"how-to" activities (as examples - on Feb. 5 Sherly will talk about assembling MAGs, and last year Peter Larsen from ANL gave an intro to machine learning )
presentation of research projects and/or practicing seminars/job talks etc (as examples - Viviana talked about her research last week, and got some input about the figures she's planning for her paper, and Scott has signed up to talk probably about his own rhizosphere research Feb. 12)
discussions/papers about new techniques/frontiers in methodology that are up and coming broadly in microbial science (e.g. if you hear about something amazing at a meeting or on twitter, share it with the group, we could read something about it, or even invite someone from afar to Zoom-participate in discussing it... As an example, last year we had Ken Kenmer from ANL Zoom in to talk about quantum dots in the context of the ANL Advanced Photon Source upgrade)
"journal-club" - like presentations of papers, but with a twist requiring some planning. If you want to present a paper from the lit., we'll institute a "thumbs up" or "thumbs down" voting process to try to encourage selection of papers that will engender a lot of discussion by diverse interested parties. We'll see whether it works to conduct a vote via a MicroEco Slack channel - thumbs up and thumbs down (or a lipstick print kiss vs. thumb-sideways, or a skull and crossbones...the options are endless.).
Re: the Slack "thumbs up/down", we need your vote to be a well-considered "thumbs up" and "thumbs down" from everyone, so that we don't get monochromatic in our discussions and lose sight of the interdisciplinarity that MicroEco is trying to support.
We'll send around a separate email about the Slack Channel (including links if you haven't used Slack before).
Also this web site "papers" page will continue to be maintained
Feb 5 ___Sherlynette Perez Castro - assembling MAGs______
From Sherly:
For the upcoming MicroEco, I will be presenting a workflow that I have been developing since my arrival at MBL to reconstruct metagenome-assembled genomes from microbiomes, focusing on quality check, assembly and the binning steps. The workflow is available online https://hackmd.io/5zX0j2nmQjWGWd3VJOh9VA?both. It is designed for Illumina (short-read) sequences, and it is tailored to the servers and clusters of the Bay Paul Center computing facility, using unix command-line. I encourage participants with access to the Bay Paul Center servers to bring one sample (R1.fastq & R2.fastq) to use during the presentation.
Disclosure* I am a soil scientist with a background in microbial ecology. My bioinformatics knowledge has been mostly self-trained. I recently participated in the Evomics Genomics Workshop:
http://evomics.org/2020-workshop-on-genomics-cesky-krumlov-czech-republic/
(all the workshop materials are available on the link).
... multiple tools (packages) used in the pipeline:
metaWRAP, CONCOCT, MaxBin2, metaBAT, CheckM, SPAdes, MegaHIT, FastQC, PRINSEQ, MetaQUAST, etc.
Resources:
Unix-Linux Command Reference
Papudeshi et al. (2017) Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes. BMC Genomics 18:915. DOI 10.1186/s12864-017-4294-1
Feb 12__MAGs with Sherly, continued!_________
Feb 19___Emil Ruff ( DOE Career grant discussion)____________________
Feb 26___Scott Klasek (rhizosphere research)
March 4____Joan Roughgarden and Zoe Cardon (Holobiont as unit of selection)__
Ever wonder how a holobiont (host-microbial associations) might "evolve" ? How selective forces shape complex, even fluid, symbiotic interactions?
If you want an introduction to some of the ideas, you could also look at this Biological Theory paper, but that's just "for fun" if you're dying of curiosity:
March 11___Fernando Rodriquez _(Eukaryotic genome curation - rotifer style)____
Delmont TO and Eren AM (2016) Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ 4:e1839; DOI 10.7717/peerj.1839
March 18_____(postponed) ________________
March 25_____(postponed)___________________
April 1_______Jessica Mark Welch_- by Zoom!_____
It's voting time! On the slack channel, Jessica would like your input on which of two papers you think would be best for MicroEco April 1.
Vote done! We're discussing:
Gorter FA, Manhart M, Ackermann M. 2020 Understanding the evolution of interspecies interactions in microbial communities. Phil. Trans. R. Soc. B 375: 20190256. http://dx.doi.org/10.1098/rstb.2019.0256
As a reminder:
We've enabled that anybody with @mbl.edu can join the workspace where the #microeco channel is.
We've also sent direct invitations to several participants off campus.
If you are new to slack, you might want to take a peek at this info:
April 8______(postponed)_________________
April 15______Colleen Cavanaugh___________________
Colleen will be talking about what's known about transmission of Coronavirus. She provided two pieces of background:
--An excellent and balanced lay review of recent studies and the potential for airborne transmission by Nell Greenfieldboyce (NPR)
--Scientific review for perusal. (pre-COVID-19)
Tellier et al. 2019. Recognition of aerosol transmission of infective agents: a commentary. BMC Infectious Diseases
April 22________Scott Klasek_______________
Crits-Christoph A, Olm M, Diamond S, Bouma-Gregson K, and Banfield J. Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow. bioRxiv https://doi.org/10.1101/695478
April 29_____Joe Vallino__________________
Joe will talk about his own research, expanding on his AGU talk ""The Importance of Incorporating Planktonic Temporal Strategies in Marine Ecosystem Models"
If you're interested in some background material just FYI, you might look at:
Kolody et al. (2019) Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME J 13:2817-2833.
May 6____Joe Vineis___________________
Joe will present research he and Ashley Bulseco are preparing for publication:
Microbes combine carbon fixation with coupled nitrogen and sulfur respiration in nitrate enriched sediment
Abstract
Carbon storage in salt marsh sediments is dependent on the metabolic activity of microbial organisms. Nitrate is a limiting nutrient for microbial carbon mineralization and anthropogenic inputs to coastal sediments could increase respiratory rates of the heterotrophic community resulting in decreased carbon storage potential. Alternatively, the nitrate could serve as an energy source, used to fix inorganic carbon by stimulating chemoautotrophic activity. We recovered MAGs from communities both enriched and unenriched with nitrate to characterize the heterotrophic and autotrophic genomic potential. We found that the heterotrophic community had a limited potential to access carbon from diverse sources and CO2 fixation was widespread. The inorganic carbon fixing community included several members of the Thioalkalivibrio, Sedimenticola, and Chlorobium. Several of the MAGs are representatives of novel families and genera including members of the candidate phyla and we speculate that the autotrophic microbial community in salt marsh sediments could reduce the amount of carbon lost due to increases in heterotrophic activity when exposed to nitrate enrichment. The presence of a microbial driven carbon cycle in these sediments has important implications for carbon storage.
May 13 _____Joe Vineis, continued...
May 20 ____Emil Ruff - current research exploring scaling in microbial phylogeny
June 3 ____Zoe Cardon -- current research and thoughts on "fitness alignment" (holobiont evolution)
Overview: De Mita, S (2012) For better or for worse: cooperation and competition in the legume-rhizobium symbiosis. New Phytologist 194(4):885-887.
Meta-analysis: Friesen ML (2012) Widespread fitness alignment in the legume-rhizobium symbiosis. New Phytologist 194:1096-1111.
Context: Bourrat P and Griffiths PE (2018) Multispecies individuals. HPLS 40:33
June 10 ____postponed (to accommodate march in Waterfront Park)
June 17 ____Sherlynette Castro
Heterotrophic thermophiles with the potential for polymeric C degradation
June 24 ____Blair Paul____retroelements that drive protein variation in cyanobacteria
Blair Paul will be leading a discussion of his work in this preprint:
https://www.biorxiv.org/content/10.1101/2020.05.26.117283v1
He notes "While this work is based purely on genomic analysis of putative hypervariable proteins, our goal is to follow up with several experiments on function. A tangent paper (not required reading!) recently uncovered a functional role of the Hanks-type kinases, which are related to the types of proteins diversified by DGRs.
https://www.frontiersin.org/articles/10.3389/fmicb.2019.03140/full"
July 1___ Brooke Weigel -- current research
