Predictable functional biogeography of marine microbial heterotrophs

Zakem, Emily J.; McNichol, Jesse; Weissman, J.L.; Raut, Yubin; Xu, Liang; Halewood, Elisa R.; Carlson, Craig A.; Dutkiewicz, Stephanie; Fuhrman, Jed A.; Levine, Naomi M.

doi:10.1101/2024.02.14.580411

Cited by 3 publications

(2 citation statements)

References 55 publications

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“…Overall, these intermediate growth clusters appeared to be more flexible metabolically and faster-growing than the slow-growing specialist clusters but more specialized and slower growing than the fast-growing generalist cluster. The intermediate growth clusters corroborate a recent modeling study which suggested that the dominant heterotrophic group in the subsurface ocean might be slow-growing copiotrophs 2 .…”

Section: Emergent Metabolic Clusterssupporting

confidence: 88%

“…Classification of heterotrophic microbes into metabolic functional guilds can provide a framework for coalescing diverse microbial communities 1 into more tractable units for incorporation into biogeochemical models 2 . Historically, we have grouped marine microbial heterotrophs into copiotrophic organisms, which thrive in high resource environments and generally have faster growth rates with flexible metabolisms, and oligotrophic organisms, which dominate resource poor environments and have slower growth rates 3 .…”

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confidence: 99%

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Emergent Metabolic Niches for Marine Heterotrophs

Reynolds,

Weiss,

James

et al. 2024

Preprint

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Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, enables us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.

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Section: Emergent Metabolic Clusterssupporting

confidence: 88%

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confidence: 99%

Emergent Metabolic Niches for Marine Heterotrophs

Reynolds,

Weiss,

James

et al. 2024

Preprint

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Phosphate starvation stops bacteria digesting algal fucan that sequesters carbon

Xu,

Schultz-Johansen,

Yao

et al. 2024

Preprint

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Algae provide a solar powered pathway to capture and sequester carbon by injecting stable fucan made from carbon dioxide into the ocean1–4. Stability of the pathway is at odds with the presence of marine bacteria with genes of enzymes that can digest fucan and release the carbon dioxide5. Biochemical explanations for stable fucan remain hypothetical6. We assembled a biological carbon cycle model and found phosphate limitation enhanced fucan synthesis by algae, stopped digestion by bacteria and thereby stabilized the fucan carbon sequestration pathway. Marine microalgaeGlossomastixsp. PLY432 increased synthesis of fucan, a part of its extracellular matrix, under nutrient-growth limiting conditions. Rate and extent of fucan digestion by a marine, isolated bacterium of theAkkermansiaceaefamily decreased with decreasing phosphate concentration. Phosphate starvation restricted bacterial growth rate, biomass yield and in turn increased the amount of stable fucan. Phosphate is universally required for growth but rare relative to glycan carbon in photosynthesis-derived ecosystems. The fact that phosphate is required for replication, transcription and translation explains why bacteria can digest gigatons of laminarin with a few enzymes, but not fucan during nutrient limited algal blooms. We conclude phosphate starvation constrains the ability of bacteria to digest fucan, which evolves to maintain stability around algal cells and consequentially also to keep carbon dioxide in the ocean.

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Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information

Xu,

Zakem,

Weissman

2024

Preprint

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Microbial maximum growth rates vary widely across species and are key parameters for ecosystem modeling. Measuring these rates is challenging, but genomic features like codon usage statistics provide useful signals for predicting growth rates for as-yet uncultivated organisms,s though current predictors often show high variance. To improve accuracy, we integrate phylogenetic signals, leveraging the evolutionary relationships among species to refine trait predictions. We present Phydon, which combines codon statistics and phylogenetic information to enhance the precision of maximum growth rate estimates, especially when a close relative with a known growth rate is available. We construct the largest and most taxonomically broad database of temperature-corrected growth rate estimates for 111,349 microbial species. The results reveal a bimodal distribution of maximum growth rates, resolving distinct groups of fast and slow growers. Our hybrid approach advances the accuracy of genome-based growth rate predictions and presents a new framework for accurate genome-based trait prediction.

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Predictable functional biogeography of marine microbial heterotrophs

Cited by 3 publications

References 55 publications

Emergent Metabolic Niches for Marine Heterotrophs

Emergent Metabolic Niches for Marine Heterotrophs

Phosphate starvation stops bacteria digesting algal fucan that sequesters carbon

Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information

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