Ecology

eLife assessment

This study presents valuable findings on the contrasting responses of two bacteria to the phytoplankton-derived compound azelaic acid. Metabolomics and transcriptomics evidence convincingly shows the assimilation pathway in one marine bacterium and a stress response in a second bacterium. The study provides evidence that azelaic acid can alter marine microbial community structure in mesocosm experiments, though the mechanisms underlying this shift in community structure remain to be explored in future studies.

eLife assessment

This useful study presents findings regarding the impact of forest cover and fragmentation on the prevalence of malaria in non-human primates. The evidence supporting the claims of the authors is solid.

eLife assessment

This valuable work on the paleovegetation history of Iceland has implications for the field of paleoecology, and the deglaciation history of Iceland and additional localities in Northern America and Europe via woody shrub colonization. The study uses a sedimentary ancient DNA metabarcoding approach to study this historic process. The strength of evidence is solid, with the methods (analysis of sedimentary DNA) and data analyses broadly supporting the claims.

eLife assessment

This important, large experimental study examines the effects of plant species richness, plant genotypic richness, and soil water availability on herbivory patterns for Piper species in several tropical sites. The authors find solid evidence that water availability, as well as intra- and interspecific plant diversity, influence herbivory and herbivore diversity, but that the effects differ geographically.

eLife assessment

This work presents a useful finding on non-breeding itinerant behavior of a migratory raptor. With its extensive dataset and analytical framework, this work is of interest to researchers investigating the ecological drivers of bird migration. However, the main claim on a novel migration pattern (so-called 'fox-trot migration') is incomplete in light of current knowledge on bird migratory behavior.

eLife assessment

This paper will be of interest to scientists in the fields of virology, entomology, ecology and epidemiology as the paper explores the drivers of viral and host composition in natural and disturbed ecosystems. The data are of high quality and have been rigorously assessed.However, important additional information on the transmission ecology of these viruses and their relationship with the environment is lacking, making it difficult to interpret the results from a disease ecology perspective.

eLife assessment

This manuscript presents a valuable new microfluidic tool that will allow researchers from different fields to rapidly quantify the chemotactic response of microbes to chemical gradients that have different strengths. Using planktonic bacteria, this paper convincingly shows that a multiplexed microfluidic device produces similar results to previously described microfluidic devices that generate only one gradient at a time. By performing on-chip dilutions, this device allows data for six different gradient strengths to be generated simultaneously, potentially reducing both experimental effort and biological variability.

eLife assessment

This fundamental study advances the analytic toolset and understanding of long-term series of biological (freshwater) communities, and the impact of humans on these. The authors highlight the value of including not only spatiotemporal scales in biodiversity assessments but also some of the possible drivers of biodiversity loss. Analyzing their joint contribution as environmental stressors, the authors provide compelling evidence that ecosystem assessment methods currently used by environmental regulators throughout Europe are not fit-for-purpose, and they identify several alternatives, more robust indicators of freshwater ecosystem health. The work is timely and will be of interest to ecologists, modelers and global warming scientists in general.

eLife assessment

This work presents a fundamental meta-analysis on the causes of glucocorticoid variations in birds and mammals. It provides convincing evidence that an increase in metabolic rates increases glucocorticoid concentrations. The work will be of broad interest to animal physiologists.

eLife assessment

This useful study aims to characterize patterns of demographic aging in naked mole rats by quantifying mortality rates in a captive colony, up to approximately the median age of death. The study system is a fascinating case of unusual longevity and physiology in mammals, but because of limited sampling at older ages and missing analyses, the evidence for the main conclusion – that naked mole rats do not experience actuarial senescence – is incomplete for younger animals and inadequate for older animals. The work nevertheless provides data of interest to biodemographers and biomedical researchers interested in naked mole rats as a model for aging.

eLife assessment

There is a tremendous need to increase agricultural productivity with means that are both practical and efficient. Drawing on data from variable field environments, this important study provides a theoretical framework for the identification of new factors with presumed relevance for crop growth. This framework can be applied in the context of both agricultural and ecological studies. There is solid evidence for several of the authors' claims, but the impact of the study is limited due to missing functional validation of candidate species in the field. Plant biologists and ecologists working in agricultural and natural environments will find the work interesting.

eLife assessment

This study presents important findings regarding the quantification of dynamics in fish communities in changing ecosystems by combining a large-scale environmental DNA metabarcoding time series with novel statistical approaches. The methods are convincing, with controlled experiments, thorough statistical analyses, and a substantial dataset covering two years of detailed observation, which can provide sufficient power to detect fine-scale ecological interactions. This work is relevant for informing future research on assessing community stability under climate change.

eLife assessment

This useful study uses untargeted metabolomics to help us understand how some herbivores are able to be generalists, rather than specializing in the metabolism of specific plant species. This is an important area, since little is known about how generalist insect species metabolize their food. In its current form, the study lacks ecological relevance due to the exclusive use of refined sampling procedures, and the metabolomic analysis is incomplete.

eLife assessment

This important study proposes a phenomenologically motivated theoretical framework to explain observed patterns of the temperature dependence of microbial diversity. The methodology is overall convincing, but the explanations of approximations and assumptions, and of their regime of validity, are incomplete. The manuscript should be of interest to microbial ecologists.

eLife assessment

This fundamental work reports an analysis of microbial abundance similarities among individuals over time in a longitudinal wild baboon cohort from Amboseli, Kenya. The authors provide compelling evidence that there are remarkably consistent dynamic associations over time in microbial abundances between baboons, despite individual baboons having individualized microbial signatures. The authors further identify universal microbial associations that appear to go beyond the studied baboon cohort, extending to human microbiomes. This study adopts a novel powerful statistical approach to analyzing longitudinal microbial dynamics at the individual level, which will likely make this work become a key reference study in the field of microbial ecology.

eLife assessment

The work by Lindmark et al. provides us with an important natural experiment on fish that challenges current literature on relationships between temperature, growth rate, and size. The strength of their results is compelling, as Lindmark et al. mixed a unique warming setup with a large battery of models and statistics. The work will be of interest to ecologists and physiologists interested in the impacts of global warming on natural communities.

eLife assessment

This valuable study presents a potentially interesting contribution on animal caching behaviour. At present, evidence that the flying squirrels themselves modified the nuts is incomplete, but there are clear video observations of them associating with the nuts. Either way, the images of the modified nuts and the detailed descriptions of the caching behaviour describe a new technique for storing nuts in a tropical rainforest.

eLife assessment

This useful theoretical and numerical study shows that evolution can stabilize predator and prey populations in a generalized Lotka-Volterra framework with high variance species-species interactions. It demonstrates an example of evolutionary bet hedging, rescuing species at risk of extinction due to destabilizing predator-prey interactions. The methodology is solid, but some modeling choices are quite specific, limiting direct applicability to concrete systems. The study should be useful to the community working on theoretical ecology and evolution, and the ecology-evolution coupling should resonate with a broader audience.

Evaluation Summary:

This paper will be of interest to marine biologists, and has particular relevance to those studying symbiotic corals. The use of compelling experimental optical measurements performed in situ allows testing of previous predictions on protein-based pigments that are found in many coral species. Specifically, the study analyzes the role of two classes of pigments, the Red Fluorescent Proteins (RFPs) and the Chromo proteins. It provides direct measurement data that suggest that RFPs can indeed provide additional light to the symbionts by converting the prevalent blue-green light at depth in orange-red light that penetrates more in the tissues of the polyps, thus increasing the number of photons available for photosynthesis. The authors also provide evidence based on light measurement for a possible photoprotective role of Chromoproteins, although the study does not yet provide any direct evidence for an ecological benefit of such light conversion/light protective functions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

eLife Assessment:

This manuscript will be of interest to microbial ecologists and biogeochemists working on soil carbon cycling and responses to climate warming. This study uses an elegant experiment to show that standing variation, both phylogenetic and phenotypic, enables microbial community adaptation to higher temperatures. The authors' conclusions are supported by the data, and this work lays a foundation for future experimental and modeling studies.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)