Biogeochemistry articles within Nature Communications

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  • Article |

    Some nutrient budgets and fluxes in aquatic environments are poorly constrained. Here, the authors identify a novel pathway of reactive nitrogen sequestration in lakes of the Sierra Nevada, and investigate the relative reactivity of dissolved organic carbon.

    • S.J. Goldberg
    • , G.I. Ball
    •  & L.I. Aluwihare

  • Article |

    The microbial carbon pump may play an important role in carbon sequestration in the deep ocean, but quantifying organic matter in this dark realm is difficult. Here, the authors use fluorescence spectroscopy to investigate the turnover time of fluorescent dissolved organic matter.

    • Teresa S. Catalá
    • , Isabel Reche
    •  & X. Antón Álvarez-Salgado

  • Article |

    Understanding how corals may react to ocean acidification is hampered due to a lack of insight into how corals source the inorganic carbon required to build their skeletons. Here, the authors show that corals are able to concentrate dissolved carbon and that bicarbonate contributes to the carbon pool used to build their skeletons.

    • Nicola Allison
    • , Itay Cohen
    •  & Alexander W. Tudhope

  • Article |

    The preservation of soft tissues during fossilization is the outcome of a race between decay and mineralization. Here the authors show that differential preservation of the Gaojiashan fossil Conotubus hemiannulatuswas influenced by the duration of tissue degradation through bacterial sulfate reduction.

    • James D. Schiffbauer
    • , Shuhai Xiao
    •  & Alan J. Kaufman

  • Article |

    Trace elements and their isotopes are powerful as tracers in the modern ocean and proxies for oceans of the past, although there are limited data for elements such as copper. Here, the authors present copper isotope data from both seawater and rainwater, providing insight into marine biogeochemical cycling.

    • Shotaro Takano
    • , Masaharu Tanimizu
    •  & Yoshiki Sohrin

  • Article |

    Aquatic methane originates in anoxic sediments and bottom waters, but some studies suggest it may also come from the oxic water column. Here, the authors experimentally confirm this hypothesis, and explore the rates, controls and biochemical pathways of oxic water methanogenesis.

    • Matthew J Bogard
    • , Paul A del Giorgio
    •  & Alison M Derry

  • Article
    | Open Access

    Excessive nutrient loading is a threat to aquatic ecosystems; however, denitrification may be key in removing large amounts of reactive nitrogen and, therefore, mitigating consequent eutrophication. Here, the authors explore how meiofauna may impact the rate of denitrification in sediments.

    • S. Bonaglia
    • , F. J. A Nascimento
    •  & V. Brüchert

  • Article |

    Methane is a significant contributor to greenhouse forcing, and determining its fluxes and reservoirs is important in understanding the methane cycle. Here, the authors investigate microbial methane oxidation in carbonates of the deep sea that represent a previously unrecognized biological sink for methane.

    • Jeffrey J. Marlow
    • , Joshua A. Steele
    •  & Victoria J. Orphan

  • Article |

    Tropical forest deforestation is a major source of CO2emissions, yet potential additional emissions through the creation of forest edge areas has been largely overlooked. Here, the authors combine remote sensing and knowledge on spatial processes to estimate carbon loss due to forest fragmentation.

    • Sandro Pütz
    • , Jürgen Groeneveld
    •  & Andreas Huth

  • Article |

    To date, covariance of carbonate and organic carbon isotope records has been assumed to denote fidelity of the original signal. This study shows that post-depositional alteration can create strong correlations, raising doubts about the use of correlated records to imply important changes in past global carbon cycling.

    • Amanda M. Oehlert
    •  & Peter K. Swart

  • Article
    | Open Access

    Although it has been widely suggested that the mid-Holocene minimum methane emissions are associated with hydrological change, direct evidence is missing. Here, the authors present evidence from the Tibetan Plateau using tracers of methanogenesis and methanotrophy, in combination with climate simulations.

    • Yanhong Zheng
    • , Joy S. Singarayer
    •  & Richard D. Pancost

  • Article |

    Methyl iodide is a fumigant registered for use in many countries and its usage is increasing. Here, the authors identify a new pathway of mercury methylation via methyl iodide in sunlit water, suggesting the necessity for a more comprehensive risk assessment for the use of methyl iodide as a fumigant.

    • Yongguang Yin
    • , Yanbin Li
    •  & Guibin Jiang

  • Article |

    Studies suggest almost the same amount of biomass is present in subterranean settings as on Earth’s surface. Here, the authors propose that a large intraterrestrial microbial system was responsible for mineralization in southern Spain, and that microbes may play a major role in sub-surface ore-forming processes.

    • Fernando Tornos
    • , Francisco Velasco
    •  & Juan Manuel Escobar

  • Article |

    Methane levels in the oceans’ surface waters are higher than those in the atmosphere, which is puzzling. Here the authors show that marine bacteria of the ubiquitous SAR11 group can release significant amounts of methane when feeding on phosphorus-containing compounds such as methylphosphonic acid.

    • Paul Carini
    • , Angelicque E. White
    •  & Stephen J. Giovannoni

  • Article |

    The potential preservation of viruses in the fossil record is poorly understood. Here, the authors perform metagenomic and microscopic analyses of viruses in living microbial mats and after mineralization, and propose criteria for identifying fossilized viruses.

    • Muriel Pacton
    • , David Wacey
    •  & Crisogono Vasconcelos

  • Article |

    Typically, microbial methane production occurs under oxygen-free conditions and abiotic methane production occurs under harsh conditions. Here, the authors show methane production from organosulphur compounds under ambient conditions, suggesting a role for these compounds in methane formation in the environment.

    • Frederik Althoff
    • , Kathrin Benzing
    •  & Frank Keppler

  • Article |

    The organic geochemical biomarker IP25 has been widely applied in the reconstruction of Arctic sea ice, yet its source remains undetermined. Here, the authors report the identification of IP25in common pan-Arctic sea ice diatoms, thus establishing its applicability as a palaeo Arctic sea ice proxy.

    • T. A. Brown
    • , S. T. Belt
    •  & C. J. Mundy

  • Article |

    Peatlands both store and emit potent greenhouse gases, yet their contribution to carbon dynamics during the past is poorly constrained. Here, Packalen et al.present new age constraints for peat development in the Hudson Bay Lowlands and quantify carbon storage and methane emissions during the Holocene.

    • Maara S. Packalen
    • , Sarah A. Finkelstein
    •  & James W. McLaughlin

  • Article
    | Open Access

    Arctic sea ice has been in rapid decline in recent decades, yet the impact on biogeochemical cycling is unknown due to insufficient sampling. Watanabe et al.combine year-long mooring observations with numerical models to show that an eddy-induced biological pump would be enhanced by sea ice retreat.

    • Eiji Watanabe
    • , Jonaotaro Onodera
    •  & Michio J. Kishi

  • Article
    | Open Access

    Seagrass beds are effective blue-carbon sinks, yet their role as a lime mud source in the tropical carbonate factory is less well known. Here, the authors demonstrate that the species Thalassia testudinumcan significantly contribute to carbonate production via the precipitation of aragonite needles.

    • Susana Enríquez
    •  & Nadine Schubert

  • Article |

    As global population and food demand rises, it is increasingly unclear how reactive nitrogen pollution will be mitigated. Bodirsky et al.run a series of model simulations and show that even under ambitious mitigation, reactive nitrogen pollution is likely to exceed critical environmental thresholds in the year 2050.

    • Benjamin Leon Bodirsky
    • , Alexander Popp
    •  & Miodrag Stevanovic

  • Article |

    Lakes play an important role in the global carbon cycle and understanding their organic matter cycling is vital. Kellerman et al.apply an ultrahigh-resolution technique to 120 lakes across Sweden and show that the molecular composition is shaped by water dynamics and temperature.

    • Anne M. Kellerman
    • , Thorsten Dittmar
    •  & Lars J. Tranvik

  • Article
    | Open Access

    The world’s tropical forests represent a terrestrial carbon sink, yet its size is uncertain. Espírito-Santo et al.characterize full Amazon disturbances combining forest inventories and remote sensing data, and use statistical modelling to quantify the Amazon aboveground forest carbon balance.

    • Fernando D.B. Espírito-Santo
    • , Manuel Gloor
    •  & Oliver L. Phillips

  • Article |

    Little is known about extracellular electron uptake by microbes. Here Bose et al. show that the anoxygenic photoautotroph Rhodopseudomonas palustrisTIE-1 accepts electrons from a poised electrode, which can be uncoupled from photosynthesis, and the pioABC system has a role in this uptake.

    • A. Bose
    • , E.J. Gardel
    •  & P.R. Girguis

  • Article |

    The microbes responsible for releasing the potent greenhouse gas methane from thawing permafrost remain largely unknown. Mondav and Woodcroft et al. investigate methane flux across a thaw gradient in Sweden and recover a near-complete genome of the dominant methanogen Candidatus ‘Methanoflorens stordalenmirensis’.

    • Rhiannon Mondav
    • , Ben J. Woodcroft
    •  & Gene W. Tyson

  • Article
    | Open Access

    Ocean acidification is affecting the stability of coral reefs, but the exact mineralogical response is poorly understood. Diaz-Pulido et al.show that, under warming conditions, the relative abundance of dolomite increases by as much as 200% and could therefore slow the climate-induced break-up of coral reefs.

    • Guillermo Diaz-Pulido
    • , Merinda C. Nash
    •  & Ulrike Troitzsch

  • Article |

    Iron emitted from hydrothermal vents is stabilized by organic matter and dispersed into the world ocean, yet the pathways leading to iron–carbon interactions are unknown. Dick et al.propose that a new ‘microbial iron pump’ is responsible for converting hydrothermal iron into bioavailable forms.

    • Meng Li
    • , Brandy M. Toner
    •  & Gregory J. Dick

  • Article |

    Methane emission occurs in natural wetlands on a large scale, but the corresponding trace element emissions have not been studied. Here, the authors study selenium and arsenic emission in a pristine peatland and show that this causes large amounts of those trace elements to enter the biogeochemical cycle.

    • Bas Vriens
    • , Markus Lenz
    •  & Lenny H.E. Winkel

  • Article
    | Open Access

    Clay-sized particles bind organic matter and sequester carbon and nitrogen in soils, yet extent and localization of organic matter coverage remain unclear. Using NanoSIMS, Vogel et al.chemically image soils at ultra-high resolution and show that only particles with rough surfaces react with organic matter.

    • Cordula Vogel
    • , Carsten W. Mueller
    •  & Ingrid Kögel-Knabner

  • Article |

    Africa is one of the fastest growing regions for the voluntary carbon market. Here, Greve et al.quantify the potential for aboveground C stocking across tropical Africa and assess the optimal placement of carbon-stocking projects when also taking co-benefits and feasibility into account.

    • Michelle Greve
    • , Belinda Reyers
    •  & Jens-Christian Svenning

  • Article |

    Recent increases in the dissolved organic carbon (DOC) content of northern aquatic systems are likely to lead to increases in CO2 emissions, yet the mechanisms are poorly understood. Here, evidence from hundreds of Canadian aquatic systems suggests a causal link between DOC concentrations and CO2flux.

    • Jean-François Lapierre
    • , François Guillemette
    •  & Paul A. del Giorgio

  • Article |

    The presence of earthworms in soil may significantly increase CO2 emissions, but the impacts of earthworms on net carbon sequestration are poorly understood. Zhang et al. introduce a new concept by which the effects of earthworms on the balance of carbon mineralization and stabilization can be quantified.

    • Weixin Zhang
    • , Paul F. Hendrix
    •  & Shenglei Fu

  • Article |

    Isoprene and monoterpenes, emitted by terrestrial plants, have an important role in both plant biology and environment, but they are poorly quantified at the ecosystem level. Peñuelas et al.show that the photochemical reflectance index can be used to indirectly estimate foliar isoprenoid emissions remotely.

    • Josep Peñuelas
    • , Giovanni Marino
    •  & Iolanda Filella

  • Article |

    Deep oceanic crust could host a wealth of microbial life, but biogeochemical reactions therein are poorly understood. Orcutt et al.combine measurements of sedimentary oxygen and pore water chemistry from basement crust with a reactive transport box model to shed light on oxygen consumption in basaltic crust.

    • Beth N. Orcutt
    • , C. Geoffrey Wheat
    •  & Wolfgang Bach

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