Deciphering microbial interactions using a label-free microbead sorting approach Abstract. Microorganisms form communities, and their interactions shape the function and stability of these communities. Understanding these interactions c

Deciphering microbial interactions using a label-free microbead sorting approach academic.oup.com/ismecommun/a... #jcampubs

Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests journals.plos.org/ploscompbiol...

Cross-feeding options define genome evolution and community assembly of deep groundwater microbiome - Environmental Microbiome Background Deep groundwaters populated by diverse and active microbes are among the most energy and nutrient-limited ecosystems. Characteristics of this ecosystem (including nutrient and dispersal lim...

Cross-feeding options define genome evolution and community assembly of deep groundwater microbiome
#microbiology #microbiome #MicroSky
@microbiomej.bsky.social
link.springer.com/article/10.1...

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :

www.nature.com/articles/s41...

See the linked threads for more details!

Digging deeper into soil metagenomics: opportunities and limitations for studying the genomic potential of soil bacteria and archaea - Biology and Fertility of Soils Soil microbial ecology has been transformed by recent progress in sequencing and metagenomics, reshaping our understanding of soil microbial functions. This article examines how metagenomics can be us...

Metagenomics is great, but applying it to soil is... complicated 🦠⛏️ Our new Perspective Article is out, diving into the the opportunities and limitations of metagenomics to study soil bacteria and archaea
link.springer.com/article/10.1...

Community structure of bacteria and fungi.

Quantifying microbiota impact on plant traits for the guidance of breeding programs

Blouin et al.

nph.onlinelibrary.wiley.com/doi/10.1111/...

www.nature.com/articles/s41...

Very neat agricultural microbiome research. There was legacy effect of potato plant vigor based on what production field it was grown in.

Image of the cover of the 1st volume of ISME Host Microbe a new official journal of the International Society for Microbial Ecology. Cover images shows a plant stomata with bacteria around and entering.

Excited to announce our new journal from @isme-microbes.bsky.social ISME Host Microbe is live and now accepting submissions. Look forward to receiving your papers! #Microsky 🧫 🦠

Nanodomain-localized formin gates symbiotic microbial entry in legume and solanaceous plants Colonization of plant roots by symbionts requires substantial morphodynamic reorganization. Examples are actin-scaffolded microcompartments called infection pockets formed during root nodule symbiosis...

Happy to share our latest work in collaboration with the lab of @pengbo10.bsky.social. Here, we describe that a formin protein mediates the polarity switch from root hair to infection thread growth during symbiotic interactions.
www.science.org/doi/10.1126/...

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...

Are you a postdoc in a plant-related field such as🌿 Plant Biology 🌿 Agriculture & Crop Sciences 🌿 Ecology & Environment 🌿 Plant Pathology & Protection or 🌿 Biotechnology ?

We invite you to join a community of 700+ postdoctoral researchers from around the world at www.plantpostdocs.com

Domestication timing and multivariate phenotypic divergence index for the 13 species.

Evolution of crop phenotypic spaces through domestication

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Wojcik et al.

@maudtenaillon.bsky.social #PlantScience

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

This is an incredible resource:

The MicrobeAtlas Database www.cell.com/cell/fulltex...

Gopher tortoise influence on soil biodiversity is constrained by historical land use - Biodiversity and Conservation Keystone species and ecosystem engineers play critical roles in maintaining and enhancing biodiversity by modifying their environment and creating ecological niches that support a wide range of organi...

Hot off the press! If you’ve ever wondered how ecosystem-engineering gopher tortoises shape soil microbial and nematode communities, this paper is for you! 🐢💚

link.springer.com/article/10.1...

How citrus rewires its vascular system to fight huanglongbing Huanglongbing (HLB) is one of the most destructive diseases threatening global citrus production, yet how citrus plants respond to the pathogen at the cellular level has remained unclear.

How #citrus rewires its vascular system to fight #huanglongbing ...

| #pathogen | #bacteria | #Liberibacter | Via eurekalert .org

Epiphytic bacterial community diversity patterns of Myriophyllum spicatum along the latitudinal gradient.

Latitudinal patterns of surface bacterial community

Li et al.

nph.onlinelibrary.wiley.com/share/WHUPK2...

Anthropogenic disturbance alters the diversity, composition, and abundance of microbes as well as the edaphic properties of the soil.

#TansleyReview: Why, when, and how microbes can benefit ecological restorations: current approaches and future directions

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Crawford et al.

@kerricrawford.bsky.social @collingdice.bsky.social
Figure created in biorender.com/iwso49n.

Mojave Desert microbial communities show high resistance and resilience over three years despite widespread plant mortality following the Dome Fire - Fire Ecology Background High severity desert fires are uncommon but typically chart a new successional trajectory altering plant communities for at least 65 years. These aboveground vegetation shifts can have larg...

Take a look at our paper on the soil microbiomes associated with the eastern Joshua tree after the 2020 dome fire! @arikchou.bsky.social @pulidofabs.bsky.social Lynn Sweet melanie davis link.springer.com/article/10.1...

A novel analysis workflow for simultaneous parsing prokaryotic and eukaryotic microbial genes from metagenomes peerj.com/articles/207... #jcampubs

From death comes diversity - Nature Ecology & Evolution A high-throughput laboratory experiment tracking the assembly of soil-derived communities shows that species-rich bacterial necromass supports increasingly diverse communities, with each additional de...

From death comes diversity! 🦠🧪🌐🌏

www.nature.com/articles/s41...

Community conservatism is widespread across microbial phyla and environments - Nature Ecology & Evolution This study reveals that closely related microorganisms tend to inhabit similar communities across all major environments and phyla. The authors term this phenomenon ‘community conservatism’, extending...

Community conservatism is widespread across microbial phyla and environments
#microbiology #microbes #MicroSky
@natecoevo.nature.com
www.nature.com/articles/s41...

(1/8) 🚨Thrilled to share our new research, now published on the cover of @science.org ! 🌳🦠
We discovered that tree #Bark — largely regarded as inert — hosts vast #Microbial communities that actively interact with the atmosphere. 🧵👇 www.science.org/doi/10.1126/...

Constructing a “periodic table” of bacteria to map diversity in trait space Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen

New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...

The Lariviere lab at UMiami is recruiting PhD students! Incoming students will join us in studying host-microbe interactions in the honey bee gut, using molecular and genetic approaches. Please see the attached flyer for more details.

#Symbiosis #SymbioSky #MicroSky #PhDOpportunity #AcademicJobs

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases | Science Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform ...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases | Science

Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6

www.asps.org.au/phytogen/oct...

Newly published in @globalchangebio.bsky.social, we look within seeds of historic herbarium specimens for changes in the prevalence of beneficial fungal symbionts in response to climate change drivers. onlinelibrary.wiley.com/doi/10.1111/...