@MicrobeCookie

LBNL Postdoc Researcher; Environmental microbiologist

 Berkeley, CA
Joined November 2022
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  • Following287
  • Followers149
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We show that hypophosphite, a naturally occurring reduced phosphorus compound, selectively inhibits syntrophic methanogenesis by suppressing formate metabolism, suggesting an overlooked geochemical control on methane production and climate warming. biorxiv.org/content/10.64898…
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Ocean depth modifies host-microbiome ecology and evolution biorxiv.org/content/10.64898…

Ocean depth modifies host-microbiome ecology and evolution

A major unsolved question in ecology and evolution is how similar free-living and symbiotic microbial communities are. In marine systems, depth homogenises free-living communities due to stronger...

biorxiv.org
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Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model biorxiv.org/content/10.64898…

Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model

Prokaryotic genomes encode a vast repertoire of noncoding elements such as ribozymes, riboswitches, and CRISPR RNAs. The sequence-level diversity of these intergenic elements precludes alignment-ba...

biorxiv.org
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A giant virus with a 4-megabase genome and a vastly expanded repeatome. biorxiv.org/content/10.64898…

A giant virus with a 4-megabase genome and a vastly expanded repeatome.

Abstract Giant viruses of the phylum Nucleocytoviricota have expanded the boundaries of virology, yet the mechanisms underlying the gigantism of their genomes remain poorly understood. Here we...

biorxiv.org
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Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning biorxiv.org/content/10.64898…

Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding...

Microbial communities drive essential ecosystem processes, yet community-level behavior often deviates from predictions based on single-species studies. This mismatch reflects the context-dependent...

biorxiv.org
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Polysaccharide release factors drive lipid-carrier recycling in bacteria biorxiv.org/content/10.64898…

Polysaccharide release factors drive lipid-carrier recycling in bacteria

Gram-negative bacteria build their cell envelope by transporting various sugar-based precursors across the inner membrane on the shared lipid carrier undecaprenyl (also known as C55). Because the...

biorxiv.org
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A cold-adapted Cas9 nuclease from the deep ocean biorxiv.org/content/10.64898…

A cold-adapted Cas9 nuclease from the deep ocean

The abundance of CRISPR systems in bacteria and archaea fuels the search for Cas nucleases that perform where established enzymes fail. Deep Ocean 1 Cas9 (DO1Cas9) is to our knowledge the first Cas9...

biorxiv.org
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Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome biorxiv.org/content/10.64898…

Genomically and ecologically cohesive subspecies as biologically meaningful units in the global...

Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities....

biorxiv.org
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Herbicide degradation is driven by communication-mediated division of labor in synthetic communities nature.com/articles/s41467-0…

Herbicide degradation is driven by communication-mediated division of labor in synthetic communities

Nature Communications - Herbicide residues threaten soil health. Researchers constructed two SynComs that degrade multiple herbicides via quorum sensing-mediated metabolic division of labor, and...

nature.com
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Thiamine cross-feeding drives microbial coexistence in the leaf microbiome nature.com/articles/s41564-0…

Thiamine cross-feeding drives microbial coexistence in the leaf microbiome

Nature Microbiology - Evolution of nutrient cross-feeding between a yeast and oomycete mediates microbial coexistence and leaf microbiome stability.

nature.com
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Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere biorxiv.org/content/10.64898…

Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere

Hydrostatic pressure is a defining feature of the deep ocean, yet how it structures microbial activity across the subseafloor biosphere is poorly understood. Here, we assess pressure effects on...

biorxiv.org
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Ruiwen Hu, PhD retweeted
Yongyu Zhang@yongyu_zhangSep 29
Escalating Herbicide Loads as Underappreciated Global Disruptors of Marine Phytoplankton and Biogeochemical Cycles pubs.acs.org/esthag/article-…

Escalating Herbicide Loads as Underappreciated Global Disruptors of Marine Phytoplankton and...

Abstract. Under accelerating climate change and anthropogenic pressures, the global oceans face unprecedented threats from land-to-ocean contaminant discha

pubs.acs.org
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Ruiwen Hu, PhD retweeted
Vivek Mutalik@vivek_mutalikSep 29
annualreviews.org/content/jo… Scaling Phage-Bacteria Interaction Contexts: From Pairwise Mechanisms to Community Dynamics

Scaling Phage-Bacteria Interaction Contexts: From Pairwise Mechanisms to Community Dynamics

Bacteriophages (phages), viruses that parasitize bacteria, hold tremendous potential as antimicrobial agents, microbiome modulators, and industrial biocontrol tools; yet clinical and environmental...

annualreviews.org
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Spaghettification: How extreme replichore imbalance impacts bacterial replication and morphology biorxiv.org/content/10.64898…

Spaghettification: How extreme replichore imbalance impacts bacterial replication and morphology

Bacterial chromosomes are typically organized into two similarly sized replichores to synchronize bidirectional replication and fusion within a Tus/ ter- defined termination zone. Previous studies...

biorxiv.org
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Environmental history can counteract nutrient quality in shaping the evolution of bacterial growth rates biorxiv.org/content/10.64898…
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Satellite-gene abundance fusion reveals global hotspots of ocean ecosystem services biorxiv.org/content/10.64898…
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Hypoxia and acidification antagonistically suppress nitrification but enhance its N2O production in coastal waters | Science Advances science.org/doi/full/10.1126…

Hypoxia and acidification antagonistically suppress nitrification but enhance its N2O production in...

The concurrent intensification of hypoxia and acidification poses a growing threat to estuarine-coastal ecosystems globally, yet their interactive impacts on nitrification, a key process in the...

science.org
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Ruiwen Hu, PhD retweeted
Yongyu Zhang@yongyu_zhangSep 24
I am pleased to share our paper just published in Science Advances, titled "Global dispersal of macroalgae-derived recalcitrant DOC may substantially contribute to deep-ocean carbon storage". science.org/doi/10.1126/scia…

Global dispersal of macroalgae-derived recalcitrant DOC may substantially contribute to deep-ocean...

Macroalgae, the dominant primary producers of Earth’s most productive coastal vegetated ecosystems and a vital component driving ocean carbon sequestration, produce ∼5 to 80% of their net primary...

science.org
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Hypoxia and acidification antagonistically suppress nitrification but enhance its N2O production in coastal waters | Science Advances science.org/doi/full/10.1126…

Hypoxia and acidification antagonistically suppress nitrification but enhance its N2O production in...

The concurrent intensification of hypoxia and acidification poses a growing threat to estuarine-coastal ecosystems globally, yet their interactive impacts on nitrification, a key process in the...

science.org
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Ruiwen Hu, PhD retweeted
Frederik Schulz
@frederikschuSep 22
New study supported by our lab published in Cell: Incendiamoeba cascadensis, a newly described geothermal amoeba, divides at 63°C, setting a new upper temperature record for eukaryotic life. Comparative genomics and cell-biological analyses reveal adaptations linked to protein homeostasis, genome stability, and environmental sensing. sciencedirect.com/science/ar…
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Ruiwen Hu, PhD retweeted
Vivek Mutalik@vivek_mutalikSep 19
Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them....Our new preprint takes this on 🧵👇
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