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Frederik Bak

@fredebak.bsky.social
176 followers 149 following 50 posts

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

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Reposted by Frederik Bak
Marie Simonin @microbialmarie.bsky.social · 23/06/2026
📆 Save The Date! The Plant-Bacteria Interaction Meeting (18th RPB) in Aussois, Savoie will take place from January 11 to 15th, 2027 👉 More info on the keynote speakers & sessions: plants-bacteria-2027.symposium.inrae.fr Deadline: September 25th @inrae-dpt-spe.bsky.social @sfp-france.bsky.social
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Amelia Rotaru @ameliarotaru.bsky.social · 18/03/2026
Please help spread the word about this 3-year postdoc position in my team. If your expertise & interest lie in studying how organisms from different domains of life (Bacteria and Archaea) communicate, come join us this summer in cozy Odense, Denmark. Job post: www.nature.com/naturecareer...
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Frederik Bak @fredebak.bsky.social · 01/03/2026
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...
academic.oup.com
Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner
Abstract. The root microbiome is important for plant development. The impact of the root microbiome is the result of multiple complex interactions among mi
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Frederik Bak @fredebak.bsky.social · 05/02/2026
Submitted a grant proposal yessterday.🤞 12000/12000 characters. That has to count for something 🥸 right?
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Reposted by Frederik Bak
Amelia Rotaru @ameliarotaru.bsky.social · 03/02/2026
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...
fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com
Two postdoctoral positions (3-year) in Experimental Evolution of Methanogenic Microbiomes in Bioelectrochemical Systems
Application deadline: 4 March 2026 at 23:59 hours local Danish time
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Reposted by Frederik Bak
Paul Carini @uncultured.carinilab.com · 15/01/2026
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...
isme.live.ws-django.co.uk
ISME20: The art and science of microbial persuasion | International Society for Microbial Ecology
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Reposted by Frederik Bak
Mark A. Hanson @hansonmark.bsky.social · 13/01/2026
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
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Frederik Bak @fredebak.bsky.social · 14/01/2026
We will soon have to do RNA-seq on RNA from wheat roots. Does anyone have recommendations for good European sequencing companies?
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Reposted by Frederik Bak
Mark A. Hanson @hansonmark.bsky.social · 11/11/2025
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/...
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.
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Frederik Bak @fredebak.bsky.social · 12/11/2025
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?
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Reposted by Frederik Bak
Team Thomma @teamthomma.bsky.social · 05/11/2025
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...
fems-microbiology.org
Editor-in-Chief for FEMS Microbiology Reviews - FEMS
The Federation of European Microbiological Societies (FEMS) is looking for an Editor-in-Chief to join its prestigious journal FEMS Microbiology Reviews for an initial period of three years, starting i...
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Reposted by Frederik Bak
The Global Soil Biodiversity Initiative @thegsbi.bsky.social · 02/11/2025
🎉 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/
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Frederik Bak @fredebak.bsky.social · 02/10/2025
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.
employment.ku.dk
Postdoc in Microbial bioinformatics
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Alex Probst @alexjprobst.bsky.social · 26/09/2025
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!
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Courtney Herms @courtneyherms.bsky.social · 16/09/2025
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/...
journals.asm.org
NRPS gene dynamics in the wheat rhizoplane show increased proportion of viscosin NRPS genes of importance for root colonization during drought | mSphere
To harness beneficial plant–microbe interactions for improved plant resilience, we need to advance our understanding of key factors required for successful root colonization. Bacterial-produced second...
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Reposted by Frederik Bak
Cecile Gubry-Rangin @micecoevo.bsky.social · 11/09/2025
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...
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Reposted by Frederik Bak
Soil Microbial Ecology Group @soilmicrobes.bsky.social · 09/09/2025
📢 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
soilmicrobes.fr
ISVC2026
International Soil Virus Conference 2026! We are excited to announce and provide RSVP details for the next International Soil Virus Conference that will be held in Saint-Loup Lamaire, France on Jun…
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Reposted by Frederik Bak
Courtney Herms @courtneyherms.bsky.social · 27/08/2025
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!
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Frederik Bak @fredebak.bsky.social · 25/08/2025
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.
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Reposted by Frederik Bak
Courtney Herms @courtneyherms.bsky.social · 05/08/2025
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
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Frederik Bak @fredebak.bsky.social · 01/07/2025
And here it is: environmentalmicrobiome.biomedcentral.com/articles/10.... Enjoy reading it.
environmentalmicrobiome.biomedcentral.com
Meloidogyne incognita parasitism is affected by Pseudomonas protegens CHA0 and its effects on tomato-associated microbiota - Environmental Microbiome
Background The multitrophic interactions in plant rhizosphere and endosphere can be beneficial or deleterious for the plant health. The parasitism by root-feeding nematodes is on the negative end of t...
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Frederik Bak @fredebak.bsky.social · 30/06/2025
Impacts of diverse undersown cover crops on seasonal soil microbial properties url: academic.oup.com/femsec/artic...
academic.oup.com
Impacts of diverse undersown cover crops on seasonal soil microbial properties
Abstract. Positive relationships between plant diversity, microbial diversity, and ecosystem functioning have widely been observed in experimental grasslan
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Frederik Bak @fredebak.bsky.social · 19/06/2025
Great final talk of the #rhizosphere6 conference. It was very rewarding to participste and hope to make it to Vienna in 4 years.
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Frederik Bak @fredebak.bsky.social · 16/06/2025
Paper accepted. #Nematode #Plantmicrobiome
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Frederik Bak @fredebak.bsky.social · 13/06/2025
#See#microbiome environmentalmicrobiome.biomedcentral.com/articles/10....
environmentalmicrobiome.biomedcentral.com
Defining the cultured and uncultured bacterial fractions in Cannabis seeds - Environmental Microbiome
Background Seeds provide a unique environment shaped by co-evolutionary processes, hosting diverse microbial communities. While microbiome studies have uncovered an extensive diversity of microorganis...
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Reposted by Frederik Bak
Courtney Herms @courtneyherms.bsky.social · 22/04/2025
Above all, I hope that the collection of 112 wheat-derived, complete Pseudomonas genomes will be a useful and interesting tool for others. Download them here: t.co/iFMgxWqnk4
t.co
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1108081
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Courtney Herms @courtneyherms.bsky.social · 22/04/2025
My 1st first-author research article is published in Applied Soil Ecology! This paper has been my constant companion over the past 4 years, but I'm so happy to send it off into the world 👇 www.sciencedirect.com/science/arti...
sciencedirect.com
Pseudomonas taxonomic and functional microdiversity in the wheat rhizosphere is cultivar-dependent and links to disease resistance profile and root diameter
Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, the…
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Tillmann Lueders @luederslab.bsky.social · 19/03/2025
Microbiology Postdocs from all over Europe and the Globe! 🦠😎👍 Application for the FEMS SSPD 2025 “Harnessing microbial solutions in environmental research and One Health” is now open 👇 2 – 10 Sept 2025 on Lake Ohrid, North Macedonia Co-Directors: Joana Falcao Salles and @luederslab.bsky.social
fems-microbiology.org
FEMS Summer School for Postdocs 2025 - FEMS
Menu: Introduction – Applications – Programme This has been the most valuable and enjoyable scientific event I’ve attended so far. The atmosphere was incredible, with inspiring co-directors and mentor...
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Marie Simonin @microbialmarie.bsky.social · 06/03/2025
📢 Open PhD Position With @fly-florian.bsky.social, we are recruiting a PhD student to develop CRISPR-Based Microbiome Editing to Study Microbial Interactions in Early Plant Life 🧬 🌿 Join us in Angers, France in the @emersys-irhs.bsky.social at @inrae-france.bsky.social 🗓️ Deadline 03/31 More info 👇
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Frederik Bak @fredebak.bsky.social · 06/03/2025
An opnion worth reading, on how to improve the planning microbiome data analysis and the use of statistics www.nature.com/articles/s41...
nature.com
Planning and describing a microbiome data analysis - Nature Microbiology
We provide guidance on the planning, execution and description of statistical analyses in microbiome studies.
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Frederik Bak @fredebak.bsky.social · 27/02/2025
#PhD position in #Microbial Interactions group. #Wheat #Microbiome #Phosphorous RT appreciated employment.ku.dk/phd?show=163...
employment.ku.dk
PhD fellowship in Microbial ecology and plant-microbe interactions in the wheat rhizosphere
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Frederik Bak @fredebak.bsky.social · 27/02/2025
#PhD positions at UCPH - Department of Plant and Envrionmental Sciences #Microbiome #Biodiversity #Pathogens jobportal.ku.dk/phd/?show=16...
jobportal.ku.dk
PhD fellowships at the Department of Plant & Environmental Sciences.
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Frederik Bak @fredebak.bsky.social · 19/02/2025
👨‍🎓 in 🌾🦠! Soon there will be an available #phd position in #plant #microbiome in out research group @ucph.bsky.social More details in a couple of weeks.
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Frederik Bak @fredebak.bsky.social · 19/02/2025
Metabolism of hemicelluloses by root-associated Bacteroidota species academic.oup.com/ismej/advanc...
academic.oup.com
Metabolism of hemicelluloses by root-associated Bacteroidota species
Abstract. Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression.
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Frederik Bak @fredebak.bsky.social · 19/02/2025
Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum academic.oup.com/ismej/advanc...
academic.oup.com
Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum
Abstract. In nature, cooperation is an essential way for species, whether they belong to the same kingdom or to different kingdoms, to overcome the scarcit
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Frederik Bak @fredebak.bsky.social · 19/02/2025
Agricultural practices and pollinators modulate the anthosphere microbiome academic.oup.com/ismecommun/a...
academic.oup.com
Agricultural practices and pollinators modulate the anthosphere microbiome
Abstract. The flower microbiome is pivotal in plant health, influencing reproductive success, fruit quality, and pathogen vulnerability. However, the impac
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Frederik Bak @fredebak.bsky.social · 19/02/2025
Invertebrate Decline Has Minimal Effects on Oak-Associated Microbiomes enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Invertebrate Decline Has Minimal Effects on Oak‐Associated Microbiomes
Reduced invertebrate biomass impacts oak-associated microbial communities: oak compartment specific bacterial and fungal communities showed divergent reactions to insect decline within an experimenta....
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Reposted by Frederik Bak
Cameron Thrash @jcamthrash.bsky.social · 19/02/2025
Ten simple rules for fostering creativity in research labs journals.plos.org/ploscompbiol... #jcampubs
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Frederik Bak @fredebak.bsky.social · 13/02/2025
I am looking for a paper on the pH and oxygen gradients around a germinating #seed. Does anyone know of one? #microbiome #plant
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Cecile Gubry-Rangin @micecoevo.bsky.social · 31/01/2025
Fully funded PhD studentships in the University of Aberdeen in microbial adaptation: www.findaphd.com/phds/project...
findaphd.com
QUARTILES DLA: Microbial thermal tolerance in the context of climate change at University of Aberdeen on FindAPhD.com
PhD Project - QUARTILES DLA: Microbial thermal tolerance in the context of climate change at University of Aberdeen , listed on FindAPhD.com
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Frederik Bak @fredebak.bsky.social · 31/01/2025
Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession academic.oup.com/ismecommun/a...
academic.oup.com
Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession
Abstract. Grazing exclusion and land abandonment are commonly adopted to restore degraded ecosystems in semiarid and arid regions worldwide. However, the t
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Frederik Bak @fredebak.bsky.social · 31/01/2025
Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans academic.oup.com/ismej/advanc...
academic.oup.com
Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans
Abstract. Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans str
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Frederik Bak @fredebak.bsky.social · 31/01/2025
Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery bmcmicrobiol.biomedcentral.com/articles/10....
bmcmicrobiol.biomedcentral.com
Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery - BMC Microbiology
Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential syner...
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Frederik Bak @fredebak.bsky.social · 31/01/2025
Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation microbiomejournal.biomedcentral.com/articles/10....
microbiomejournal.biomedcentral.com
Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation - Microbiome
Background Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germinat...
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Frederik Bak @fredebak.bsky.social · 31/01/2025
Commercial bioinoculants improve colonization but do not alter the arbuscular mycorrhizal fungal community of greenhouse-grown grapevine root environmentalmicrobiome.biomedcentral.com/articles/10....
environmentalmicrobiome.biomedcentral.com
Commercial bioinoculants improve colonization but do not alter the arbuscular mycorrhizal fungal community of greenhouse-grown grapevine roots - Environmental Microbiome
Background Arbuscular mycorrhizal fungi (AMF) are beneficial root symbionts contributing to improved plant growth and development and resistance to abiotic and biotic stresses. Commercial bioinoculant...
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 27/01/2025
Pls ahre: Pls share: Tenure-Track Assistant Professor of Microbiology, Hofstra University, NY Full ad and application link: hofstra.peopleadmin.com/postings/5041
hofstra.peopleadmin.com
Assistant Professor of Microbiology
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Kati Retzer @katarzynaretzer.bsky.social · 27/01/2025
Looking forward to share my experience as #translationalscientist #roots #plantscience #appliedscience #plantsoil #sustainability #barleymicrobreed #droughtstress @bokuvienna.bsky.social At the @plantaeofficial.bsky.social platform thx @katarinakurtovic.bsky.social plantae.org/plantaeprese...
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Elisabeth Bik @elisabethbik.bsky.social · 27/01/2025
‘Stamp out paper mills’ — science sleuths on how to fight fake research By Anna Abalkina, René Aquarius, Elisabeth Bik, David Bimler, Dorothy Bishop, Jennifer Byrne, Guillaume Cabanac, Adam Day, Cyril Labbé & Nick Wise @nature.com www.nature.com/articles/d41...
nature.com
‘Stamp out paper mills’ — science sleuths on how to fight fake research
A group of scientists who are experts at spotting fraudulent research outline five essential steps to combat industrialized scientific misconduct.
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Frederik Bak @fredebak.bsky.social · 18/01/2025
Had the pleasure to attend the inaugural lecture by Bo Markussen (Applied statistics) yesterday at @ucph.bsky.social Super interesting, and great to see our microbiome data can be used for developing new statistical tests. I am thankful for the Data Science Lab at @ucph.bsky.social
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