Ecology

eLife assessment

This manuscript from Ramírez-Flandes will be of interest to marine biologists, deep ocean ecologists, conservation biologists, and biogeographers. At times, the comparison of merely a pair of samples or sampling locales can substantially widen our view of biological and ecological systems and processes. In the case of this study, the pattern of metazoan diversity from eDNA samples from across the water columns in comparable series from two deep trench systems (to below 8000 m) is markedly different, including evidence of substantial biological diversity deep in the Atacama Trench (to a much greater extent than observed in the Kermadec Trench), contradicting existing paradigms about biodiversity potential in abyssal-hadal regions.

eLife assessment

The manuscript makes an important contribution to understanding the roles of the bee host and microbiome in degrading amygdalin, a dietary secondary metabolite. Several bacterial strains and their enzymes responsible for the deglycosylation of amygdalin are identified. Conclusions are reached convincingly through a comprehensive combination of in vitro and in vivo experiments including gene-expression analysis, proteomics, HPLC-MS, and the use of recombinant E. coli to test enzyme function. As the consequences of microbial-derived amygdalin metabolisation on host health remain uncertain from the experiments conducted, the manuscript could be improved through a clearer discussion of future work needed and in parts more careful wording to not prematurely suggest benefits to the host.

eLife assessment

The authors present a rich investigation of the evolution of social-movement rules in animal societies under pathogen pressure. The study should be of interest to a broad readership.

eLife assessment

We admired the study by Krehenwinkel and colleagues for its novelty, depth, and ecological breadth, but have questions regarding the laboratory, bioinformatic and statistical methodologies that require clarification. It is likely to make a substantial impact in the field of plant-based arthropod metabarcoding, revealing ecological insights that can be derived from existing bio-banked material. The work, which creatively exploits herbarium material to track arthropod communities, will be interesting to a general audience in addition to ecologists, foresters, phytopathologists, and industry.

Evaluation Summary:

This manuscript has the potential to be of interest to a broad range of behavioral scientists. It provides insights into how biases can affect value-based behavior in invertebrates, similar to what has been reported in humans. However, there are a number of potential confounders that need to be addressed before drawing robust conclusions from the data reported.

(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 #1, Reviewer #2 and Reviewer #4 agreed to share their name with the authors.)

Evaluation Summary:

This paper is of broad interest to biologists and climate modelers that study the impact of environmental stress (especially multiple stressors) on marine life. The authors show that exposure to low pH (ocean acidification) decreases the ability of two mussel species to survive freezing stress. The authors measure multiple biochemical parameters to try and identify the mechanisms underlying the change in freeze tolerance, but future work will be needed to resolve the underlying mechanism in detail.

(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.)

Evaluation Summary:

This paper will be of interest to urban foresters, ecologists, and planners. It provides an urban tree dataset across US cities that can be used to address questions on urban biodiversity and ecosystem services. It contains clear descriptions about the data processing and structures in general, but would need further clarifications about the sample completeness and representativeness of the data.

(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.)

Evaluation Summary:

The paper describes an interesting, but very abstract extension of normative choice theories. By linking economic and foraging theory, the paper would potentially be of interest to a broad audience in behavioral economics and neuroscience. However, the results in their current form have several important limitations: the lack of a significant validation, such as an account for well-known behavioral or neural effects that would not be explained by alternative theories, a quantitative performance comparison between the proposed EDM and other models in realistic behavioral situations, and a specific link between the actual processes and limitations of real brains and the EDM.

(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.)

Evaluation Summary:

This manuscript identifies pH as a common factor that underlies eco-evolutionary dynamics related to priority effects, which play an important role in community assembly. Using multiple lines of evidence, the data support the overall conclusions of the manuscript that pH-mediated priority effects in the nectar microbiome are the drivers of alternative community states. This manuscript will be of broad interest to readers in ecology and evolutionary biology.

(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.)

Evaluation Summary:

In this paper, the authors use a mathematical model of plant and water dynamics in drylands to show that drylands adaptive capacity to respond to changes, via spatial self-organization in space, has also beneficial effects in preserving its biodiversity and ecosystem functions. The current study extends previous work by considering a trait diversity gradient that ranges from stress-tolerant to fast-growing plant species.

(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 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

This study provides a comprehensive analysis of the effects of polymorphism in an immune gene (the immunoglobulin E receptor Fcer1a) on immune responses, resistance to infection, and reproductive fitness in a wild rodent population. The authors claim to have found evidence for sex-specific effects of Fcer1a polymorphism, a result that would have broad implications for our understanding of the maintenance of genetic variation. The support for this claim is currently rather weak.

(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.)

Evaluation Summary:

Using an impressive experimental design, Tang et al. analyzed the effects of intraspecific (genetic) and interspecific (species) diversity in ecosystem processes carried out by forest communities. The results show that both species and genotype diversity influence productivity via changes in overall functional diversity, herbivory, and soil fungal diversity. This study will be important to ecologists and environmentalists interested in ecosystem processes and restoration efforts.

(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.)

Evaluation Summary:

This paper is of potential interest to people working at the interface between agronomy, ecology, and evolution. By growing experimental mixtures of crop species, i.e., intercrops, the study aims at testing whether positive interactions between species grown in association strengthen over generations of coexistence. The data are original and of high quality, and the statistical analysis are rigorous. The interpretation of the Results as well as the Discussion and Conclusions currently ignore an important discrepancy in the results for competition versus overall yield.

(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 #3 agreed to share their name with the authors.)

Evaluation Summary:

Kruse and Herzschuh apply LAVESI, a machine-intensive and spatially-explicit simulation of individual Siberian trees at the tundra-forest boundary, to call attention to the rapid reduction in the tundra biome as climate warming pushes forests toward the Arctic Ocean. This detailed modelling study predicts dramatic losses of tundra area by the middle of the millenium even under an ambitious climate mitigation scenario and highlights considerable risks of extinction.

(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 #1 agreed to share their name with the authors.)

Evaluation Summary:

This study will be of interest to wildlife ecologists and conservation practitioners. The authors took a collaborative approach and collated a large dataset of wildlife camera trap recordings across cities in the USA. The analyses reveal variability in diel activity among species and cities, providing important insights into the effects of urbanization.

(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 #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Hoverflies are a group of insects that provide crucial ecosystem services such as pollination and crop protection. Their migratory behavior in western countries is well characterized, but in eastern Asia, the annual summer monsoon provides a 'highway' of favorable winds for the airborne transport of migratory organisms, and the migration of hoverflies in this large region has not been well studied. This study addresses hoverfly migration in this region and its consequences using a variety of suitable methods. The work will be of great interest to insect migration biologists and pollination ecologists.

(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 #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The manuscript reports that when lowland plants were transplanted into alpine turfs under lowland climatic conditions, they rapidly increase soil microbial decomposition of carbon stocks due to root exudates feeding the microbes. The authors conclude that when lowland plants migrate to alpine sites and these warm up, they may also cause a pulse of carbon loss from soil. An alternative explanation of their findings might be that when alpine plants are transplanted into alpine turfs under lowland climatic conditions, these are unable to increase soil microbial decomposition as much as lowland plants because the latter are better adapted to their climatic home environment.

(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 #1 and Reviewer #4 agreed to share their names with the authors.)

Evaluation Summary:

Manipulations of sex hormones in animals in ecologically relevant environments usually involve long-term manipulations using chronic implants or injections of esterified steroids with longer half-lives than the endogenous hormones. This has been done in line with the prevailing idea of the long-lasting effects of steroids mediated by the transcritpional actions of their liganded receptors. The specific novelty of this study lies in the transiency of hormone availability (testosterone's half-life is about 2 hours). This might suggest that the observed effects depend on a mode of action different from the mode of action during chronic sex hormone exposure. It should also be noted that any study in natural settings is significantly more difficult to perform than in the lab. However, as all brain/hormonal functions evolved in natural environments, these studies are absolutely crucial to understand the function of the respective systems.

(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.)

Evaluation Summary:

Urbanization has broad impacts for macroecology but its consequences for wildlife microbial ecology remain unclear. Dillard et al. hypothesize that humans living in an urban setting may transfer their microbes to wildlife with potential adverse effects. They analyze 16S rRNA gene sequencing data from humans, crested anoles, and coyotes, leading to the discovery of multiple bacteria that fit the pattern of urbanization and inter-species transfer.

(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 #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Zhou et al. provide a robust study on isotopic and metabolic changes of a soil community across a gradient of different land-use types in Sumatra, Indonesia. By mixing community-based analyses of stable isotopes and size-based metabolic measures, they are able to elucidate, for the first time, important links among plants and the soil food web in tropical ecosystems. This study is of importance to tropical biologists, ecosystem ecologists and biodiversity conservationists aiming to understand the impacts of humans on tropical forests.

(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.)