Ecology

Multiplexed microfluidic screening of bacterial chemotaxis

1. Michael R Stehnach
2. Richard J Henshaw
3. Sheri A Floge
4. Jeffrey S Guasto

• Curated by eLife

  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.

Reviewed by eLife

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

1. Masayuki Ushio
2. Testuya Sado
3. Takehiko Fukuchi
4. Sachia Sasano
5. Reiji Masuda
6. Yutaka Osada
7. Masaki Miya

• Curated by eLife

  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.

Reviewed by eLife

Learning the functional landscape of microbial communities

1. Abigail Skwara
2. Karna Gowda
3. Mahmoud Yousef
4. Juan Diaz-Colunga
5. Arjun S. Raman
6. Alvaro Sanchez
7. Mikhail Tikhonov
8. Seppe Kuehn

Reviewed by Arcadia Science

Metabolic consequences of various fruit-based diets in a generalist insect species

1. Laure Olazcuaga
2. Raymonde Baltenweck
3. Nicolas Leménager
4. Alessandra Maia-Grondard
5. Patricia Claudel
6. Philippe Hugueney
7. Julien Foucaud

• Curated by eLife

  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.

Reviewed by eLife

Universal gut microbial relationships in the gut microbiome of wild baboons

1. Kimberly E Roche
2. Johannes R Bjork
3. Mauna R Dasari
4. Laura Grieneisen
5. David Jansen
6. Trevor J Gould
7. Laurence R Gesquiere
8. Luis B Barreiro
9. Susan C Alberts
10. Ran Blekhman
11. Jack A Gilbert
12. Jenny Tung
13. Sayan Mukherjee
14. Elizabeth A Archie

• Curated by eLife

  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.

Reviewed by eLife

Larger but younger fish when growth outpaces mortality in heated ecosystem

1. Max Lindmark
2. Malin Karlsson
3. Anna Gårdmark

• Curated by eLife

  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.

Reviewed by eLife

Flying squirrels use a mortise-tenon structure to fix nuts on understory twigs

1. Han Xu
2. Lian Xia
3. John R Spence
4. Mingxian Lin
5. Chunyang Lu
6. Yanpeng Li
7. Jie Chen
8. Tushou Luo
9. Yide Li
10. Suqin Fang

• Curated by eLife

  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.

Reviewed by eLife

Eco-evolutionary feedback can stabilize diverse predator-prey communities

1. Stephen Martis

• Curated by eLife

  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.

Reviewed by eLife

High genetic diversity in the pelagic deep-sea fauna of the Atacama Trench revealed by environmental DNA

1. Salvador Ramírez-Flandes
2. Carolina E. González
3. Montserrat Aldunate
4. Julie Poulain
5. Patrick Wincker
6. Ronnie N. Glud
7. Rubén Escribano
8. Sophie Arnaud Haond
9. Osvaldo Ulloa

• Curated by eLife

  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.

Reviewed by eLife

Host-microbiome metabolism of a plant toxin in bees

1. Erick VS Motta
2. Alejandra Gage
3. Thomas E Smith
4. Kristin J Blake
5. Waldan K Kwong
6. Ian M Riddington
7. Nancy Moran

• Curated by eLife

  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.

Reviewed by eLife