Articles | Volume 12, issue 21
Research article 05 Nov 2015
Research article | 05 Nov 2015
Microbial carbon recycling: an underestimated process controlling soil carbon dynamics – Part 2: A C3-C4 vegetation change field labelling experiment
A. Basler et al.
A. Basler, M. Dippold, M. Helfrich, and J. Dyckmans
Biogeosciences, 12, 5929–5940,
Natalie Orlowski, Lutz Breuer, Nicolas Angeli, Pascal Boeckx, Christophe Brumbt, Craig S. Cook, Maren Dubbert, Jens Dyckmans, Barbora Gallagher, Benjamin Gralher, Barbara Herbstritt, Pedro Hervé-Fernández, Christophe Hissler, Paul Koeniger, Arnaud Legout, Chandelle Joan Macdonald, Carlos Oyarzún, Regine Redelstein, Christof Seidler, Rolf Siegwolf, Christine Stumpp, Simon Thomsen, Markus Weiler, Christiane Werner, and Jeffrey J. McDonnell
Hydrol. Earth Syst. Sci., 22, 3619–3637,Short summary
To extract water from soils for isotopic analysis, cryogenic water extraction is the most widely used removal technique. This work presents results from a worldwide laboratory intercomparison test of cryogenic extraction systems. Our results showed large differences in retrieved isotopic signatures among participating laboratories linked to interactions between soil type and properties, system setup, extraction efficiency, extraction system leaks, and each lab’s internal accuracy.
Dominika Lewicka-Szczebak, Jens Dyckmans, Jan Kaiser, Alina Marca, Jürgen Augustin, and Reinhard Well
Biogeosciences, 13, 1129–1144,Short summary
Oxygen isotopic signatures of N2O are formed in complex multistep enzymatic reactions and depend on isotopic fractionation during enzymatic reduction of nitrate to N2O and on the oxygen isotope exchange with soil water. We propose a new method for quantification of oxygen isotope exchange, with simultaneous determination of oxygen isotopic signatures, to decipher the mechanism of oxygen isotopic fractionation. We indicate the differences between fractionation mechanisms by various pathways.
A. Basler, M. Dippold, M. Helfrich, and J. Dyckmans
Biogeosciences, 12, 5929–5940,
Related subject area
Biogeochemistry: Organic BiogeochemistrySeasonal variability and sources of in situ brGDGT production in a permanently stratified African crater lakeNovel hydrocarbon-utilizing soil mycobacteria synthesize unique mycocerosic acids at a Sicilian everlasting fireAlkenone isotopes show evidence of active carbon concentrating mechanisms in coccolithophores as aqueous carbon dioxide concentrations fall below 7 μmol L−1Sediment release of dissolved organic matter to the oxygen minimum zone off PeruBetter molecular preservation of organic matter in an oxic than in a sulfidic depositional environment: evidence from Thalassiphora pelagica (Dinoflagellata, Eocene) cystsAssessing branched tetraether lipids as tracers of soil organic carbon transport through the Carminowe Creek catchment (southwest England)The nonconservative distribution pattern of organic matter in the Rajang, a tropical river with peatland in its estuaryPredominance of hexamethylated 6-methyl branched glycerol dialkyl glycerol tetraethers in the Mariana Trench: source and environmental implicationHigh-pH and anoxic conditions during soil organic matter extraction increases its electron-exchange capacity and ability to stimulate microbial Fe(III) reduction by electron shuttlingSterol preservation in hypersaline microbial matsStructural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs)Distribution and degradation of terrestrial organic matter in the sediments of peat-draining rivers, Sarawak, Malaysian BorneoValidation of carbon isotope fractionation in algal lipids as a pCO2 proxy using a natural CO2 seep (Shikine Island, Japan)Composition and cycling of dissolved organic matter from tropical peatlands of coastal Sarawak, Borneo, revealed by fluorescence spectroscopy and parallel factor analysisLatitudinal variations in δ30Si and δ15N signatures along the Peruvian shelf: quantifying the effects of nutrient utilization versus denitrification over the past 600 yearsDiapycnal dissolved organic matter supply into the upper Peruvian oxyclineComposition and vertical flux of particulate organic matter to the oxygen minimum zone of the central Baltic Sea: impact of a sporadic North Sea inflowMain drivers of transparent exopolymer particle distribution across the surface Atlantic OceanBiochemical and structural controls on the decomposition dynamics of boreal upland forest moss tissuesSpatiotemporal transformation of dissolved organic matter along an alpine stream flow path on the Qinghai–Tibet Plateau: importance of source and permafrost degradationA quest for the biological sources of long chain alkyl diols in the western tropical North Atlantic OceanLong-chain diols in rivers: distribution and potential biological sourcesLeaf wax n-alkanes in modern plants and topsoils from eastern Georgia (Caucasus) – implications for reconstructing regional paleovegetationThe role of diatom resting spores in pelagic–benthic coupling in the Southern OceanCalcium content and high calcium adaptation of plants in karst areas of southwestern Hunan, ChinaSubstrate potential of last interglacial to Holocene permafrost organic matter for future microbial greenhouse gas productionVariation pattern of particulate organic carbon and nitrogen in oceans and inland watersC5 glycolipids of heterocystous cyanobacteria track symbiont abundance in the diatom Hemiaulus hauckii across the tropical North AtlanticMolecular fingerprinting of particulate organic matter as a new tool for its source apportionment: changes along a headwater drainage in coarse, medium and fine particles as a function of rainfallsVariations and determinants of carbon content in plants: a global synthesisThe Holocene sedimentary record of cyanobacterial glycolipids in the Baltic Sea: an evaluation of their application as tracers of past nitrogen fixationTechnical note: An inverse method to relate organic carbon reactivity to isotope composition from serial oxidationA mechanistic model of an upper bound on oceanic carbon export as a function of mixed layer depth and temperatureNew molecular evidence for surface and sub-surface soil erosion controls on the composition of stream DOM during storm eventsSource, composition, and environmental implication of neutral carbohydrates in sediment cores of subtropical reservoirs, South ChinaIsoprenoid emission response to changing light conditions of English oak, European beech and Norway spruceOrigin and processing of terrestrial organic carbon in the Amazon system: lignin phenols in river, shelf, and fan sedimentsParticle export fluxes to the oxygen minimum zone of the eastern tropical North AtlanticSpatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lakeRole of zooplankton in determining the efficiency of the biological carbon pumpContrasting composition of terrigenous organic matter in the dissolved, particulate and sedimentary organic carbon pools on the outer East Siberian Arctic ShelfBVOC emissions from English oak (Quercus robur) and European beech (Fagus sylvatica) along a latitudinal gradientFate of terrigenous organic matter across the Laptev Sea from the mouth of the Lena River to the deep sea of the Arctic interiorSource, transport and fate of soil organic matter inferred from microbial biomarker lipids on the East Siberian Arctic ShelfFast-freezing with liquid nitrogen preserves bulk dissolved organic matter concentrations, but not its compositionChemodiversity of dissolved organic matter in the Amazon BasinIdentification and analysis of low-molecular-weight dissolved organic carbon in subglacial basal ice ecosystems by ion chromatographyEvolution of dissolved and particulate chromophoric materials during the VAHINE mesocosm experiment in the New Caledonian coral lagoon (south-west Pacific)Evidence for methane production by the marine algae Emiliania huxleyiMolecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS
Loes G. J. van Bree, Francien Peterse, Allix J. Baxter, Wannes De Crop, Sigrid van Grinsven, Laura Villanueva, Dirk Verschuren, and Jaap S. Sinninghe Damsté
Biogeosciences, 17, 5443–5463,Short summary
Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are used as a paleothermometer based on their temperature dependence in global soils, but aquatic production complicates their use in lakes. BrGDGTs in the water column of Lake Chala, East Africa, respond to oxygen conditions and mixing. Changes in their signal can be linked to bacterial community composition rather than membrane adaptation to changing conditions. Their integrated signal in the sediment reflects mean air temperature.
Nadine T. Smit, Laura Villanueva, Darci Rush, Fausto Grassa, Caitlyn R. Witkowski, Mira Holzheimer, Adriaan J. Minnaard, Jaap S. Sinninghe Damsté, and Stefan Schouten
Revised manuscript accepted for BGShort summary
Soils from an everlasting fire (gas seep) in Sicily, Italy reveal high relative abundances of novel uncultivated mycobacteria and unique 13C depleted mycocerosic acids (multi-methyl branched fatty acids) close to the main gas seep. Our results imply, that mycocerosic acids in combination with their depleted δ13C values offer a new biomarker tool to study the role of soil mycobacteria as hydrocarbon consumers in the modern and past global carbon cycle.
Marcus P. S. Badger
Revised manuscript accepted for BGShort summary
Reconstructing ancient atmospheric CO2 is an important aim of palaeoclimate science in order to understand the Earth's climate system. One method, the alkenone proxy based on molecular fossils of coccolithophores, has been recently shown to be ineffective at low to moderate CO2 levels. In this paper I show that this is likely due to changes in the biogeochemistry of the coccolithophores when there is low carbon availability, but for much of the Cenozoic the alkenone proxy should have utility.
Alexandra N. Loginova, Andrew W. Dale, Frédéric A. C. Le Moigne, Sören Thomsen, Stefan Sommer, David Clemens, Klaus Wallmann, and Anja Engel
Biogeosciences, 17, 4663–4679,Short summary
We measured dissolved organic carbon (DOC), nitrogen (DON) and matter (DOM) optical properties in pore waters and near-bottom waters of the eastern tropical South Pacific off Peru. The difference between diffusion-driven and net fluxes of DOC and DON and qualitative changes in DOM optical properties suggested active microbial utilisation of the released DOM at the sediment–water interface. Our results suggest that the sediment release of DOM contributes to microbial processes in the area.
Gerard J. M. Versteegh, Alexander J. P. Houben, and Karin A. F. Zonneveld
Biogeosciences, 17, 3545–3561,Short summary
Anoxic sediments mostly contain much more organic matter than oxic ones, and therefore organic matter in anoxic settings is often considered to be preserved better than in oxic settings. However, through the analysis of the same fossil dinoflagellate cyst species from both oxic and anoxic settings, we show that at a molecular level the preservation in the oxic sediments may be better since in the anoxic setting the cyst macromolecule has been altered by postdepositional modification.
Jingjing Guo, Miriam Glendell, Jeroen Meersmans, Frédérique Kirkels, Jack J. Middelburg, and Francien Peterse
Biogeosciences, 17, 3183–3201,Short summary
The fluxes of soil organic carbon (OC) transport from land to sea are poorly constrained, mostly due to the lack of a specific tracer for soil OC. Here we evaluate the use of specific molecules derived from soil bacteria as a tracer for soil OC in a small river catchment. We find that the initial soil signal is lost upon entering the aquatic environment. However, the local environmental history of the catchment is reflected by these molecules in the lake sediments that act as their sink.
Zhuo-Yi Zhu, Joanne Oakes, Bradley Eyre, Youyou Hao, Edwin Sien Aun Sia, Shan Jiang, Moritz Müller, and Jing Zhang
Biogeosciences, 17, 2473–2485,Short summary
Samples were collected in August 2016 in the Rajang River and its estuary, with tropical forest in the river basin and peatland in the estuary. Organic matter composition was influenced by transportation in the river basin, whereas peatland added clear biodegraded parts to the fluvial organic matter, which implies modification of the initial lability and/or starting points in the subsequent degradation and alternation processes after the organic matter enters the sea.
Wenjie Xiao, Yasong Wang, Yongsheng Liu, Xi Zhang, Linlin Shi, and Yunping Xu
Biogeosciences, 17, 2135–2148,Short summary
The hadal zone (6–11 km depth) is the least explored habitat on Earth. We studied microbial branched glycerol dialkyl glycerol tetraethers (brGDGTs) in the Challenger Deep, Mariana Trench. One unique feature is the strong predominance of 6-methyl brGDGT, which likely reflects an adaption of brGDGT-producing bacteria to alkaline seawater and low temperature. BrGDGTs, with elemental and isotopic data, suggest an autochthonous product for brGDGT. A new approach is proposed for brGDGT sourcing.
Yuge Bai, Edisson Subdiaga, Stefan B. Haderlein, Heike Knicker, and Andreas Kappler
Biogeosciences, 17, 683–698,Short summary
Biogeochemical processes of SOM are key for greenhouse gas emission and water quality. We extracted SOM by water or by NaOH–HCl under oxic–anoxic conditions. Chemical and anoxic extractions lead to higher SOM electron exchange capacities, resulting in stimulation of microbial Fe(III) reduction. Therefore, aqueous pH-neutral SOM extracts should be used to reflect environmental SOM redox processes, and artifacts of chemical extractions need to be considered when evaluating SOM redox processes.
Yan Shen, Volker Thiel, Pablo Suarez-Gonzalez, Sebastiaan W. Rampen, and Joachim Reitner
Biogeosciences, 17, 649–666,Short summary
Today, sterols are widespread in plants, animals, and fungi but are almost absent in the oldest rocks. Microbial mats, representing the earliest complex ecosystems on Earth, were omnipresent in Precambrian marine environments and may have degraded the sterols at that time. Here we analyze the distribution of sterols through a microbial mat. This provides insight into how variations in biological and nonbiological factors affect the preservation of sterols in modern and ancient microbial mats.
Sarah Coffinet, Travis B. Meador, Lukas Mühlena, Kevin W. Becker, Jan Schröder, Qing-Zeng Zhu, Julius S. Lipp, Verena B. Heuer, Matthew P. Crump, and Kai-Uwe Hinrichs
Biogeosciences, 17, 317–330,Short summary
This study deals with two membrane lipids called BDGTs and PDGTs. Membrane lipids are molecules forming the cell envelope of all organisms. Different organisms produce different lipids thus they can be used to detect the presence of specific organisms in the environment. We analyzed the structure of these new lipids and looked for potential producers. We found that they are likely made by microbes emitting methane below the sediment surface and could be used to track these specific microbes.
Ying Wu, Kun Zhu, Jing Zhang, Moritz Müller, Shan Jiang, Aazani Mujahid, Mohd Fakharuddin Muhamad, and Edwin Sien Aun Sia
Biogeosciences, 16, 4517–4533,Short summary
Our understanding of terrestrial organic matter (TOM) in tropical peat-draining rivers remains limited, especially in Southeast Asia. We explored the characteristics of TOM via bulk parameters and lignin phenols of sediment in Malaysia. This showed that the most important plant source of the organic matter in these rivers is woody angiosperm C3 plants with limited diagenetic alteration. This slower degradation of TOM may be a link to higher total nitrogen content, especially for the small river.
Caitlyn R. Witkowski, Sylvain Agostini, Ben P. Harvey, Marcel T. J. van der Meer, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 16, 4451–4461,Short summary
Carbon dioxide concentrations (pCO2) in the atmosphere play an integral role in Earth system dynamics, especially climate. Past climates help us understand future ones, but reconstructing pCO2 over the geologic record remains a challenge. This research demonstrates new approaches for exploring past pCO2 via the carbon isotope fractionation in general algal lipids, which we test over a high CO2 gradient from a naturally occurring CO2 seep.
Yongli Zhou, Patrick Martin, and Moritz Müller
Biogeosciences, 16, 2733–2749,Short summary
We found that peatlands in coastal Sarawak, Borneo, export extremely humified organic matter, which dominates the riverine organic matter pool and conservatively mixes with seawater, while the freshly produced fraction is low and stable in concentration at all salinities. We estimated that terrigenous fractions, which showed high photolability, still account for 20 % of the coastal dissolved organic carbon pool, implying the importance of peat-derived organic matter in the coastal carbon cycle.
Kristin Doering, Claudia Ehlert, Philippe Martinez, Martin Frank, and Ralph Schneider
Biogeosciences, 16, 2163–2180,
Alexandra N. Loginova, Sören Thomsen, Marcus Dengler, Jan Lüdke, and Anja Engel
Biogeosciences, 16, 2033–2047,Short summary
High primary production in the Peruvian upwelling system is followed by rapid heterotrophic utilization of organic matter and supports the formation of one of the most intense oxygen minimum zones (OMZs) in the world. Here, we estimated vertical fluxes of oxygen and dissolved organic matter (DOM) from the surface to the OMZ. Our results suggest that DOM remineralization substantially reduces oxygen concentration in the upper water column and controls the shape of the upper oxycline.
Carolina Cisternas-Novoa, Frédéric A. C. Le Moigne, and Anja Engel
Biogeosciences, 16, 927–947,Short summary
We investigate the composition and vertical fluxes of POM in two deep basins of the Baltic Sea (GB: Gotland Basin and LD: Landsort Deep). The two basins showed different O2 regimes resulting from the intrusion of oxygen-rich water from the North Sea that ventilated the deep waters in GB, but not in LD. In GB, O2 intrusions lead to a high abundance of manganese oxides that aggregate with POM, altering its composition and vertical flux and contributing to a higher POC transfer efficiency in GB.
Marina Zamanillo, Eva Ortega-Retuerta, Sdena Nunes, Pablo Rodríguez-Ros, Manuel Dall'Osto, Marta Estrada, Maria Montserrat Sala, and Rafel Simó
Biogeosciences, 16, 733–749,Short summary
Many marine microorganisms produce polysaccharide-rich transparent exopolymer particles (TEPs) for rather unknown reasons but with important consequences for the ocean carbon cycle, sea–air gas exchange and formation of organic aerosols. Here we compare surface–ocean distributions of TEPs and physical, chemical and biological variables along a N–S transect in the Atlantic Ocean. Our data suggest that phytoplankton and not bacteria are the main TEP producers, and solar radiation acts as a sink.
Michael Philben, Sara Butler, Sharon A. Billings, Ronald Benner, Kate A. Edwards, and Susan E. Ziegler
Biogeosciences, 15, 6731–6746,Short summary
We explored the relationship between chemical composition and the temperature sensitivity of moss decomposition using 959-day lab incubations. Mass loss was low despite the predominance of carbohydrates, indicating the persistence of labile C. Scanning electron microscopy revealed little change in the moss cell-wall structure. These results suggest that the moss cell-wall matrix protects labile C from decomposition, contributing to the globally important stocks of moss-derived C.
Yinghui Wang, Robert G. M. Spencer, David C. Podgorski, Anne M. Kellerman, Harunur Rashid, Phoebe Zito, Wenjie Xiao, Dandan Wei, Yuanhe Yang, and Yunping Xu
Biogeosciences, 15, 6637–6648,Short summary
With global warming, thawing of permafrost releases dissolved organic matter (DOM) into streams. By analyzing DOM along an alpine stream on the Qinghai–Tibet Plateau, we found DOM was mainly from the active layer, but with deepening of the active layer, the contribution of the deep permafrost layer increased, causing a change in the chemical composition of DOM. From the head- to downstream, DOM is undergoing rapid degradation, but some components are persistent and can be transported downstream.
Sergio Balzano, Julie Lattaud, Laura Villanueva, Sebastiaan W. Rampen, Corina P. D. Brussaard, Judith van Bleijswijk, Nicole Bale, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 5951–5968,Short summary
We tried to identify the microbes which biosynthesize a class of lipids widespread in seawater, the long chain alkyl diols (LCDs). We could not find any microorganism likely involved in the production of LCDs. The amounts of LCDs found are too high to be produced by living organisms and are likely to be part of the refractory organic matter persisting for long periods in the water column.
Julie Lattaud, Frédérique Kirkels, Francien Peterse, Chantal V. Freymond, Timothy I. Eglinton, Jens Hefter, Gesine Mollenhauer, Sergio Balzano, Laura Villanueva, Marcel T. J. van der Meer, Ellen C. Hopmans, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 4147–4161,Short summary
Long-chain diols (LCDs) are biomarkers that occur widespread in marine environments and also in lakes and rivers. In this study, we looked at the distribution of LCDs in three river systems (Godavari, Danube, and Rhine) in relation to season, precipitation, and temperature. We found out that the LCDs are likely being produced in calm areas of the river systems and that marine LCDs have a different distribution than riverine LCDs.
Marcel Bliedtner, Imke K. Schäfer, Roland Zech, and Hans von Suchodoletz
Biogeosciences, 15, 3927–3936,Short summary
In this study, we systematically analyze leaf wax derived n-alkane patterns in eastern Georgia to test their potential for paleoenvironmental reconstructions in the semi-humid to semi-arid central southern Caucasus region. We investigated the influence of vegetation types on the leaf wax signal in modern plants and topsoil material. Our results show distinct and systematic differences in the n-alkane patterns between vegetation types and prove their potential for vegetation reconstructions.
Mathieu Rembauville, Stéphane Blain, Clara Manno, Geraint Tarling, Anu Thompson, George Wolff, and Ian Salter
Biogeosciences, 15, 3071–3084,Short summary
Sinking phytoplankton from the surface ocean provide the principal energy source to deep-ocean ecosystems. Our aim was to understand how different phytoplankton communities impact the chemical nature of this sinking material. We show certain types of phytoplankton can preferentially export energy-rich storage compounds to the seafloor. Any climate-driven effects on phytoplankton community structure could thus impact remote deep-ocean ecosystems thousands of kilometres beneath the surface.
Xiaocong Wei, Xiangwen Deng, Wenhua Xiang, Pifeng Lei, Shuai Ouyang, Hongfang Wen, and Liang Chen
Biogeosciences, 15, 2991–3002,Short summary
Karst is a kind of typical calcium-rich environment, which is widely distributed. We measured the Ca2+ content of 41 plant species, as well as soil total Ca2+ and exchange Ca2+. We found out that different plants have different ways to high Ca2+ adaptation. According to the different high Ca2+ adaptation of the 17 dominant species, we divided them into 3 categories: Ca-indifferent plants, high-Ca plants and low-Ca plants. Our results can provide a theoretical basis for vegetation restoration.
Janina G. Stapel, Georg Schwamborn, Lutz Schirrmeister, Brian Horsfield, and Kai Mangelsdorf
Biogeosciences, 15, 1969–1985,Short summary
Climate warming in the Arctic results in thawing of permafrost deposits. This promotes the accessibility of freeze-locked old organic matter (OM) accumulated during the past. Characterizing OM of different depositional ages, we were able to show that OM from last glacial Yedoma deposits possess the highest potential to provide organic substrates such as acetate for microbial greenhouse gas production and therefore to accelerate the carbon–climate feedback cycle during ongoing global warming.
Changchun Huang, Quanliang Jiang, Ling Yao, Hao Yang, Chen Lin, Tao Huang, A-Xing Zhu, and Yimin Zhang
Biogeosciences, 15, 1827–1841,Short summary
The latitudinal dependency of POC / PON in ocean and inland water is significant, regulated by trophic state and climate, etc. factors. POC / PON significantly increased from coastal water (6.89 ± 2.38) to open ocean (7.59 ± 4.22) with the increasing rate of 0.0024 / km. The re-examination of the global relationship between, and variations in, POC and PON could be important for the global and regional coupling between the carbon and nitrogen cycles in the ocean and freshwater.
Nicole J. Bale, Tracy A. Villareal, Ellen C. Hopmans, Corina P. D. Brussaard, Marc Besseling, Denise Dorhout, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 1229–1241,Short summary
Associations between diatoms and N-fixing cyanobacteria (diatom–diazotroph associations, DDAs) play an important role in the N cycle of the tropical North Atlantic. Heterocysts are the site of N fixation and contain unique glycolipids. We measured these glycolipids in the water column and surface sediment from the tropical North Atlantic. We found a significant correlation between the concentration of glycolipid and of DDAs, strengthening their application as biomarkers.
Laurent Jeanneau, Richard Rowland, and Shreeram Inamdar
Biogeosciences, 15, 973–985,Short summary
The source of particulate organic matter in headwaters during storm events remains an open question. We use the molecular composition of organic matter sampled during four spring–summer storms and compare it to potential sources. We identify litter, streambed and vicinal soils as the main sources of particulate organic matter. Their proportions depend on (i) the size of the catchment and (ii) the rain event.
Suhui Ma, Feng He, Di Tian, Dongting Zou, Zhengbing Yan, Yulong Yang, Tiancheng Zhou, Kaiyue Huang, Haihua Shen, and Jingyun Fang
Biogeosciences, 15, 693–702,Short summary
Plant carbon (C) content is critical to the assessment of the global C cycle. Our results showed that the global average C contents in organs were significantly lower than a canonical value of 50 %. Plant C content tended to decrease with increasing latitude, and life form explained more variation than climate. Our findings suggest that specific C content values of different organs and life forms should be incorporated into the estimations of regional and global vegetation biomass C stocks.
Martina Sollai, Ellen C. Hopmans, Nicole J. Bale, Anchelique Mets, Lisa Warden, Matthias Moros, and Jaap S. Sinninghe Damsté
Biogeosciences, 14, 5789–5804,Short summary
The Baltic Sea is characterized by recurring summer phytoplankton blooms, dominated by a few cyanobacterial species. These bacteria are able to use dinitrogen gas as the source for nitrogen and produce very specific lipids. We analyzed these lipids in a sediment core to study their presence over the past 7000 years. This reveals that cyanobacterial blooms have not only occurred in the last decades but were common at times when the Baltic was connected to the North Sea.
Jordon D. Hemingway, Daniel H. Rothman, Sarah Z. Rosengard, and Valier V. Galy
Biogeosciences, 14, 5099–5114,Short summary
The balance between organic matter (OM) fixation and decay is a major control on atmospheric CO2 concentrations. Understanding the environmental, chemical, and physical mechanisms that control the distribution of OM decay rates is therefore critical for constraining the global carbon cycle. In this manuscript, we derive a method to relate OM reactivity to its isotope composition using a kinetic model and provide a novel framework to discern the controls on OM decay rates.
Zuchuan Li and Nicolas Cassar
Biogeosciences, 14, 5015–5027,
Marie Denis, Laurent Jeanneau, Patrice Petitjean, Anaëlle Murzeau, Marine Liotaud, Louison Yonnet, and Gérard Gruau
Biogeosciences, 14, 5039–5051,Short summary
The results of this study highlight the changes of DOM composition in soil solutions and surface runoff, probably controlled by water-table dynamics and pre-event hydrological conditions. These changes should be taken into account for a better understanding of micropollutant mobility. Moreover, this work has implications for modeling DOM export in headwater catchments, as many studies assume that DOM transfer during storm events consists of the flushing of pre-existing soil solution DOM.
Dandan Duan, Dainan Zhang, Yu Yang, Jingfu Wang, Jing'an Chen, and Yong Ran
Biogeosciences, 14, 4009–4022,Short summary
Neutral carbohydrates, carbon isotopic composition, and algal productivity proxies in three reservoir sediment cores, South China, were investigated. Monosaccharide compositions and diagnostic parameters indicate a predominant contribution of phytoplankton in the sediment cores. Algal monosaccharide content is highly related to the algal productivity and increasing mean air temperature, but not to nutrient input, demonstrating the effect of climate warming in low-latitude regions.
Ylva van Meeningen, Guy Schurgers, Riikka Rinnan, and Thomas Holst
Biogeosciences, 14, 4045–4060,Short summary
Leaf scale measurements have been performed on English oak, European beech and Norway spruce at a field site in Denmark to study the release of volatile compounds in response to a change in light. Whilst some compounds, like isoprene and sabinene, increased with increasing light, other compounds, like camphene, showed no light response for most of the trees. This can help to increase our knowledge of how species and compounds respond to light and to possibly improve how they can be modeled.
Shuwen Sun, Enno Schefuß, Stefan Mulitza, Cristiano M. Chiessi, André O. Sawakuchi, Matthias Zabel, Paul A. Baker, Jens Hefter, and Gesine Mollenhauer
Biogeosciences, 14, 2495–2512,
Anja Engel, Hannes Wagner, Frédéric A. C. Le Moigne, and Samuel T. Wilson
Biogeosciences, 14, 1825–1838,Short summary
To better understand the role of oxygen for the biological carbon pump, we studied particle fluxes through hypoxic waters in the eastern tropical North Atlantic. Attenuation of organic carbon fluxes over depth was lower than expected from seawater temperatures, indicating co-effects of oxygen concentration. Differences were observed for individual organic components, suggesting that future carbon export fluxes may depend on changes in surface ocean organic matter quality under global change.
Julie Tolu, Johan Rydberg, Carsten Meyer-Jacob, Lorenz Gerber, and Richard Bindler
Biogeosciences, 14, 1773–1792,Short summary
In this study, we demonstrated that the composition of sediment organic matter can vary significantly within a single lake, in a close relationship with the spatial patterns of elemental inorganic geochemistry. This results from a combination of different bio-, geo- and physicochemical lake factors, and our results highlight that the potential for large spatial variability across lakes should be considered when studying carbon, nutrient and trace element cycling at lake and global scales.
Emma L. Cavan, Stephanie A. Henson, Anna Belcher, and Richard Sanders
Biogeosciences, 14, 177–186,Short summary
The biological carbon pump (BCP) plays a key role in regulating atmospheric CO2. Controls on the efficiency at which this occurs are poorly known. Here we combine in situ observations with an ecosystem model to show that zooplankton have an important role in regulating the efficiency of the BCP. Predicted future changes in ocean conditions, such as expansion of oxygen minimum zones, may decrease the role of zooplankton in the BCP globally, increasing its efficiency and altering atmospheric CO2.
Joan A. Salvadó, Tommaso Tesi, Marcus Sundbom, Emma Karlsson, Martin Kruså, Igor P. Semiletov, Elena Panova, and Örjan Gustafsson
Biogeosciences, 13, 6121–6138,Short summary
Fluvial discharge and coastal erosion of the permafrost-dominated East Siberian Arctic delivers large quantities of terrigenous organic carbon (Terr-OC) to marine waters. We assessed its fate and composition in different marine pools with a suite of biomarkers. The dissolved organic carbon is transporting off-shelf “young” and fresh vascular plant material, while sedimentary and near-bottom particulate organic carbon preferentially carries old organic carbon released from thawing permafrost.
Ylva van Meeningen, Guy Schurgers, Riikka Rinnan, and Thomas Holst
Biogeosciences, 13, 6067–6080,Short summary
English oak and European beech are common European trees known to release volatile compounds such as isoprene and monoterpenes. By doing leaf chamber measurements at three sites in Europe, the aim was to study how the emission differed for cloned trees growing at different sites. The measured emission rates from clones varied between sites, but the relative compound contribution was stable both within and between sites. This can help to increase our knowledge of emission pattern variability.
Lisa Bröder, Tommaso Tesi, Joan A. Salvadó, Igor P. Semiletov, Oleg V. Dudarev, and Örjan Gustafsson
Biogeosciences, 13, 5003–5019,Short summary
Thawing permafrost may release large amounts of terrestrial organic carbon (TerrOC) to the Arctic Ocean. We assessed its fate in the marine environment with a suite of biomarkers. Across the Laptev Sea their concentrations in surface sediments decreased significantly and showed a trend to qualitatively more degraded TerrOC with increasing water depth. We infer that the degree of degradation of TerrOC is a function of the time spent under oxic conditions during protracted cross-shelf transport.
Juliane Bischoff, Robert B. Sparkes, Ayça Doğrul Selver, Robert G. M. Spencer, Örjan Gustafsson, Igor P. Semiletov, Oleg V. Dudarev, Dirk Wagner, Elizaveta Rivkina, Bart E. van Dongen, and Helen M. Talbot
Biogeosciences, 13, 4899–4914,Short summary
The Arctic contains a large pool of carbon that is vulnerable to warming and can be released by rivers and coastal erosion. We study microbial lipids (BHPs) in permafrost and shelf sediments to trace the source, transport and fate of this carbon. BHPs in permafrost deposits are released to the shelf by rivers and coastal erosion, in contrast to other microbial lipids (GDGTs) that are transported by rivers. Several further analyses are needed to understand the complex East Siberian Shelf system.
Lisa Thieme, Daniel Graeber, Martin Kaupenjohann, and Jan Siemens
Biogeosciences, 13, 4697–4705,Short summary
Freezing can affect dissolved organic matter properties and concentrations. Nevertheless, water samples are regularly frozen for sample preservation. To test, if fast-freezing with liquid nitrogen instead of normal freezing at −18 °C can prevent changes in DOM characteristics, we compared fresh and differently frozen terrestrial water samples. We found that fast-freezing with liquid nitrogen can prevent bulk organic matter concentrations but not its spectroscopic properties.
Michael Gonsior, Juliana Valle, Philippe Schmitt-Kopplin, Norbert Hertkorn, David Bastviken, Jenna Luek, Mourad Harir, Wanderley Bastos, and Alex Enrich-Prast
Biogeosciences, 13, 4279–4290,Short summary
We present in this study a highly diverse and complex chemodiversity of dissolved organic matter (DOM) in the Amazon Basin analyzed by modern ultrahigh-resolution mass spectrometry and optical property analyses. DOM within the Rio Madeira (white water), Rio Negro (black water) and Rio Tapajós (clear water) area showed a large overlap of thousands of molecular formulae, but also unique signatures were apparent for each region, with significant correlations to colored DOM.
Emily C. O'Donnell, Jemma L. Wadham, Grzegorz P. Lis, Martyn Tranter, Amy E. Pickard, Marek Stibal, Paul Dewsbury, and Sean Fitzsimons
Biogeosciences, 13, 3833–3846,Short summary
We use a novel ion chromatographic analysis that provides the first identification and quantification of major low-molecular-weight dissolved organic carbon (LMW-DOC) compounds in basal ice. LMW-DOC concentrations were dependent on the bioavailability of the overridden organic carbon, which in turn was influenced by the type of overridden material. The overridden material may thus act as a direct (abiotic leaching) and indirect (microbial cycling) source of DOC to the subglacial environment.
Marc Tedetti, Lauriane Marie, Rüdiger Röttgers, Martine Rodier, France Van Wambeke, Sandra Helias, Mathieu Caffin, Véronique Cornet-Barthaux, and Cécile Dupouy
Biogeosciences, 13, 3283–3303,Short summary
In the framework of the VAHINE project, we investigated the spectral characteristics and the variability of dissolved and particulate chromophoric materials throughout a 23-day mesocosm experiment conducted in the south-west Pacific at the mouth of the New Caledonian coral lagoon. We found that the dynamics of CDOM and particulate matter absorption were strongly coupled with those of cyanobacteria Synechococcus spp. and bacterial production.
Katharina Lenhart, Thomas Klintzsch, Gerald Langer, Gernot Nehrke, Michael Bunge, Sylvia Schnell, and Frank Keppler
Biogeosciences, 13, 3163–3174,Short summary
In this study we investigated marine algae as a source of CH4 in oxic surface waters of oceans. Algae-derived CH4 may explain the CH4 oversaturating state within the surface mixed layer, sometimes also termed the "oceanic methane paradox". This finding of an overlooked source of CH4 in marine environments will be of considerable importance to scientists in many disciplines because algae play a crucial role in organic matter cycling in marine and freshwater ecosystems.
Norbert Hertkorn, Mourad Harir, Kaelin M. Cawley, Philippe Schmitt-Kopplin, and Rudolf Jaffé
Biogeosciences, 13, 2257–2277,Short summary
Wetlands commonly feature high levels of natural dissolved organic matter (DOM), a critical component in their biogeochemical functions. Here we describe the first detailed, comparative, molecular characterization of DOM in three sub-tropical, pulsed, wetlands, using optical properties, high field nuclear magnetic resonance and ultrahigh resolution mass spectrometry, and compare compositional features to variations in organic matter sources and flooding characteristics.
Amelung, W. and Zhang, X.: Determination of amino acid enantiomers in soils, Soil Biol. Biochem., 33, 553–562, 2001.
Amelung, W., Cheshire, M. V., and Guggenberger, G.: Determination of neutral and acidic sugars in soil by capillary gas-liquid chromatography after trifluoroacetic acid hydrolysis, Soil Biol. Biochem., 28, 1631–1639, 1996.
Amelung, W., Brodowski, S., Sandhage-Hofmann, A., and Bol, R.: Combining Biomarker with Stable Isotope Analyses for Assesing the Transformation and Turnover of Soil Organic Matter, in: Advances in Agronomy, Adv. Agron, Elsevier Acacemic Press Inc, 100, 155–250, 2008.
Apostel, C., Dippold, M., and Kuzyakov, Y.: Biochemistry of hexose and pentose transformations in soil analyzed by position-specific labeling and 13C-PLFA, Soil Biol. Biochem., 80, 199–208, https://doi.org/10.1016/j.soilbio.2014.09.005, 2015.
Baisden, W. T., Amundson, R., Cook, A. C., and Brenner, D. L.: Turnover and storage of C and N in five density fractions from California annual grassland surface soils, Global Biogeochem. Cy., 16, 64-1–64-16, https://doi.org/10.1029/2001GB001822, 2002.
Baldock, J. A., Oades, J. M., Nelson, P. N., Skene, T. M., Golchin, A., and Clarke, P.: Assessing the extent of decomposition of natural organic materials using solid-state 13C NMR spectroscopy, Aust. J. Soil Res., 35, 1061–1083, https://doi.org/10.1071/S97004, 1997.
Balesdent, J. and Mariotti, A.: Measurement of soil organic matter turnover using Measurement of soil organic matter turnover using 13C natural abundance, in: Mass spectrometry of soils, edited by: Boutton, T. W. and Yamasaki, S.-I., Books in soils, plants, and the environment, M. Dekker, New York, 83–111, 1996.
Basler, A. and Dyckmans, J.: Compound-specific delta C-13 analysis of monosaccharides from soil extracts by high-performance liquid chromatography/isotope ratio mass spectrometry, Rapid Commun. Mass Sp., 27, 2546–2550, https://doi.org/10.1002/rcm.6717, 2013.
Basler, A., Dippold, M., Helfrich, M., and Dyckmans, J.: Microbial carbon recycling – an underestimated process controlling soil carbon dynamics – Part 1: A long-term laboratory incubation experiment, Biogeosciences, 12, 5929–5940, https://doi.org/10.5194/bg-12-5929-2015, 2015.
Boschker, H., Moerdijk-Poortvliet, T., van Breugel, P., Houtekamer, M., and Middelburg, J. J.: A versatile method for stable carbon isotope analysis of carbohydrates by high-performance liquid chromatography/isotope ratio mass spectrometry, Rapid Commun. Mass Sp., 22, 3902–3908, 2008.
Bowman, S. M. and Free, S. J.: The structure and synthesis of the fungal cell wall, Bioessays, 28, 799–808, https://doi.org/10.1002/bies.20441, 2006.
Brookes, P., Landman, A., Pruden, G., and Jenkinson, D. S.: Chloroform fumigation and the release of soil nitrogen: A rapid direct extraction method to measure microbial biomass nitrogen in soil, Soil Biol. Biochem., 17, 837–842, https://doi.org/10.1016/0038-0717(85)90144-0, 1985.
Caesar-Tonthat, T. C.: Soil binding properties of mucilage produced by a basidiomycete fungus in a model system, Mycol. Res., 106, 930–937, https://doi.org/10.1017/S0953756202006330, 2002.
Chenu, C.: Influence of a fungal polysaccharide, scleroglucan, on clay microstructures, Soil Biol. Biochem., 21, 299–305, https://doi.org/10.1016/0038-0717(89)90108-9, 1989.
Cheshire, M. V.: Origins and stability of soil polysaccharide, J. Soil Sci., 28, 1–10, https://doi.org/10.1111/j.1365-2389.1977.tb02290.x, 1977.
Cheshire, M. V.: Nature and origin of carbohydrates in soils, Academic Pr, London, 216 pp., 1979.
Coelho, R. R., Linhares, L. F., and Martin, J. P.: Sugars in hydrolysates of fungal melanins and soil humic acids, Plant Soil, 106, 127–133, https://doi.org/10.1007/BF02371204, 1988.
Derrien, D. and Amelung, W.: Computing the mean residence time of soil carbon fractions using stable isotopes: impacts of the model framework, Eur. J. Soil Sci., 62, 237–252, https://doi.org/10.1111/j.1365-2389.2010.01333.x, 2011.
Derrien, D., Marol, C., and Balesdent, J.: The dynamics of neutral sugars in the rhizosphere of wheat. An approach by C-13 pulse-labelling and GC/C/IRMS, Plant Soil, 267, 243–253, 2004.
Derrien, D., Marol, C., Balabane, M., and Balesdent, J.: The turnover of carbohydrate carbon in a cultivated soil estimated by 13C natural abundances, Eur. J. Soil Sci., 57, 547–557, 2006.
Derrien, D., Marol, C., and Balesdent, J.: Microbial biosyntheses of individual neutral sugars among sets of substrates and soils, Geoderma, 139, 190–198, 2007.
Dippold, M. and Kuzyakov, Y.: Biogeochemical transformations of amino acids in soil assessed by position-specific labelling, Plant Soil, 373, 385–401, https://doi.org/10.1007/s11104-013-1764-3, 2013.
Engelking, B., Flessa, H., and Joergensen, R. G.: Formation and use of microbial residues after adding sugarcane sucrose to a heated soil devoid of soil organic matter, Soil Biol. Biochem., 40, 97–105, https://doi.org/10.1016/j.soilbio.2007.07.009, 2008.
Glaser, B., Turrion, M. B., Solomon, D., Ni, A., and Zech, W.: Soil organic matter quantity and quality in mountain soils of the Alay Range, Kyrgyzia, affected by land use change, Biol. Fertil. Soils, 31, 407–413, 2000.
Gleixner, G., Poirier, N., Bol, R., and Balesdent, J.: Molecular dynamics of organic matter in a cultivated soil, Org. Geochem., 33, 357–366, 2002.
Golchin, A., Oades, J. M., Skjemstad, J. O., and Clarke, P.: Soil structure and carbon cycling, Aust. J. Soil Res., 32, 1043–1068, https://doi.org/10.1071/SR9941043, 1994a.
Golchin, A., Oades, J. M., Skjemstad, J. O., and Clarke, P.: Study of free and occluded particulate organic-matter in soils by solid-state C-13 CP/MAS NMR-spectroscopy and scanning electron-microscopy, Aust. J. Soil Res., 32, 285–309, https://doi.org/10.1071/SR9940285, 1994b.
Guggenberger, G., Christensen, B. T., and Zech, W.: Land-use effects on the composition of organic matter in particle-size separates of soil: I. Lignin and carbohydrate signature, Eur. J. Soil Sci., 45, 449–458, https://doi.org/10.1111/j.1365-2389.1994.tb00530.x, 1994.
Helfrich, M., Ludwig, B., Buurman, P., and Flessa, H.: Effect of land use on the composition of soil organic matter in density and aggregate fractions as revealed by solid-state C-13 NMR spectroscopy, Geoderma, 136, 331–341, 2006.
Hobbie, E. A., Weber, N. S., Trappe, J. M., and van Klinken, Gert J.: Using radiocarbon to determine the mycorrhizal status of fungi, New Phytol., 156, 129–136, https://doi.org/10.1046/j.1469-8137.2002.00496.x, 2002.
IUSS Working Group WRB: World reference base for soil resources 2014: International soil classification system for naming soils and creating legends for soil maps, World soil resources reports, FAO, Rome, Online-Ressource, 2014.
John, B., Yamashita, T., Ludwig, B., and Flessa, H.: Storage of organic carbon in aggregate and density fractions of silty soils under different types of land use, Geoderma, 128, 63–79, https://doi.org/10.1016/j.geoderma.2004.12.013, 2005.
Kiem, R. and Kögel-Knabner, I.: Contribution of lignin and polysaccharides to the refractory carbon pool in C-depleted arable soils, Soil Biol. Biochem., 35, 101–118, 2003.
Kramer, C. and Gleixner, G.: Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils, Soil Biol. Biochem., 38, 3267–3278, https://doi.org/10.1016/j.soilbio.2006.04.006, 2006.
Ludwig, B., Helfrich, M., and Flessa, H.: Modelling the Long-Term Stabilization of Carbon from Maize in a Silty Soil, Plant Soil, 278, 315–325, https://doi.org/10.1007/s11104-005-8808-2, 2005.
Moers, M. E. C., Baas, M., Deleeuw, J. W., Boon, J. J., and Schenck, P. A.: Occurrence and origin of carbohydrates in peat samples from a red mangrove environment as reflected by abundances of neutral monosaccharides, Geochim. Cosmochim. Ac., 54, 2463–2472, 1990.
Muramaya, S.: Microbial synthesis of saccharides in soils incubated with 13C-labelled glucose, Soil Biol. Biochem., 20, 193–199, https://doi.org/10.1016/0038-0717(88)90036-3, 1988.
Oades, J. M.: Soil organic matter and structural stability: mechanisms and implications for management, Plant Soil, 76, 319–337, 1984.
Osaku, C. A., Sassaki, G. L., Zancan, G. T., and Iacomini, M.: Studies on neutral exopolysaccharides produced by the ectomycorrhiza Thelephora terrestris, FEMS Microbiol. Lett., 216, 145–149, https://doi.org/10.1111/j.1574-6968.2002.tb11428.x, 2002.
R Core Team: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, available at: http://www.R-project.org, 2013.
Rethemeyer, J., Kramer, C., Gleixner, G., John, B., Yamashita, T., Flessa, H., Andersen, N., Nadeau, M.-J., and Grootes, P. M.: Transformation of organic matter in agricultural soils: radiocarbon concentration versus soil depth, Geoderma, 128, 94–105, https://doi.org/10.1016/j.geoderma.2004.12.017, 2005.
Sauheitl, L., Glaser, B., and Bol, R.: Short-term dynamics of slurry-derived plant and microbial sugars in a temperate grassland soil as assessed by compound-specific delta C-13 analyses, Rapid Commun. Mass Sp., 19, 1437–1446, 2005.
Schmidt, M. W., Torn, M. S., Abiven, S., Dittmar, T., Guggenberger, G., Janssens, I. A., Kleber, M., Kögel-Knabner, I., Lehmann, J., Manning, David, A. C., Nannipieri, P., Rasse, D. P., Weiner, S., and Trumbore, S. E.: Persistence of soil organic matter as an ecosystem property, Nature, 478, 49–56, https://doi.org/10.1038/nature10386, 2011.
Six, J. and Jastrow, J. D.: Organic matter turnover, in: Encyclopedia of soil science, edited by: Lal, R., Dekker, New York, NY, 936–942, 2002.
Six, J., Conant, R. T., Paul, E. A., and Paustian, K.: Stabilization mechanisms of soil organic matter: Implications for C-saturation of soils, Plant Soil, 241, 155–176, https://doi.org/10.1023/A:1016125726789, 2002.
Six, J., Bossuyt, H., Degryze, S., and Denef, K.: A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics, Soil Till. Res., 79, 7–31, https://doi.org/10.1016/j.still.2004.03.008, 2004.
Sollins, P., Homann P., and Caldwell, B. A.: Stabilization and destabilization of soil organic matter: mechanisms and controls, Geoderma, 74, 65–105, https://doi.org/10.1016/S0016-7061(96)00036-5, 1996.
Stevenson, F. J.: Humus chemistry: Genesis, composition, reactions, 2nd Ed., Wiley, New York, 496 pp., 1994.
Stribley, D. P. and Read, D. J.: The Biology of Mycorrhiza in the Ericaceae III, Movement of Carbon-14 from Host to Fungus, New Phytol., 73, 731–741, https://doi.org/10.1111/j.1469-8137.1974.tb01301.x, 1974.
Takano, Y., Chikaraishi, Y., Ogawa, N. O., Nomaki, H., Morono, Y., Inagaki, F., Kitazato, H., Hinrichs, K.-U., and Ohkouchi, N.: Sedimentary membrane lipids recycled by deep-sea benthic archaea, Nat. Geosci., 3, 858–861, https://doi.org/10.1038/ngeo983, 2010.
Tisdall, J. M. and Oades, J. M.: Organic matter and water-stable aggregates in soils, J. Soil Sci., 33, 141–163, https://doi.org/10.1111/j.1365-2389.1982.tb01755.x, 1982.
Vance, E., Brookes, P., and Jenkinson, D. S.: An extraction method for measuring soil microbial biomass C, Soil Biol. Biochem., 19, 703–707, https://doi.org/10.1016/0038-0717(87)90052-6, 1987
von Lützow, M. von Kögel-Knabner, I., Ekschmitt, K., Matzner, E., Guggenberger, G., Marschner, B., and Flessa, H.: Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions – a review, Eur. J. Soil Sci., 57, 426–445, https://doi.org/10.1111/j.1365-2389.2006.00809.x, 2006.