Biogeochemistry articles within Nature Communications

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  • Article
    | Open Access

    Despite growing interest in environmental metabolomics, we lack conceptual frameworks for considering how metabolites vary across space and time in ecological systems. Here, the authors apply (species) community assembly concepts to metabolomics data, offering a way forward in understanding the assembly of metabolite assemblages.

    • Robert E. Danczak
    • , Rosalie K. Chu
    •  & James C. Stegen

  • Article
    | Open Access

    Iron minerals trap carbon in permafrost, preventing microbial degradation and release to the atmosphere as CO2, but the stability of this carbon as permafrost thaws is unclear. Here the authors use nanoscale analyses to show that thaw conditions stimulate Fe-reducing bacteria that trigger carbon release.

    • Monique S. Patzner
    • , Carsten W. Mueller
    •  & Casey Bryce

  • Article
    | Open Access

    Excess fertilizer use causes subsurface contamination. Here, the authors conduct an assessment of water quality vulnerability across Europe, finding that 75% of agricultural regions are susceptible to nitrate contamination for least one-third of the year, two times more than using standard estimation procedure.

    • R. Kumar
    • , F. Heße
    •  & S. Attinger

  • Article
    | Open Access

    The fate of subducted CO2 remains debated, with estimates mainly from numerical predictions varying from wholesale decarbonation of the shallow subducting slab to massive deep subduction of CO2. Here, the authors present field-based data and show that ~40% to ~65% of the CO2 in subducting crust is released via metamorphic decarbonation reactions at forearc depths.

    • E. M. Stewart
    •  & Jay J. Ague

  • Article
    | Open Access

    A Southern Ocean influences on the carbon cycle is considered a key component of deglacial changes. Here, the authors show spatial differences in glacial Southern Ocean carbon storage that dissipated rapidly 14.6 kyr ago, revealing a South Indian Ocean contribution to rapid deglacial atmospheric CO2 increases.

    • Julia Gottschalk
    • , Elisabeth Michel
    •  & Samuel L. Jaccard

  • Article
    | Open Access

    Historically it has been maintained that soil organic carbon (SOC) is stabilized through interactions with mineral interfaces. Here the authors use cryo-electron microscopy and spectroscopy to show that SOC interactions can also occur between organic forms in patchy, disordered structure.

    • Angela R. Possinger
    • , Michael J. Zachman
    •  & Johannes Lehmann

  • Article
    | Open Access

    Photosynthetic formation of manganese (Mn) oxides from dissolved Mn ions was proposed to occur in ancestral photosystems before oxygenic photosynthesis evolved. Here, the authors provide evidence for this hypothesis by showing that photosystem II devoid of the Mn cluster oxidises Mn ions leading to formation of Mn-oxide nanoparticles.

    • Petko Chernev
    • , Sophie Fischer
    •  & Holger Dau

  • Article
    | Open Access

    Zooplankton biomass in the dark ocean is thought to be low and weakly coupled to epipelagic primary production, but recent evidence suggests otherwise. Here the authors analyse data from the Malaspina Circumnavigation Expedition and published data to estimate bathypelagic zooplankton biomass and assess its relationship to primary production, currently not well accounted for in oceanic C budget.

    • S. Hernández-León
    • , R. Koppelmann
    •  & C. M. Duarte

  • Article
    | Open Access

    Antarctic krill are known to be important to the carbon cycle, but the exact contribution is not known. Here the authors show that krill moulting is a major vector of carbon export in the Southern Ocean, together with krill faecal pellets accounting for almost 90% of annual particulate organic carbon flux.

    • C. Manno
    • , S. Fielding
    •  & G. A. Tarling

  • Article
    | Open Access

    As the climate warms, soil carbon stores will likely be degraded by microbes and released as CO2, but these predictions are based on laboratory incubations that might not reflect real rates. Here the authors optimize model projections using dozens of short- and long-term incubations in forest and grasslands.

    • Siyang Jian
    • , Jianwei Li
    •  & Melanie A. Mayes

  • Article
    | Open Access

    Warming in the high latitudes is expected to stimulate soil organic matter decomposition which leads to enhanced carbon emissions. Here, the authors show that short-term experiments do not capture the complexity of vegetation dynamics in the Arctic and might thus not provide a full picture of long term processes.

    • Nicholas J. Bouskill
    • , William J. Riley
    •  & Robert F. Grant

  • Perspective
    | Open Access

    Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.

    • Emily J. Zakem
    • , Martin F. Polz
    •  & Michael J. Follows

  • Perspective
    | Open Access

    Reducing soil degradation and improving soil management could make an important contribute to climate change mitigation. Here the authors discuss opportunities and challenges towards implementing a global climate mitigation strategy focused on carbon sequestration in agricultural soils, and propose a framework for guiding region- and soil-specific management options.

    • W. Amelung
    • , D. Bossio
    •  & A. Chabbi

  • Article
    | Open Access

    Phytoplankton are biogeochemically important but the drivers of their seasonal cycles in the Southern Ocean are poorly resolved. Here the authors use seven years of ARGO float data to measure bloom initiation, decline and termination throughout the Southern Ocean, finding that bloom dynamics are especially sensitive to the coupling between cell division rates and loss processes.

    • Lionel A. Arteaga
    • , Emmanuel Boss
    •  & Jorge L. Sarmiento

  • Article
    | Open Access

    Coastal systems have enormous carbon-sequestering potential, but any positive climate effects can be countered by methane emissions. Here the authors use sea level rise manipulation mesocosms in tidal wetlands to show that shifts in plant community composition have the greatest effect on methane emissions.

    • Peter Mueller
    • , Thomas J. Mozdzer
    •  & J. Patrick Megonigal

  • Article
    | Open Access

    The Si cycle is important to ocean productivity and nutrient cycling, however there are uncertainties in global budgets. Here the authors use a multi-isotope approach on seafloor sediments and pore fluids, finding that an unappreciated source of Si to the ocean is the degradation of seafloor serpentinites.

    • Sonja Geilert
    • , Patricia Grasse
    •  & Catriona D. Menzies

  • Article
    | Open Access

    Carbon stored in the Arctic is threatened by climate change, but models do not capture the local-scale heterogeneity that influences carbon dynamics. Here the authors refine tundra models to account for heterogeneity, finding improved projections and decreased uncertainty in assessing the fate of carbon.

    • M. J. Lara
    • , A. D. McGuire
    •  & S. D. Wullschleger

  • Article
    | Open Access

    Mechanisms and consequences of the acclimation of soil respiration to warming are unclear. Here, the authors combine soil respiration, metagenomics, and functional gene results from a 7-year grassland warming experiment to a microbial-enzyme decomposition model, showing functional gene information to lower uncertainty and improve fit.

    • Xue Guo
    • , Qun Gao
    •  & Jizhong Zhou

  • Article
    | Open Access

    Soil age is thought to be an important driver of ecosystem development. Here, the authors perform a global survey of soil chronosequences and meta-analysis to show that, contrary to expectations, soil age is a relatively minor ecosystem driver at the biome scale once other drivers such as parent material, climate, and vegetation type are accounted for.

    • Manuel Delgado-Baquerizo
    • , Peter B. Reich
    •  & Noah Fierer

  • Article
    | Open Access

    Permafrost locks away the largest reservoir of mercury on the planet, but climate warming threatens to thaw these systems. Here the authors use models to show that unconstrained fossil fuel burning will dramatically increase the amount of mercury released into future ecosystems.

    • Kevin Schaefer
    • , Yasin Elshorbany
    •  & Elsie M. Sunderland

  • Article
    | Open Access

    Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

    • Yanfen Zheng
    • , Jinyan Wang
    •  & Xiao-Hua Zhang

  • Article
    | Open Access

    Africa houses approximately one third of the global cattle, sheep and goat population. Here the authors show that manure accumulation in livestock enclosures can emit significant quantities of the greenhouse gas N2O for decades after abandonment, totaling 5% of continental anthropogenic N2O emissions.

    • Klaus Butterbach-Bahl
    • , Gretchen Gettel
    •  & Lutz Merbold

  • Review Article
    | Open Access

    Accounting guidelines exist for carbon flows in terrestrial and coastal ecosystems, but not shelf sea sediments. In this Review, the authors explore whether effective management of carbon stocks accumulating in shelf seas could contribute to a nation’s greenhouse gas emissions reduction targets.

    • Tiziana Luisetti
    • , Silvia Ferrini
    •  & Emmanouil Tyllianakis

  • Article
    | Open Access

    Phosphorus is an essential nutrient critical for agriculture, but because it is non-renewable its future availability is threatened. Here the authors show that across the globe most nations have net losses of phosphorus, with soil erosion as the major route of loss in Europe, Africa and South America.

    • Christine Alewell
    • , Bruno Ringeval
    •  & Pasquale Borrelli

  • Article
    | Open Access

    The universality of the trade-off between early growth and lifespan in trees and its implications are disputed. Analysing a global tree ring dataset and performing data-driven simulations, the authors demonstrate the pervasiveness of the trade-off and challenge current earth system models that predict a continuation of the carbon sink into mature forests under warming and increasing CO2.

    • R. J. W. Brienen
    • , L. Caldwell
    •  & E. Gloor

  • Article
    | Open Access

    Ocean uptake of carbon dioxide impacts the climate, but flux estimates from surface measurements have not been corrected for temperature differences between surface and water sampling depth. Making that correction, the authors find previous estimates for ocean uptake have been substantially underestimated.

    • Andrew J. Watson
    • , Ute Schuster
    •  & Lonneke Goddijn-Murphy

  • Article
    | Open Access

    Predicting the fate of carbon in peatlands relies on assumptions of behaviour in response to temperature. Here, the authors show that the temperature dependency of respiratory carbon losses shift strongly over day-night cycles, an overlooked facet causing bias in peatland carbon cycle simulations.

    • Järvi Järveoja
    • , Mats B. Nilsson
    •  & Matthias Peichl

  • Article
    | Open Access

    Mangroves and the carbon they store are threatened by deforestation, but the efficacy of policies to protect them is unknown. Here the authors assess changes in mangrove carbon stocks between 1996 and 2016 and show less loss than previous methods estimated, indicating conservation has had a positive effect.

    • Daniel R. Richards
    • , Benjamin S. Thompson
    •  & Lahiru Wijedasa

  • Article
    | Open Access

    Soil microbial communities remain active throughout much of the Arctic winter, and Arctic winters are warming dramatically. Here, the authors show that persistently warm winter soils can lead to labile carbon starvation and reduced microbial respiration, despite the high carbon content of most Arctic soils.

    • Patrick F. Sullivan
    • , Madeline C. Stokes
    •  & Michael N. Weintraub

  • Article
    | Open Access

    Some palaeotemperature proxies suffer from inaccuracies related to kinetic fractionations occurring during carbonate mineral growth. Here, the authors show that dual clumped isotope thermometry can identify the origin of these kinetic biases and allows for the reconstruction of accurate environmental temperatures.

    • David Bajnai
    • , Weifu Guo
    •  & Jens Fiebig

  • Article
    | Open Access

    Ocean cold seeps are poorly understood relative to related systems like hydrothermal vents. Here the authors use high pressure bioreactors and microbial communities from a cold seep mud volcano and find a previously missing step of methane conversion to acetate that likely fuels heterotrophic communities.

    • Shanshan Yang
    • , Yongxin Lv
    •  & Yu Zhang

  • Article
    | Open Access

    Geological sources of H2 and abiotic CH4 have had a critical role in the evolution of life and sustainability of the deep subsurface biosphere, yet the origins of these sources remain largely unconstrained. Here the authors show that deep serpentinization (40–80 km) during subduction generates significant amounts of H2 and abiotic CH4, potentially providing energy to the overlying subsurface biosphere.

    • A. Vitale Brovarone
    • , D. A. Sverjensky
    •  & I. Daniel

  • Article
    | Open Access

    Soil organism biodiversity contributes to ecosystem function, but biodiversity and function have not been equivalently studied across the globe. Here the authors identify locations, environment types, and taxonomic groups for which there is currently a lack of biodiversity and ecosystem function data in the existing literature.

    • Carlos A. Guerra
    • , Anna Heintz-Buschart
    •  & Nico Eisenhauer

  • Article
    | Open Access

    How the tropical mixed layer of the ocean reacts to near-inertial waves has rarely been observed directly. Here, the authors present new data that shows strongly elevated vertical diffusive heat flux in the presence of near-inertial waves, causing a cooling of the mixed layer that is particularly strong in summer.

    • Rebecca Hummels
    • , Marcus Dengler
    •  & Peter Brandt

  • Article
    | Open Access

    Cement plays a dual role in the carbon cycle like a sponge. Here, the authors employ a dynamic model to quantify such sponge effect and concluded that deep decarbonization of the global cement cycle will require radical technology advancements and widespread deployment of material efficiency measures.

    • Zhi Cao
    • , Rupert J. Myers
    •  & Gang Liu

  • Article
    | Open Access

    Ocean warming could enable the release of methane related to hydrate dissociation from the ocean floor, a process thought to have triggered abrupt climate changes in Earth history. Here the authors detect this process in action, observing a massive release of methane from a site in the South Atlantic Ocean.

    • Marcelo Ketzer
    • , Daniel Praeg
    •  & José A. Cupertino

  • Article
    | Open Access

    Ocean oxygen minimum zones (OMZs) are known to emit the powerful greenhouse gas N2O, but global emission dynamics are not constrained. Here the authors use air trajectory analyses and find that air masses pick up N2O as they pass over OMZs, and that overall concentrations are elevated during La Niña events.

    • Andrew R. Babbin
    • , Elisabeth L. Boles
    •  & Ray F. Weiss

  • Article
    | Open Access

    Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.

    • Luiz A. Domeignoz-Horta
    • , Grace Pold
    •  & Kristen M. DeAngelis

  • Article
    | Open Access

    Microbial ammonia oxidation is important in marine nutrient cycling and greenhouse gas dynamics, but the responses to ocean warming are unclear. Here coast to open ocean incubations show that projected year 2100 temperatures might be too hot for these microbes in oligotrophic regions to handle, but may facilitate oxidation rates in coastal waters.

    • Zhen-Zhen Zheng
    • , Li-Wei Zheng
    •  & Shuh-Ji Kao

  • Article
    | Open Access

    Monomethylmercury is a toxin that humans can be exposed to after consumption of seafood in which it has bioaccumulated. Here the authors show that amphipods in the deepest point of the global ocean contain monomethylmercury with surface origins, suggesting rapid sinking of this toxin on particles.

    • Ruoyu Sun
    • , Jingjing Yuan
    •  & Congqiang Liu

  • Article
    | Open Access

    Massive stores of carbon and nutrients in permafrost could be released by global warming. Here the authors show that though warming across the Tibetan alpine permafrost region accelerates nitrogen liberation, contrary to expectations the elevated nutrients do not alleviate plant nitrogen limitation.

    • Dan Kou
    • , Guibiao Yang
    •  & Yuanhe Yang

  • Article
    | Open Access

    Terrestrial carbon uptake as high inter-annual variability which can be used to help understand future responses to climate change. Here the authors’ modeling reveals a large portion of this variability is driven by human land use changes and management, and not captured by other models.

    • Chao Yue
    • , Philippe Ciais
    •  & Alexander A. Nassikas

  • Article
    | Open Access

    Satellites can observe marine phytoplankton, but observations are sparse in seasonally dark, cloudy environments like the Southern Ocean. These authors use Argo floats to track the fate of phytoplankton blooms off Antarctica and determine 10% of biomass is exported, while 90% is prey to grazing.

    • Sébastien Moreau
    • , Philip W. Boyd
    •  & Peter G. Strutton

  • Article
    | Open Access

    The environmental changes at the Permian–Triassic boundary are thought to have been caused primarily by volcanic eruptions. Here the authors develop a model to show that the loss of ecosystems on land and consequent massive terrestrial biomass oxidation triggered large biogeochemical changes in the oceans at the time of the marine mass extinction.

    • Jacopo Dal Corso
    • , Benjamin J. W. Mills
    •  & Paul B. Wignall

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