are widespread and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long-term monitoring has yielded time series for the concentrations of biologically important compounds; however, the underlying metabolite fluxes remain poorly quantified.

A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models.

As the size of phylogenetic trees and comparative data continue to grow and more complex models are developed to investigate the processes that gave rise to them, macroevolutionary analyses are becoming increasingly limited by computational requirements. Here, we introduce a novel algorithm, based on the "flow" of the differential equations that describe likelihoods along tree edges in backward time, to reduce redundancy in calculations and efficiently compute the likelihood of various macroevolutionary models. Our algorithm applies to several diversification models, including birth-death models and models that account for state- or time-dependent rates, as well as many commonly used models of discrete-trait evolution, and provides an alternative way to describe macroevolutionary model likelihoods.

Circumventing kinetics in biogeochemical modeling.

Microbial metabolism drives biogeochemical fluxes in virtually every ecosystem. Modeling these fluxes is challenged by the incredible diversity of microorganisms, whose kinetic parameters are largely unknown. In poorly mixed systems, such as stagnant water columns or sediments, however, long-term bulk microbial metabolism may become limited by physical transport rates of substrates across space.

A census-based estimate of Earth's bacterial and archaeal diversity.

The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.

Bacterial diversification through geological time.

Numerous studies have estimated plant and animal diversification dynamics; however, no comparable rigorous estimates exist for bacteria-the most ancient and widespread form of life on Earth. Here, we analyse phylogenies comprising up to 448,112 bacterial lineages to reconstruct global bacterial diversification dynamics. To handle such large phylogenies, we developed methods based on the statistical properties of infinitely large trees.

Function and functional redundancy in microbial systems.

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms.

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.

The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs.