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Ruiwen Hu, PhD

@MicrobeCookie

LBNL Postdoc Researcher; Environmental microbiologist

 Berkeley, CA
Joined November 2022
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Photo by Ruiwen Hu, PhD (@MicrobeCookie)Photo by Ruiwen Hu, PhD (@MicrobeCookie)
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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The microbial making and breaking of dimethylsulfoniopropionate and related compounds nature.com/articles/s41564-0…
The microbial making and breaking of dimethylsulfoniopropionate and related compounds

The microbial making and breaking of dimethylsulfoniopropionate and related compounds

Nature Microbiology - This Review reports the current understanding of the microbially mediated dimethylsulfoniopropionate cycle—the biodiversity, regulation and importance of genes and...

nature.com
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Global change reshapes marine microbial communities, functions and One Health outcomes nature.com/articles/s41579-0…
Global change reshapes marine microbial communities, functions and One Health outcomes

Global change reshapes marine microbial communities, functions and One Health outcomes

Nature Reviews Microbiology - Global change is transforming marine microbial communities. In this Review, Peixoto and colleagues explore the effects of climate and anthropogenic stressors on...

nature.com
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Toward planetary microbial systems biology: Cell cell.com/cell/fulltext/S0092…
Toward planetary microbial systems biology

Toward planetary microbial systems biology

Planetary microbial systems biology, encompassing multi-omics, AI, and field-to-lab interaction, is proposed as a framework to study Earth’s interconnected microbiomes at a planetary scale.

cell.com
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The Braarudosphaera bigelowii genome reveals cellular remodeling around a nitrogen-fixing organelle biorxiv.org/content/10.64898…
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Evolutionary oxidation of proteins in Earth’s history nature.com/articles/s41467-0…

Evolutionary oxidation of proteins in Earth’s history

Nature Communications - The Great Oxidation Event about 2.4 billion years ago transformed Earth’s atmosphere and forced early life to adapt. This study shows that proteins across the tree of...

nature.com
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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

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

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

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

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 describe...

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...

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

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

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...

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

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

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

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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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

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...

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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