L&O Special Issue: “Linking metagenomics to aquatic microbial ecology and biogeochemical cycles”

 

Ramon Massana, SINGEK coordinator and supervisor of ESR1, will be Special Editor in the Limnology & Oceanography Special Issue entitled “Linking metagenomics to aquatic microbial ecology and biogeochemical cycles” and jointly edited by Special Editors Hans-Peter Grossart (Leibniz-Institute of Freshwater Ecology and Inland Fisheries), Katherine McMahon (University of Wisconsin-Madison) and David Walsh (Concordia University, Canada).

The emphasis of the 2020 Special Issue for Limnology and Oceanography will be on the use of metagenomics to increase our understanding of aquatic microbiology and ecosystem functioning. A general aim of microbial ecology is to observe, understand, and predict the distribution and interactions of microorganisms in the context of environmental conditions. Taxonomic profiling of different microbial communities often reveals significant but unexplained variations across aquatic environments both in space and time. Functional differences among organisms are often invoked as an explanation; and variation in gene content (assessed by metagenomics) often reveals dynamic relationships between metabolic pathways and environmental conditions, the strength of which typically depends on the magnitude of the environmental change between communities. However, a major challenge in microbial ecology remains. Many taxa that appear functionally redundant at the metabolic pathway level show significant variation across environments with different ecological features. Possible explanations include dispersal limitation, biotic interactions, and rapid adaptation to environmental conditions that are not easily predictable based on gene content alone. The special issue will explore recent advances and current limitations about how large-scale meta-omics analyses can be integrated into biogeochemical and eco-evolutionary frameworks to better predict taxonomic and functional diversity patterns across aquatic ecosystems from lakes and rivers to oceans and from viruses and microbes to protists. Reviews, meta-analyses, and perspectives are welcome in addition to standard manuscripts that use primary data.

Submissions from all interested researchers who work in this area are welcome!!

The deadline for manuscript submission is January 28, 2019. Manuscripts may be submitted earlier, and accepted papers will be published online upon acceptance with a print issue expected in January 2020. Articles should be submitted through ScholarOne at the Wiley Limnology & Oceanography website: https://mc.manuscriptcentral.com/lo. Please identify your submission for consideration in the “metagenomics” issue.

For more information: https://aslo.org/blog/2020-l&o-special-issue

 

Congratulations Luis and Puri for that a new SINGEK paper published in Genome Biology and Evolution:

“Evolutionary genomics of Metchnikovella incurvata
(Metchnikovellidae), an early branching microsporidium”

L. J. Galindo, G. Torruella, D. Moreira, H. Timpano, G. Paskerova, A. Smirnov, E. Nassonova, P. López-García

 

Heatmap illustrating the conservation of pathways and structures in metchnikovellids
and neighbor lineages. It is based on 73 Gene Ontology terms (GO), identified using EggNOG
(Huerta-Cepas et al. 2017) for 12 Holomycota representative proteomes. Sequences obtained
in this study are highlighted in black. Colors indicate the percentage of annotated genes with
a GO term.

Metchnikovellids are highly specialized hyperparasites, which infect and reproduce inside gregarines (Apicomplexa) inhabiting marine invertebrates. Their phylogenetic affiliation was under constant discussion until recently, when analysis of the first near-complete metchnikovellid genome, that of Amphiamblys sp., placed it in a basal position with respect to most Microsporidia. Microsporidia are a highly diversified lineage of extremely reduced parasites related to Rozellida (Rozellosporidia = Rozellomycota = Cryptomycota) within the Holomycota clade of Opisthokonta. By sequencing DNA from a single-isolated infected gregarine cell we obtained an almost complete genome of a second metchnikovellid species, and the first one of a taxonomically described and well-documented species, Metchnikovella incurvata. Our phylogenomic analyses show that, despite being considerably divergent from each other, M. incurvata forms a monophyletic group with Amphiamplys sp., and confirm that metchnikovellids are one of the deep branches of Microsporidia. Comparative genomic analysis demonstrates that, like most Microsporidia, metchnikovellids lack mitochondrial genes involved in energy transduction and are thus incapable of synthesizing their own ATP via mitochondrial oxidative phosphorylation. They also lack the horizontally acquired ATP transporters widespread in most Microsporidia. We hypothesize that a family of mitochondrial carrier proteins evolved to transport ATP from the host into the metchnikovellid cell. We observe the progressive reduction of genes involved in DNA repair pathways along the evolutionary path of Microsporidia, which might explain, at least partly, the extremely high evolutionary rate of the most derived species. Our data also suggest that genome reduction and acquisition of novel genes co-occurred during the adaptation of Microsporidia to their hosts.

Interdisciplinary meeting to explore the use of single cell technologies to understand the function, diversity and interactions of microbes. By bringing together physicists who manipulate cells, microbiologists who seek to understand the nature of microbial communities and genomicists who are developing new approaches to study individual cells we will achieve a greater understanding of the potential of this new field.

There will be a poster session at 16:15 on Monday 10 December. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team with the subject heading “Single cell ecology: poster abstract” no later than Monday 22 October 2018. Please note that places are limited and posters are selected at the scientific organiser’s discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.

Recorded audio of the presentations will be available here after the meeting has taken place.

Meeting papers will be published in a future issue of Philosophical Transactions B.

 

Single cell approaches are changing how we study many biological problems. This meeting will bring together biophysicists, molecular biologists and microbial ecologists who are using these technologies to understand the natural world. The aim of this satellite meeting is to report progress, identify areas for synergy and lay down the foundations for further developing this interdisciplinary science.

 

Both venues will be an exciting and stimulating meeting for all SINGEK members and participants.

Register now!

 

 

The Ramon Margalef Summer Colloquium (RMSC) has been running yearly since 2013 and aims at training young researchers in Ecology, as well as promoting their networking and debate with invited lecturers as well as among themselves. The Colloquium is inspired in the figure of Ramon Margalef (Barcelona, 1919-2004), who was one of the founders of modern ecology. He broke paradigms and contributed with innovative theories about the spatio-temporal structure of ecosystems, the relationships between diversity, biodiversity, stability and connectivity, the fundamental role of energy in biological productivity as well as the interrelationships between ecological succession and evolution. He recognized the importance of the physical environment to understand the behavior of species and ecosystems. He wrote ca. 400 papers and books, working for many years at the Institut de Ciències del Mar and the University of Barcelona.

This 6^th Colloquium will, again, be an excellent opportunity to foster learning and discussions on the relevance of an interdisciplinary perspective in Ecology & Evolution.

 

Central topic: Ecology through the omics lens

The use of omics techniques has spread rapidly across the field of Ecology and Evolution during the last decade, but there is substantial work ahead to link the obtained results with the existent ecological theory. During the 2018 Ramon Margalef Summer Colloquium, we will make an effort to bridge this gap, aiming to inspire attending students to move from “what” to “why” when using omics approaches to study the ecosystem, as well as to frame their omics-based research in a theoretical ecological framework. The course will cover different environments (marine, terrestrial, host associated) as well as organismal sizes (from microbes to plants and animals), thus becoming an excellent opportunity to bring together researchers with similar questions, but working in fields that seldom communicate between each other. Furthermore, this edition of the course will focus on the feedbacks between ecology and evolution, and how the processes studied by both disciplines shape the structure of life on earth.

 

The scientific organization of the RMSC 2018 will be provided by Institut de Ciències del Mar (ICM-CSIC) and the logistics will be taken care by the Catalan Association of Oceanographers (ACOIO). The course organizers are Javier del Campo, Ramiro Logares (SINGEK Project Supervisor of ESR2) and Cèlia Marrasé.

 

More information at the website of the Colloquia.