A unified theory for organic matter accumulation

Zakem, Emily; Cael, B. B.; Levine, Naomi M.

doi:10.1073/pnas.2016896118

Cited by 72 publications

(53 citation statements)

References 69 publications

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“…This is because the addition of labile substrates could increase the population size of degraders, thereby enabling the recycling of more recalcitrant forms of organic matter. The implications of this hypothesis were recently explored using consumer -resource models, which can qualitatively reproduce the distribution and concentration of organic matter in the ocean (Mentges et al, 2019;Zakem et al, 2021). The underlying key assumption was that most substrates are accessible to generalists and few substrates only to specialists.…”

Section: Challenge 6 | Non-linear Growth Kineticsmentioning

confidence: 99%

Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology

Sichert

Cordero

2021

Front. Microbiol.

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Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex “landscape” of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.

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Section: Challenge 6 | Non-linear Growth Kineticsmentioning

confidence: 99%

Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology

Sichert

Cordero

2021

Front. Microbiol.

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“…Although this classification has proven useful in the study of oceanic DOC, it has not completely avoided the core problem, which is the use of the term "refractory" as a one-fits-all word for different and frequently non-complementary properties/characteristics related to DOC reactivity. Another way of addressing the reactivity of DOC is to use the DOC continuum concept instead of using a number of DOC pools based on its reactivity (Zakem et al, 2021). Several studies have discussed DOC reactivity in terms of compounds with a continuum of first order decay rates, e.g., in sediments (Boudreau and Ruddick, 1991;Middelburg et al, 1993) and lake water (Vähätalo et al, 2010;Koehler et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

What Is Refractory Organic Matter in the Ocean?

et al. 2021

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About 20% of the organic carbon produced in the sunlit surface ocean is transported into the ocean’s interior as dissolved, suspended and sinking particles to be mineralized and sequestered as dissolved inorganic carbon (DIC), sedimentary particulate organic carbon (POC) or “refractory” dissolved organic carbon (rDOC). Recently, the physical and biological mechanisms associated with the particle pumps have been revisited, suggesting that accepted fluxes might be severely underestimated (Boyd et al., 2019; Buesseler et al., 2020). Perhaps even more poorly understood are the mechanisms driving rDOC production and its potential accumulation in the ocean. On the basis of recent conflicting evidence about the relevance of DOC degradation in the deep ocean, we revisit the concept of rDOC in terms of its “refractory” nature in order to understand its role in the global carbon cycle. Here, we address the problem of various definitions and approaches used to characterize rDOC (such as turnover time in relation to the ocean transit time, molecule abundance, chemical composition and structure). We propose that rDOC should be operationally defined. However, we recognize there are multiple ways to operationally define rDOC; thus the main focus for unifying future studies should be to explicitly state how rDOC is being defined and the analytical window used for measuring rDOC, rather than adhering to a single operational definition. We also conclude, based on recent evidence, that the persistence of rDOC is fundamentally dependent on both intrinsic (chemical composition and structure, e.g., molecular properties), and extrinsic properties (amount or external factors, e.g., molecular concentrations, ecosystem properties). Finally, we suggest specific research questions aimed at stimulating research on the nature, dynamics, and role of rDOC in Carbon sequestration now and in future scenarios of climate change.

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“…This idea would suggest that the DOC accumulation in the ocean depends on the speed with which currents transport the various DOC compounds to those environments where the microbial communities possess the metabolic capability to consume those compounds (Shen & Benner, 2018). Finally, a recent study proposes a unifying theory that is based on the complexity of microbial ecosystem, explaining the conversion of functionally recalcitrant DOC to a state of complete consumption as a function microbial community or environmental changes (Zakem et al, 2021).…”

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confidence: 99%

Sensitivity of Steady State, Deep Ocean Dissolved Organic Carbon to Surface Boundary Conditions

Matsumoto

Tanioka

Gilchrist

2022

Global Biogeochemical Cycles

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Most of the organic matter produced in the surface ocean by photoautotrophs is grazed by zooplankton and recycled quickly within the upper ocean by heterotrophic microbes. The small fraction of organic matter that escapes recycling accumulates in the ocean in the dissolved phase. In terms of carbon, the oceanic inventory of the dissolved organic carbon (DOC) has been previously estimated to be 662-700 PgC (Hansell et al., 2009;Hedges, 1992). Previous estimates of the global ocean DOC export production have employed ocean models and range from roughly 20% (Hansell et al., 2009) to 27% (Yamanaka & Tajika, 1997 of the global ocean carbon export production. The potential importance of marine DOC to global climate is indicated by the fact that the marine DOC inventory rivals the atmospheric carbon inventory. Also, carbon export is a key driver of atmospheric pCO 2 . Indeed, some paleoclimate events have been attributed to changes in the marine DOC cycle (Sexton et al., 2011).The marine DOC cycle has been studied for decades, and as yet, our understanding of DOC dynamics is incomplete. DOC is a complex mixture of thousands of compounds that are chemically and structurally diverse and thus poorly characterized (e.g., Hedges et al., 2000;Hertkorn et al., 2006). Radiocarbon ( 14 C) measurements of deep ocean DOC samples indicate ages as old as 6,000 years (Williams & Druffel, 1987). Thus, accumulated DOC has somehow survived global ocean overturning multiple times.There are also aspects of the global distribution of DOC that remain unexplained. Measurements indicate that DOC in the open ocean exists at very low concentrations, typically in the range of 35-80 μmol kg −1 (Figure 1). The concentration is relatively high and variable near the surface and lower and more uniform at depth. It is typically 65-80 μmol kg −1 in the stratified, warm waters of the tropical and subtropical regions. In the subpolar surface waters, where vertical mixing is strong, the DOC concentration is lower and approaches the deep ocean values of 35∼40 μmol kg −1 . The deep ocean DOC concentration was once thought to be uniform (Martin & Fitzwater, 1992), but as Hansell and Carlson (1998) first reported, there is a modest concentration gradient representing a decrease along the path of the meridional overturning circulation from the North Atlantic to the North Pacific by approximately 14 μmol kg −1 . The surface distribution as well as the deep ocean gradient are not well explained in terms of sources and sinks of DOC. In particular, the DOC sinks (e.g., photodegradation, hydrothermal vents) and their rates are poorly understood (Lang et al., 2006;Mopper et al., 1991). In one case, a DOC

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A unified theory for organic matter accumulation

Cited by 72 publications

References 69 publications

Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology

Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology

What Is Refractory Organic Matter in the Ocean?

Sensitivity of Steady State, Deep Ocean Dissolved Organic Carbon to Surface Boundary Conditions

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