@fredebak
Assistant professor University of Copenhagen, Plant and Environmental Sciences | Visiting researcher AIT, Austrian Institute of Technology Bioresources. Plant-microbe interactions | Subsurface microbiology | Microbial ecology | Football
Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner url: academic.oup.com/ismecommun/a...
Submitted a grant proposal yessterday.🤞 12000/12000 characters. That has to count for something 🥸 right?
I’m looking for two postdoctoral scientists in experimental evolution to join my team from April 2026 (or soon after). Please share! fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/Candid...
Co-convening "The art and science of microbial persuasion" at #ISME20 with Fengping Wang. Cultivation advances: methods, media, uncultured lineages. Coaxing reluctant microbes? Submit your abstract & join us in NZ!
isme.live.ws-django.co.uk/public/confe...
isme.live.ws-django.co.uk/public/confe...
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
Cheers Eoghhan, same to you!
Thanks, will have a look at Novogene!
We will soon have to do RNA-seq on RNA from wheat roots.
Does anyone have recommendations for good European sequencing companies?
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.
A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision.
A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.
The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:
a 🧵 1/n
Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
How to deal with a co-author who claims to have written and revised part of a manuscript, when it is clearly just ChatGPT or the like?
To all visionary microbe enthusiasts: @femsmicro.org is looking for an editor-in-chief for their flagship journal FEMS Microbiology Reviews! More details can be found here: fems-microbiology.org/opportunitie...
🎉 Don't miss out on early bird registration for the 4th Global Soil Biodiversity Conference 🎉
Early bird registration is open until December 15th ,2025 🦜
Registration page 👇
globalsoilbiodiversity2026.org/registration/
A 2-y postdoc position in my former group at University of Copenhagen is available in microbial ecology and bioinformatics.
See more: employment.ku.dk/faculty/?sho...
Feel free to contact me if you have questions about the environment.
Please share the ad.
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
Hot off the press from our lab, led by @fredebak.bsky.social 👇
NRPS gene dynamics in the wheat rhizoplane show increased proportion of viscosin NRPS genes of importance for root colonization during drought | mSphere journals.asm.org/doi/10.1128/...
Post-doc position on Biological Nitrification Inhibition in rice in Aberdeen (Scotland)! Join our nice team and environment! Deadline 23rd Sept! www.abdnjobs.co.uk/vacancy/rese...
📢 We are thrilled to announce the International Soil Virus Conference 2026 in conjunction with the Saint Loup Research Institute.
🗓️ June 16 – 18, 2026
📍 Château de Saint Loup sur Thouet, France
👇 RSVP by October 31st, 2025
#virus #phage #ISVC2026
Hvordan ser det ud med billetter til i morgen?
Hot off the press!! At my exchange at @niab-uk.bsky.social, we found some interesting patterns in how root hairless wheat will use its microbiome (bacteria + fungi) to improve its phosphorus uptake.
The results in one sentence: bacteria may be cool, but AMF are the superstar!
Paper accepted! ☺️Great way to start the week.
We investigated the composition of non-ribosomal peptide synthases on the rhizoplane of #wheat during drought. Among other things, we showed that the potential to synthesize the biosurfactant #viscosin improves rhizoplane colonization during drought.
Maybe you cut more corners on this one 🙃
GPS watches don't do well on tracks ;)
Hey plant + soil people, what is your experience with RNA extraction kits? Will any ole kit work, or are some better with soil/soil-grown plants than others? We are buying our first RNA kits, drop your suggestions!! #PlantScience
So good to see you in Copenhagen!
Thanks a lot for stopping by
And here it is:
environmentalmicrobiome.biomedcentral.com/articles/10....
Enjoy reading it.
Impacts of diverse undersown cover crops on seasonal soil microbial properties url: academic.oup.com/femsec/artic...
@courtneyherms.bsky.social
Great final talk of the #rhizosphere6 conference. It was very rewarding to participste and hope to make it to Vienna in 4 years.
Paper accepted. #Nematode #Plantmicrobiome
#See#microbiome
environmentalmicrobiome.biomedcentral.com/articles/10....
A bit related to the second one: That taxa identified as hub taxa in network analysis are the most important ones/keystone species.