Biogeosciences Discussions

Journal Information
ISSN / EISSN : 1810-6277 / 1810-6285
Current Publisher: Copernicus GmbH (10.5194)
Total articles ≅ 4,379
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Yuge Bai, Edisson Subdiaga, Stefan B. Haderlein, Heike Knicker,
Published: 9 September 2019
Biogeosciences Discussions, Volume 2019, pp 1-25; doi:10.5194/bg-2019-308

Soil organic matter (SOM), including humic substances (HS), is redox-active, can be microbially reduced, and transfers electrons in an abiotic reaction to Fe(III) minerals thus serving as electron shuttle. The standard procedure to extract HS from soil and separate them into humic acids (HA) and fulvic acids (FA) involves alkaline and acidic solutions potentially leading to unwanted changes in SOM chemical and redox properties. To determine the effects of extraction conditions on the redox and electron shuttling properties of SOM extracts, we prepared HS and SOM extracts from a forest soil applying either a combination of 0.1 M NaOH and 6 M HCl, or water (pH 7). Both chemical extractions (NaOH / HCl) and water extractions were done in separate setups under either oxic or anoxic conditions. Furthermore, we applied the NaOH / HCl treatment to a subsample of the water-extracted-SOM. We found that soil extraction with NaOH lead to ca. 100 times more extracted C and the extracted HS had 2–3 times higher electron exchange capacities (EEC) than SOM extracted by water. For water-extracted SOM, anoxic extraction conditions lead to about 7 times more extracted C and 1.5 times higher EEC than under oxic extraction conditions. This difference was probably due to the occurrence of microbial reduction and dissolution of Fe(III) minerals in the soil during the water extraction at neutral pH and the concomitant release of Fe(III) mineral-bound organic matter. NaOH / HCl treatment of the water-extracted SOM lead to 2 times higher EEC values in the HA isolated from the SOM compared to the water-extracted SOM itself, suggesting the chemical treatment with NaOH and HCl caused changes of redox-active functional groups of the extracted organic compounds. Higher EEC of extracts in turn resulted in a higher stimulation of microbial Fe(III) mineral reduction by electron shuttling, i.e. faster initial Fe(III) reduction rates, and in most cases also in higher reduction extents. Our findings suggest that SOM extracted with water at neutral pH should be used to better reflect environmental SOM redox processes in lab experiments and that potential artefacts of the chemical extraction method and anoxic extraction condition need to be considered when evaluating and comparing abiotic and microbial SOM redox processes.
Kaiwen Ta, Zijun Wu, Xiaotong Peng, Zhaofu Luan
Published: 4 September 2019
Biogeosciences Discussions, Volume 2019, pp 1-50; doi:10.5194/bg-2019-315

Low-temperature hydrothermal system is dominated by Fe-Si oxyhydroxide deposits. However, the formation process and mechanism on modern hydrothermal Fe-Si oxyhydroxides at ultra-slow spreading centers remain poorly understood. The investigation presented in this paper focuses on six Fe-Si deposits collected from different sites at the Southwest Indian Ridge (SWIR). The mineralogical and geochemical evidence showed significant characteristics of a low-temperature hydrothermal origin. The Mössbauer spectra and iron speciation data further provided an insight into iron-bearing phases in all deposits. Two different types of biomineralized forms were discovered in these deposits by Scanning Electron Microscopy analysis. Energy-dispersive X-ray spectrometry and nano secondary ion mass spectrometry revealed that distinct biogenic structures were mainly composed of Fe, Si, and O, together with some trace elements. The Sr and Nd isotope compositions of Fe-Si deposits at the SWIR were closely related to interaction between hydrothermal fluids and seawater. The remarkably homogeneous Pb isotope compositions can be attributed to hydrothermal circulation. Based on these findings, we suggest that microbial activity plays a significant role in the formation of Fe-Si oxyhydroxides at the at ultra-slow spreading SWIR. Biogenic Fe-Si oxyhydroxides potentially provide insights into the origin and evolution of life in the geologic record.
, Nora Plenter, Sabrina Schilling, , Gabriele Broll,
Published: 29 August 2019
Biogeosciences Discussions, Volume 2019, pp 1-39; doi:10.5194/bg-2019-284

Inland waters are significant sources of CO2 and CH4 to the atmosphere, following recent studies this is particularly the case for small and shallow lakes. The spatial in-lake heterogeneity of CO2 and CH4 production processes and their drivers in the sediment yet remain poorly studied. We thus measured potential CO2 and CH4 production in sediment incubations from 12 sites within the small and shallow crater lake Windsborn in Germany as well as fluxes at the water-atmosphere interface at four sites. Production rates were highly variable and ranged from 7.2 and 38.5 µmol CO2 g C−1 d−1 and from 5.4 to 33.5 µmol CH4 g C−1 d−1. Fluxes lay between 4.5 and 26.9 mmol CO2 m−2 d−1 and between 0 and 9.8 mmol CH4 m−2 d−1. Both CO2 and CH4 production rates and CH4 fluxes were significantly negative (p
, Cathrine Manohar
Published: 29 August 2019
Biogeosciences Discussions, Volume 2019, pp 1-28; doi:10.5194/bg-2019-330

The Northern Indian Ocean host two recognized Oxygen Minimum Zones (OMZ): one in the Arabian Sea and the other in the Bay of Bengal region. The next-generation sequencing technique was used to understand the total bacterial diversity from the surface sediment of off Goa within the OMZ of Arabian Sea, and from off Paradip within the OMZ of Bay of Bengal. The dominant phyla identified include Firmicutes (33.06 %) and Proteobacteria (32.44 %) from the Arabian Sea, and Proteobacteria (52.51 %) and Planctomycetes (8.63 %) from the Bay of Bengal. Statistical analysis indicates that bacterial diversity from sediments of the Bay of Bengal OMZ is ~ 48 % higher than the Arabian Sea OMZ. Diverse candidate bacterial clades were also detected, whose function is unknown, but many of these were reported from other OMZs as well, suggesting their putative role in sediment biogeochemistry. Bacterial diversity from the present study reveals that the off Paradip site of Bay of Bengal OMZ is highly diverse and unexplored in comparison to the off Goa site of the Arabian Sea OMZ. Functional diversity analysis indicates that the relative percentage distribution of genes involved in methane, nitrogen, sulfur and many unclassified energy metabolisms is almost the same in both sites, reflecting a similar ecological role, irrespective of the differences in phylotypic diversity.
, Marko Kvakić, Laurent Augusto, Philippe Ciais, , Nathaniel D. Mueller, , Thomas Nesme, Nicolas Vuichard, Xuhui Wang, et al.
Published: 27 August 2019
Biogeosciences Discussions; doi:10.5194/bg-2019-298

Crossed fertilization additions are a common tool to assess nutrient interaction in a given ecosystem. Such fertilization experiments lead to the definition of nutrient interaction categories: e.g. simultaneous co-limitation, single resource response, etc. (Harpole et al., 2011). However, the implications of such categories in terms of nutrient interaction modeling are not clear. To this end, we developed a theoretical analysis of nitrogen (N) and phosphorus (P) fertilization experiments based on the computation of ratios between plant demand and soil supply for each nutrient. The theoretical analysis is developed following two mathematical formalisms of interaction: Liebig's law of minimum and multiple limitation hypothesis. As results of the theoretical framework, we defined the corresponding between most Harpole categories and the values of the limitation by each nutrient when considered alone in the control experiment (i.e. without additional nutrient supply). We showed that synergistic co-limitation could occur even using Liebig's formalism under certain conditions as a function of the amount of N and P added in fertilization experiments. We then applied our framework with global maps of soil supply and plant demand for croplands to achieve their potential yield. This allowed us to estimate the global occurrence of each limitation category, for each of the possible interaction formalism. We found that a true co-limitation could affect a large proportion of the global crop area (e.g. ~ 42 % for maize) if multiple limitation hypothesis is assumed. Our work clarifies the conditions required to achieve N and P co-limitation as function of the interaction formalism. Combined with compilation of field trials in cropland, our study would improve our understanding of nutrient limitation in cropland at the global scale.
, Laura Haffert, , Andrea Koschinsky, Sabine Kasten
Published: 20 August 2019
Biogeosciences Discussions, Volume 2019, pp 1-38; doi:10.5194/bg-2019-316

The thriving interest in harvesting deep-sea mineral resources, such as polymetallic nodules, calls for environmental impact studies, and ultimately, for regulations for environmental protection. Industrial-scale deep-sea mining of polymetallic nodules most likely has severe consequences for the natural environment. However, the effects of mining activities on deep-sea ecosystems, sediment geochemistry and element fluxes are still poorly conceived. Predicting the environmental impact is challenging due to the scarcity of environmental baseline studies as well as the lack of mining trials with industrial mining equipment in the deep sea. Thus, currently we have to rely on small-scale disturbances simulating deep-sea mining activities as a first-order approximation to study the expected impacts on the abyssal environment. Here, we investigate surface sediments in disturbance tracks of seven small-scale benthic impact experiments, which have been performed in four European contract areas for the exploration of polymetallic nodules in the Clarion-Clipperton Zone (CCZ). These small-scale disturbance experiments were performed 1 day to 37 years prior to our sampling program in the German, Polish, Belgian and French contract areas using different disturbance devices. We show that the depth distribution of solid-phase Mn in the upper 20 cm of the sediments in the CCZ provides a reliable tool for the determination of the disturbance depth, which has been proposed in a previous study (Paul et al., 2018). We found that the upper 5–15 cm of the sediments were removed during various small-scale disturbance experiments in the different exploration contract areas. Transient transport-reaction modelling for the Polish and German contract areas reveals that the removal of the surface sediments is associated with the loss of reactive labile organic carbon. As a result, oxygen consumption rates decrease significantly after the removal of the surface sediments, and consequently, oxygen penetrates up to tenfold deeper into the sediments inhibiting denitrification and Mn(IV) reduction. Our model results show that the post-disturbance geochemical re-equilibration is controlled by diffusion until the reactive labile TOC fraction in the surface sediments is partly re-established and the biogeochemical processes commence. While the re-establishment of bioturbation is essential, the geochemical re-equilibration of the sediments is ultimately controlled by the burial rates of organic matter. Hence, under current depositional conditions, the new geochemical equilibrium in the sediments of the CCZ is reached only on a millennia scale even for these small-scale disturbances simulating deep-sea mining activities.
Published: 8 August 2019
Biogeosciences Discussions; doi:10.5194/bg-2019-273

Growing evidence points to the dynamic role that kerogen is playing on the Earth's surface in controlling atmospheric chemistry over geologic time. Although quantitative constraints on weathering of kerogen remain loose, its changing weathering behavior modulated by the activity of glaciers, suggest that this largest pool of reduced carbon on Earth may have played a key part in atmospheric CO2 variability across recent glacial-interglacial times and beyond.
Tong Yu,
Published: 6 August 2019
Biogeosciences Discussions; doi:10.5194/bg-2019-278

Biological nitrogen fixation plays an important role in the global nitrogen cycle. However, the fixation rate has been usually measured or estimated at a particular observational site. To quantify the fixation amount at the global scale, a process-based model is needed. This study develops a biological nitrogen fixation model and couples it with an extant biogeochemistry model of N2O emissions to examine the fixation rate and its effects on N2O emissions. The revised N2O emission model better matches the observed data in comparison with our previous model that has not considered the fixation effects. The new model estimates that tropical forests have the highest fixation rate among all ecosystem types, and decrease from the equator to the polar region. The estimated nitrogen fixation in global terrestrial ecosystems is 61.5 Tg N yr−1 with a range of 19.8–107.9 Tg N yr−1 in the 1990s. Our estimates are relatively low compared to some early estimates using empirical approaches, but comparable to more recent estimates that involve more detailed processes in their modeling. Furthermore, we estimate that the fixation contributes to −5 % to 20 % changes in N2O emissions compared to our previous estimates, depending on ecosystem types and climatic conditions. This study highlights that there are relatively large effects of the biological nitrogen fixation on ecosystem nitrogen cycling and soil N2O emissions and calls for more comprehensive understanding of biological nitrogen fixation and more observational data for different ecosystems to improve future quantification of the fixation and its impacts.
Svetlana N. Losa, , , Julia Oelker, Mariana A. Soppa, , ,
Published: 31 July 2019
Biogeosciences Discussions; doi:10.5194/bg-2019-289

This study highlights recent advances and challenges of applying coupled physical-biogeochemical modeling for investigating the distribution of the key phytoplankton groups in the Southern Ocean, an area of strong interest for understanding biogeochemical cycling and ecosystem functioning under present climate change. Our simulations of the phenology of various Phytoplankton Functional Types (PFTs) are based on a version of the Darwin biogeochemical model coupled to the Massachusetts Institute of Technology (MIT) general circulation model (Darwin-MITgcm). The ecological module version was adapted for the Southern Ocean by: 1) improving coccolithophores abundance relative to the original model by introducing a high affinity for nutrients and an ability to escape grazing control for coccolithophores; 2) including two different (small vs. large) size classes of diatoms; and 3) accounting for two distinct life stages for Phaeocystis (single cell vs. colonial). This new model configuration describes best the competition and co-occurrence of the PFTs in the Southern Ocean. It improves significantly relative to an older version the agreement of the simulated abundance of the coccolithophores and diatoms with in situ scanning electron microscopy observations in the Subantarctic Zone as well as with in situ diatoms and haptophytes (including coccolithophores and Phaeocystis) chlorophyll a concentrations within the Patagonian Shelf and along the Western Antarctic Peninsula obtained by diagnostic pigment analysis. The modeled Southern Ocean PFT dominance also agrees well with satellite-based PFT information.
, Seeta A. Sistla, Kristen M. DeAngelis
Published: 26 July 2019
Biogeosciences Discussions; doi:10.5194/bg-2019-269

Climate change has the potential to destabilize the Earth’s massive terrestrial carbon (C) stocks, but the degree to which models project this destabilization to occur depends on the kinds and complexities of microbial processes they simulate. Of particular note is carbon use efficiency (CUE), which determines the fraction of C processed by microbes that is anabolized into microbial biomass rather than being lost to the atmosphere as carbon dioxide. The temperature sensitivity of CUE is often modeled as a homogeneous property of the community, which contrasts with empirical data and has unknown impacts on projected changes to the soil carbon cycle under global warming. We used the DEMENT model – which simulates taxon-level litter decomposition dynamics – to explore the effects of introducing organism-level heterogeneity into the CUE response to temperature for decomposition of leaf litter under 5 °C of warming. We found that allowing CUE temperature response to differ between taxa facilitated increased loss of litter C, unless fungal taxa were specifically restricted to decreasing CUE with temperature. Increased loss of litter C was observed when the growth of a larger microbial biomass pool was fueled by higher community-level average CUE at higher temperature in the heterogeneous microbial community, with effectively lower costs for extracellular enzyme production. Together these results implicate a role for diversity of taxon-level CUE responses in driving the fate of litter C in a warmer world.
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