Articles | Volume 14, issue 10
https://doi.org/10.5194/bg-14-2697-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-14-2697-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
31 May 2017
Research article |
| 31 May 2017
Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches
Valérie F. Schwab
CORRESPONDING AUTHOR
Friedrich Schiller University, Institute of Geosciences, Jena,
Germany
Friedrich Schiller University, Institute for Inorganic and
Analytical Chemistry, Jena, Germany
Martina Herrmann
Friedrich Schiller University, Institute of Ecology, Jena, Germany
German Centre for Integrative Biodiversity Research (iDiv),
Halle-Jena-Leipzig, Leipzig, Germany
Vanessa-Nina Roth
Max-Planck-Institute for Biogeochemistry, Jena, Germany
Gerd Gleixner
Max-Planck-Institute for Biogeochemistry, Jena, Germany
Robert Lehmann
Friedrich Schiller University, Institute of Geosciences, Jena,
Germany
Georg Pohnert
Friedrich Schiller University, Institute for Inorganic and
Analytical Chemistry, Jena, Germany
Susan Trumbore
Max-Planck-Institute for Biogeochemistry, Jena, Germany
Kirsten Küsel
Friedrich Schiller University, Institute of Ecology, Jena, Germany
German Centre for Integrative Biodiversity Research (iDiv),
Halle-Jena-Leipzig, Leipzig, Germany
Kai U. Totsche
Friedrich Schiller University, Institute of Geosciences, Jena,
Germany
Related authors
Martin E. Nowak, Valérie F. Schwab, Cassandre S. Lazar, Thomas Behrendt, Bernd Kohlhepp, Kai Uwe Totsche, Kirsten Küsel, and Susan E. Trumbore
Hydrol. Earth Syst. Sci., 21, 4283–4300, https://doi.org/10.5194/hess-21-4283-2017, https://doi.org/10.5194/hess-21-4283-2017, 2017
Short summary
Short summary
In the present study we combined measurements of dissolved inorganic carbon (DIC) isotopes with a set of different geochemical and microbiological methods in order to get a comprehensive view of biogeochemical cycling and groundwater flow in two limestone aquifer assemblages. This allowed us to understand interactions and feedbacks between microbial communities, their carbon sources, and water chemistry.
Luciano Emmert, Susan Trumbore, Joaquim dos Santos, Adriano Lima, Niro Higuchi, Robinson Negrón-Juárez, Cléo Dias-Júnior, Tarek El-Madany, Olaf Kolle, Gabriel Ribeiro, and Daniel Marra
EGUsphere, https://doi.org/10.5194/egusphere-2024-3234, https://doi.org/10.5194/egusphere-2024-3234, 2024
Short summary
Short summary
For the first time, we documented wind gusts with the potential to damage trees in a forest in the Central Amazon. We used meteorological data collected at crown height over 24 months. We recorded 424 gusts, which occur more frequently and intensely in higher elevated areas and during the transition from the dry to the wet season. More intense rains showed the strongest relationship with extreme winds, highlighting the role of extreme events in tree mortality.
David Ho, Michał Gałkowski, Friedemann Reum, Santiago Botía, Julia Marshall, Kai Uwe Totsche, and Christoph Gerbig
Geosci. Model Dev., 17, 7401–7422, https://doi.org/10.5194/gmd-17-7401-2024, https://doi.org/10.5194/gmd-17-7401-2024, 2024
Short summary
Short summary
Atmospheric model users often overlook the impact of the land–atmosphere interaction. This study accessed various setups of WRF-GHG simulations that ensure consistency between the model and driving reanalysis fields. We found that a combination of nudging and frequent re-initialization allows certain improvement by constraining the soil moisture fields and, through its impact on atmospheric mixing, improves atmospheric transport.
Luiz A. T. Machado, Jürgen Kesselmeier, Santiago Botía, Hella van Asperen, Meinrat O. Andreae, Alessandro C. de Araújo, Paulo Artaxo, Achim Edtbauer, Rosaria R. Ferreira, Marco A. Franco, Hartwig Harder, Sam P. Jones, Cléo Q. Dias-Júnior, Guido G. Haytzmann, Carlos A. Quesada, Shujiro Komiya, Jost Lavric, Jos Lelieveld, Ingeborg Levin, Anke Nölscher, Eva Pfannerstill, Mira L. Pöhlker, Ulrich Pöschl, Akima Ringsdorf, Luciana Rizzo, Ana M. Yáñez-Serrano, Susan Trumbore, Wanda I. D. Valenti, Jordi Vila-Guerau de Arellano, David Walter, Jonathan Williams, Stefan Wolff, and Christopher Pöhlker
Atmos. Chem. Phys., 24, 8893–8910, https://doi.org/10.5194/acp-24-8893-2024, https://doi.org/10.5194/acp-24-8893-2024, 2024
Short summary
Short summary
Composite analysis of gas concentration before and after rainfall, during the day and night, gives insight into the complex relationship between trace gas variability and precipitation. The analysis helps us to understand the sources and sinks of trace gases within a forest ecosystem. It elucidates processes that are not discernible under undisturbed conditions and contributes to a deeper understanding of the trace gas life cycle and its intricate interactions with cloud dynamics in the Amazon.
Hella van Asperen, Thorsten Warneke, Alessandro Carioca de Araújo, Bruce Forsberg, Sávio José Filgueiras Ferreira, Thomas Röckmann, Carina van der Veen, Sipko Bulthuis, Leonardo Ramos de Oliveira, Thiago de Lima Xavier, Jailson da Mata, Marta de Oliveira Sá, Paulo Ricardo Teixeira, Julie Andrews de França e Silva, Susan Trumbore, and Justus Notholt
Biogeosciences, 21, 3183–3199, https://doi.org/10.5194/bg-21-3183-2024, https://doi.org/10.5194/bg-21-3183-2024, 2024
Short summary
Short summary
Carbon monoxide (CO) is regarded as an important indirect greenhouse gas. Soils can emit and take up CO, but, until now, uncertainty remains as to which process dominates in tropical rainforests. We present the first soil CO flux measurements from a tropical rainforest. Based on our observations, we report that tropical rainforest soils are a net source of CO. In addition, we show that valley streams and inundated areas are likely additional hot spots of CO in the ecosystem.
Maximiliano González-Sosa, Carlos A. Sierra, J. Andrés Quincke, Walter E. Baethgen, Susan Trumbore, and M. Virginia Pravia
SOIL, 10, 467–486, https://doi.org/10.5194/soil-10-467-2024, https://doi.org/10.5194/soil-10-467-2024, 2024
Short summary
Short summary
Based on an approach that involved soil organic carbon (SOC) monitoring, radiocarbon measurement in bulk soil, and incubations from a long-term 60-year experiment, it was concluded that the avoidance of old carbon losses in the integrated crop–pasture systems is the main reason that explains their greater carbon storage capacities compared to continuous cropping. A better understanding of these processes is essential for making agronomic decisions to increase the carbon sequestration capacity.
Saqr Munassar, Christian Roedenbeck, Michał Gałkowski, Frank-Thomas Koch, Kai U. Totsche, Santiago Botía, and Christoph Gerbig
EGUsphere, https://doi.org/10.5194/egusphere-2024-291, https://doi.org/10.5194/egusphere-2024-291, 2024
Short summary
Short summary
CO2 mole fractions simulated over a global stations showed an overestimation of CO2 if the diurnal cycle is missing NEE. This led to biases in the estimated fluxes derived from the inversions at continental and regional scales. IAVof estimated NEE was affected by the diurnal effect. The findings point to the importance of including the diurnal variations of CO2 in the biosphere priors used in inversions to better converge flux estimates among inversions, in particular those contributing to GCB.
Ingrid Chanca, Ingeborg Levin, Susan Trumbore, Kita Macario, Jost Lavric, Carlos Alberto Quesada, Alessandro Carioca de Araújo, Cléo Quaresma Dias Júnior, Hella van Asperen, Samuel Hammer, and Carlos Sierra
EGUsphere, https://doi.org/10.5194/egusphere-2024-883, https://doi.org/10.5194/egusphere-2024-883, 2024
Short summary
Short summary
Assessing the net carbon (C) budget of the Amazon entails considering the magnitude and timing of C absorption and losses through respiration (transit time of C). Radiocarbon-based estimates of the transit time of C in the Amazon Tall Tower Observatory (ATTO) suggest a doubling of the transit time from 6 ± 2 years and 18 ± 5 years (October 2019 and December 2021, respectively). This variability indicates that only a fraction of newly fixed C can be stored for decades or longer.
Adriana Simonetti, Raquel Fernandes Araujo, Carlos Henrique Souza Celes, Flávia Ranara da Silva e Silva, Joaquim dos Santos, Niro Higuchi, Susan Trumbore, and Daniel Magnabosco Marra
Biogeosciences, 20, 3651–3666, https://doi.org/10.5194/bg-20-3651-2023, https://doi.org/10.5194/bg-20-3651-2023, 2023
Short summary
Short summary
We combined 2 years of monthly drone-acquired RGB (red–green–blue) imagery with field surveys in a central Amazon forest. Our results indicate that small gaps associated with branch fall were the most frequent. Biomass losses were partially controlled by gap area, with branch fall and snapping contributing the least and greatest relative values, respectively. Our study highlights the potential of drone images for monitoring canopy dynamics in dense tropical forests.
Shane W. Stoner, Marion Schrumpf, Alison Hoyt, Carlos A. Sierra, Sebastian Doetterl, Valier Galy, and Susan Trumbore
Biogeosciences, 20, 3151–3163, https://doi.org/10.5194/bg-20-3151-2023, https://doi.org/10.5194/bg-20-3151-2023, 2023
Short summary
Short summary
Soils store more carbon (C) than any other terrestrial C reservoir, but the processes that control how much C stays in soil, and for how long, are very complex. Here, we used a recent method that involves heating soil in the lab to measure the range of C ages in soil. We found that most C in soil is decades to centuries old, while some stays for much shorter times (days to months), and some is thousands of years old. Such detail helps us to estimate how soil C may react to changing climate.
Saqr Munassar, Guillaume Monteil, Marko Scholze, Ute Karstens, Christian Rödenbeck, Frank-Thomas Koch, Kai U. Totsche, and Christoph Gerbig
Atmos. Chem. Phys., 23, 2813–2828, https://doi.org/10.5194/acp-23-2813-2023, https://doi.org/10.5194/acp-23-2813-2023, 2023
Short summary
Short summary
Using different transport models results in large errors in optimized fluxes in the atmospheric inversions. Boundary conditions and inversion system configurations lead to a smaller but non-negligible impact. The findings highlight the importance to validate transport models for further developments but also to properly account for such errors in inverse modelling. This will help narrow the convergence of gas estimates reported in the scientific literature from different inversion frameworks.
Jeffrey Prescott Beem-Miller, Craig Rasmussen, Alison May Hoyt, Marion Schrumpf, Georg Guggenberger, and Susan Trumbore
EGUsphere, https://doi.org/10.5194/egusphere-2022-1083, https://doi.org/10.5194/egusphere-2022-1083, 2022
Preprint withdrawn
Short summary
Short summary
We compared the age of persistent soil organic matter as well as active emissions of carbon dioxide from soils across a gradient of climate and geology. We found that clay minerals are more important than mean annual temperature for both persistent and actively cycling soil carbon, and that they may attenuate the sensitivity of soil organic matter decomposition to temperature. Accounting for geology and soil development could therefore improve estimates of soil carbon stocks and changes.
Karel Castro-Morales, Anna Canning, Sophie Arzberger, Will A. Overholt, Kirsten Küsel, Olaf Kolle, Mathias Göckede, Nikita Zimov, and Arne Körtzinger
Biogeosciences, 19, 5059–5077, https://doi.org/10.5194/bg-19-5059-2022, https://doi.org/10.5194/bg-19-5059-2022, 2022
Short summary
Short summary
Permafrost thaw releases methane that can be emitted into the atmosphere or transported by Arctic rivers. Methane measurements are lacking in large Arctic river regions. In the Kolyma River (northeast Siberia), we measured dissolved methane to map its distribution with great spatial detail. The river’s edge and river junctions had the highest methane concentrations compared to other river areas. Microbial communities in the river showed that the river’s methane likely is from the adjacent land.
Rachael Akinyede, Martin Taubert, Marion Schrumpf, Susan Trumbore, and Kirsten Küsel
Biogeosciences, 19, 4011–4028, https://doi.org/10.5194/bg-19-4011-2022, https://doi.org/10.5194/bg-19-4011-2022, 2022
Short summary
Short summary
Soils will likely become warmer in the future, and this can increase the release of carbon dioxide (CO2) into the atmosphere. As microbes can take up soil CO2 and prevent further escape into the atmosphere, this study compares the rate of uptake and release of CO2 at two different temperatures. With warming, the rate of CO2 uptake increases less than the rate of release, indicating that the capacity to modulate soil CO2 release into the atmosphere will decrease under future warming.
Saqr Munassar, Christian Rödenbeck, Frank-Thomas Koch, Kai U. Totsche, Michał Gałkowski, Sophia Walther, and Christoph Gerbig
Atmos. Chem. Phys., 22, 7875–7892, https://doi.org/10.5194/acp-22-7875-2022, https://doi.org/10.5194/acp-22-7875-2022, 2022
Short summary
Short summary
The results obtained from ensembles of inversions over 13 years show the largest spread in the a posteriori fluxes over the station set ensemble. Using different prior fluxes in the inversions led to a smaller impact. Drought occurrences in 2018 and 2019 affected CO2 fluxes as seen in net ecosystem exchange estimates. Our study highlights the importance of expanding the atmospheric site network across Europe to better constrain CO2 fluxes in inverse modelling.
Sophie F. von Fromm, Alison M. Hoyt, Markus Lange, Gifty E. Acquah, Ermias Aynekulu, Asmeret Asefaw Berhe, Stephan M. Haefele, Steve P. McGrath, Keith D. Shepherd, Andrew M. Sila, Johan Six, Erick K. Towett, Susan E. Trumbore, Tor-G. Vågen, Elvis Weullow, Leigh A. Winowiecki, and Sebastian Doetterl
SOIL, 7, 305–332, https://doi.org/10.5194/soil-7-305-2021, https://doi.org/10.5194/soil-7-305-2021, 2021
Short summary
Short summary
We investigated various soil and climate properties that influence soil organic carbon (SOC) concentrations in sub-Saharan Africa. Our findings indicate that climate and geochemistry are equally important for explaining SOC variations. The key SOC-controlling factors are broadly similar to those for temperate regions, despite differences in soil development history between the two regions.
Marion Schrumpf, Klaus Kaiser, Allegra Mayer, Günter Hempel, and Susan Trumbore
Biogeosciences, 18, 1241–1257, https://doi.org/10.5194/bg-18-1241-2021, https://doi.org/10.5194/bg-18-1241-2021, 2021
Short summary
Short summary
A large amount of organic carbon (OC) in soil is protected against decay by bonding to minerals. We studied the release of mineral-bonded OC by NaF–NaOH extraction and H2O2 oxidation. Unexpectedly, extraction and oxidation removed mineral-bonded OC at roughly constant portions and of similar age distributions, irrespective of mineral composition, land use, and soil depth. The results suggest uniform modes of interactions between OC and minerals across soils in quasi-steady state with inputs.
Jinxuan Chen, Christoph Gerbig, Julia Marshall, and Kai Uwe Totsche
Geosci. Model Dev., 13, 4091–4106, https://doi.org/10.5194/gmd-13-4091-2020, https://doi.org/10.5194/gmd-13-4091-2020, 2020
Short summary
Short summary
One of the essential challenge for atmospheric CO2 forecasting is predicting CO2 flux variation on synoptic timescale. For CAMS CO2 forecast, a process-based vegetation model is used.
In this research we evaluate another type of model (i.e., the light-use-efficiency model VPRM), which is a data-driven approach and thus ideal for realistic estimation, on its ability of flux prediction. Errors from different sources are assessed, and overall the model is capable of CO2 flux prediction.
Ann-Sophie Lehnert, Thomas Behrendt, Alexander Ruecker, Georg Pohnert, and Susan E. Trumbore
Atmos. Meas. Tech., 13, 3507–3520, https://doi.org/10.5194/amt-13-3507-2020, https://doi.org/10.5194/amt-13-3507-2020, 2020
Short summary
Short summary
Volatile organic compounds (VOCs) like scents can appear and disappear quickly. For example, when a bug starts on a tree, the tree releases VOCs that warn the trees around him. Thus, one needs instruments measuring their concentration in real time and identify which VOC is measured. In our study, we compared two instruments doing that, PTR-MS and SIFT-MS. Both work similarly, but we found that the PTR-MS can measure lower concentrations, but the SIFT-MS can identify VOCs better.
Corey R. Lawrence, Jeffrey Beem-Miller, Alison M. Hoyt, Grey Monroe, Carlos A. Sierra, Shane Stoner, Katherine Heckman, Joseph C. Blankinship, Susan E. Crow, Gavin McNicol, Susan Trumbore, Paul A. Levine, Olga Vindušková, Katherine Todd-Brown, Craig Rasmussen, Caitlin E. Hicks Pries, Christina Schädel, Karis McFarlane, Sebastian Doetterl, Christine Hatté, Yujie He, Claire Treat, Jennifer W. Harden, Margaret S. Torn, Cristian Estop-Aragonés, Asmeret Asefaw Berhe, Marco Keiluweit, Ágatha Della Rosa Kuhnen, Erika Marin-Spiotta, Alain F. Plante, Aaron Thompson, Zheng Shi, Joshua P. Schimel, Lydia J. S. Vaughn, Sophie F. von Fromm, and Rota Wagai
Earth Syst. Sci. Data, 12, 61–76, https://doi.org/10.5194/essd-12-61-2020, https://doi.org/10.5194/essd-12-61-2020, 2020
Short summary
Short summary
The International Soil Radiocarbon Database (ISRaD) is an an open-source archive of soil data focused on datasets including radiocarbon measurements. ISRaD includes data from bulk or
whole soils, distinct soil carbon pools isolated in the laboratory by a variety of soil fractionation methods, samples of soil gas or water collected interstitially from within an intact soil profile, CO2 gas isolated from laboratory soil incubations, and fluxes collected in situ from a soil surface.
Shaun R. Levick, Anna E. Richards, Garry D. Cook, Jon Schatz, Marcus Guderle, Richard J. Williams, Parash Subedi, Susan E. Trumbore, and Alan N. Andersen
Biogeosciences, 16, 1493–1503, https://doi.org/10.5194/bg-16-1493-2019, https://doi.org/10.5194/bg-16-1493-2019, 2019
Short summary
Short summary
We used airborne lidar to map the three-dimensional structure and model the biomass of plant canopies across a long-term fire experiment in the Northern Territory of Australia. Our results show that late season fires occurring every 2 years reduce the amount of carbon stored above-ground by 50 % relative to unburnt control plots. We also show how increased fire intensity removes the shrub layer from savannas and discuss the implications for biodiversity conservation.
Thomas Behrendt, Elisa C. P. Catão, Rüdiger Bunk, Zhigang Yi, Elena Schweer, Steffen Kolb, Jürgen Kesselmeier, and Susan Trumbore
SOIL, 5, 121–135, https://doi.org/10.5194/soil-5-121-2019, https://doi.org/10.5194/soil-5-121-2019, 2019
Short summary
Short summary
We measured net fluxes of OCS from nine soils with different land use in a dynamic chamber system and analyzed for one soil RNA relative abundance and gene transcripts. Our data suggest that indeed carbonic anhydrase (CA) plays an important role for OCS exchange, but the role of other enzymes might have been underestimated. Our study is the first assessment of the environmental significance of different microbial groups producing and consuming OCS by various enzymes other than CA.
Boaz Hilman, Jan Muhr, Susan E. Trumbore, Norbert Kunert, Mariah S. Carbone, Päivi Yuval, S. Joseph Wright, Gerardo Moreno, Oscar Pérez-Priego, Mirco Migliavacca, Arnaud Carrara, José M. Grünzweig, Yagil Osem, Tal Weiner, and Alon Angert
Biogeosciences, 16, 177–191, https://doi.org/10.5194/bg-16-177-2019, https://doi.org/10.5194/bg-16-177-2019, 2019
Short summary
Short summary
Combined measurement of CO2 / O2 fluxes in tree stems suggested that on average 41 % of the respired CO2 was not emitted locally to the atmosphere. This finding strengthens the recognition that CO2 efflux from tree stems is not an accurate measure of respiration. The CO2 / O2 fluxes did not vary as expected if CO2 dissolution in the xylem sap was the main driver for the CO2 retention. We suggest the examination of refixation of respired CO2 as a possible mechanism for CO2 retention.
Fabio Boschetti, Valerie Thouret, Greet Janssens Maenhout, Kai Uwe Totsche, Julia Marshall, and Christoph Gerbig
Atmos. Chem. Phys., 18, 9225–9241, https://doi.org/10.5194/acp-18-9225-2018, https://doi.org/10.5194/acp-18-9225-2018, 2018
Short summary
Short summary
Retrieving surface–atmosphere fluxes from the combination of atmospheric observations with atmospheric transport models can benefit from combining multiple species in a single inversion. The underlying effect is that species such as CO2 and CO have partially overlapping emission patterns for given sectors and fuel types and so share part of the uncertainties, both related to the a priori knowledge of emissions, and to model–data mismatch error. We show this for airborne profile data from IAGOS.
Marta Camino-Serrano, Bertrand Guenet, Sebastiaan Luyssaert, Philippe Ciais, Vladislav Bastrikov, Bruno De Vos, Bert Gielen, Gerd Gleixner, Albert Jornet-Puig, Klaus Kaiser, Dolly Kothawala, Ronny Lauerwald, Josep Peñuelas, Marion Schrumpf, Sara Vicca, Nicolas Vuichard, David Walmsley, and Ivan A. Janssens
Geosci. Model Dev., 11, 937–957, https://doi.org/10.5194/gmd-11-937-2018, https://doi.org/10.5194/gmd-11-937-2018, 2018
Short summary
Short summary
Global models generally oversimplify the representation of soil organic carbon (SOC), and thus its response to global warming remains uncertain. We present the new soil module ORCHIDEE-SOM, within the global model ORCHIDEE, that refines the representation of SOC dynamics and includes the dissolved organic carbon (DOC) processes. The model is able to reproduce SOC stocks and DOC concentrations in four different ecosystems, opening an opportunity for improved predictions of SOC in global models.
Bernd Kohlhepp, Robert Lehmann, Paul Seeber, Kirsten Küsel, Susan E. Trumbore, and Kai U. Totsche
Hydrol. Earth Syst. Sci., 21, 6091–6116, https://doi.org/10.5194/hess-21-6091-2017, https://doi.org/10.5194/hess-21-6091-2017, 2017
Rebecca Elizabeth Cooper, Karin Eusterhues, Carl-Eric Wegner, Kai Uwe Totsche, and Kirsten Küsel
Biogeosciences, 14, 5171–5188, https://doi.org/10.5194/bg-14-5171-2017, https://doi.org/10.5194/bg-14-5171-2017, 2017
Short summary
Short summary
In this study we show increasing organic matter (OM) content on ferrihydrite surfaces enhances Fe reduction by the model Fe reducer S. oneidensis and a microbial consortia extracted from peat. Similarities in reduction rates between S. oneidensis and the consortia suggest electron shuttling dominates in OM-rich soils. Community profile analyses showed enrichment of fermenters with pure ferrihydrite, whereas OM–mineral complexes favored enrichment of Fe-reducing Desulfobacteria and Pelosinus sp.
Martin E. Nowak, Valérie F. Schwab, Cassandre S. Lazar, Thomas Behrendt, Bernd Kohlhepp, Kai Uwe Totsche, Kirsten Küsel, and Susan E. Trumbore
Hydrol. Earth Syst. Sci., 21, 4283–4300, https://doi.org/10.5194/hess-21-4283-2017, https://doi.org/10.5194/hess-21-4283-2017, 2017
Short summary
Short summary
In the present study we combined measurements of dissolved inorganic carbon (DIC) isotopes with a set of different geochemical and microbiological methods in order to get a comprehensive view of biogeochemical cycling and groundwater flow in two limestone aquifer assemblages. This allowed us to understand interactions and feedbacks between microbial communities, their carbon sources, and water chemistry.
Shreeya Verma, Julia Marshall, Christoph Gerbig, Christian Rödenbeck, and Kai Uwe Totsche
Atmos. Chem. Phys., 17, 5665–5675, https://doi.org/10.5194/acp-17-5665-2017, https://doi.org/10.5194/acp-17-5665-2017, 2017
Short summary
Short summary
The inverse modelling approach for estimating surface fluxes is based on transport models that have an imperfect representation of atmospheric processes like vertical mixing. In this paper, we show how assimilating commercial aircraft-based vertical profiles of CO2 into inverse models can help reduce error due to the transport model, thus providing more accurate estimates of surface fluxes. Further, the reduction in flux uncertainty due to aircraft profiles from the IAGOS project is quantified.
Lesego Khomo, Susan Trumbore, Carleton R. Bern, and Oliver A. Chadwick
SOIL, 3, 17–30, https://doi.org/10.5194/soil-3-17-2017, https://doi.org/10.5194/soil-3-17-2017, 2017
Short summary
Short summary
We evaluated mineral control of organic carbon dynamics by relating the content and age of carbon stored in soils of varied mineralogical composition found in the landscapes of Kruger National Park, South Africa. Carbon associated with smectite clay minerals, which have stronger surface–organic matter interactions, averaged about a thousand years old, while most soil carbon was only decades to centuries old and was associated with iron and aluminum oxide minerals.
Daniel Magnabosco Marra, Niro Higuchi, Susan E. Trumbore, Gabriel H. P. M. Ribeiro, Joaquim dos Santos, Vilany M. C. Carneiro, Adriano J. N. Lima, Jeffrey Q. Chambers, Robinson I. Negrón-Juárez, Frederic Holzwarth, Björn Reu, and Christian Wirth
Biogeosciences, 13, 1553–1570, https://doi.org/10.5194/bg-13-1553-2016, https://doi.org/10.5194/bg-13-1553-2016, 2016
Short summary
Short summary
Predicting biomass correctly at the landscape level in hyperdiverse and structurally complex tropical forests requires the inclusion of predictors that express inherent variations in species architecture. The model of interest should comprise the floristic composition and size-distribution variability of the target forest, implying that even generic global or pantropical biomass estimation models can lead to strong biases.
Leandro T. dos Santos, Daniel Magnabosco Marra, Susan Trumbore, Plínio B. de Camargo, Robinson I. Negrón-Juárez, Adriano J. N. Lima, Gabriel H. P. M. Ribeiro, Joaquim dos Santos, and Niro Higuchi
Biogeosciences, 13, 1299–1308, https://doi.org/10.5194/bg-13-1299-2016, https://doi.org/10.5194/bg-13-1299-2016, 2016
Short summary
Short summary
In the Amazon forest, wind disturbances can create canopy gaps of many hundreds of hectares. We show that inputs of plant litter associated with large windthrows cause a short-term increase in soil carbon stock. The degree of increase is related to soil clay content and tree mortality intensity. The higher carbon content and potentially higher nutrient availability in soils from areas recovering from windthrows may favor forest regrowth and increase vegetation resilience.
P. Kountouris, C. Gerbig, K.-U. Totsche, A. J. Dolman, A. G. C. A. Meesters, G. Broquet, F. Maignan, B. Gioli, L. Montagnani, and C. Helfter
Biogeosciences, 12, 7403–7421, https://doi.org/10.5194/bg-12-7403-2015, https://doi.org/10.5194/bg-12-7403-2015, 2015
M. E. Nowak, F. Beulig, J. von Fischer, J. Muhr, K. Küsel, and S. E. Trumbore
Biogeosciences, 12, 7169–7183, https://doi.org/10.5194/bg-12-7169-2015, https://doi.org/10.5194/bg-12-7169-2015, 2015
Short summary
Short summary
Microorganisms have been recognized as an important source of soil organic matter (SOM). Autotrophic microorganisms utilize CO2 instead of organic carbon. Microbial CO2 fixation is accompanied with high 13C isotope discrimination. Because autotrophs are abundant in soils, they might be a significant factor influencing 13C signatures of SOM. Thus, it is important to asses the importance of autotrophs for C isotope signatures in soils, in order to use isotopes as a tracer for soil C dynamics.
M. O. Andreae, O. C. Acevedo, A. Araùjo, P. Artaxo, C. G. G. Barbosa, H. M. J. Barbosa, J. Brito, S. Carbone, X. Chi, B. B. L. Cintra, N. F. da Silva, N. L. Dias, C. Q. Dias-Júnior, F. Ditas, R. Ditz, A. F. L. Godoi, R. H. M. Godoi, M. Heimann, T. Hoffmann, J. Kesselmeier, T. Könemann, M. L. Krüger, J. V. Lavric, A. O. Manzi, A. P. Lopes, D. L. Martins, E. F. Mikhailov, D. Moran-Zuloaga, B. W. Nelson, A. C. Nölscher, D. Santos Nogueira, M. T. F. Piedade, C. Pöhlker, U. Pöschl, C. A. Quesada, L. V. Rizzo, C.-U. Ro, N. Ruckteschler, L. D. A. Sá, M. de Oliveira Sá, C. B. Sales, R. M. N. dos Santos, J. Saturno, J. Schöngart, M. Sörgel, C. M. de Souza, R. A. F. de Souza, H. Su, N. Targhetta, J. Tóta, I. Trebs, S. Trumbore, A. van Eijck, D. Walter, Z. Wang, B. Weber, J. Williams, J. Winderlich, F. Wittmann, S. Wolff, and A. M. Yáñez-Serrano
Atmos. Chem. Phys., 15, 10723–10776, https://doi.org/10.5194/acp-15-10723-2015, https://doi.org/10.5194/acp-15-10723-2015, 2015
Short summary
Short summary
This paper describes the Amazon Tall Tower Observatory (ATTO), a new atmosphere-biosphere observatory located in the remote Amazon Basin. It presents results from ecosystem ecology, meteorology, trace gas, and aerosol measurements collected at the ATTO site during the first 3 years of operation.
J. F. Mori, T. R. Neu, S. Lu, M. Händel, K. U. Totsche, and K. Küsel
Biogeosciences, 12, 5277–5289, https://doi.org/10.5194/bg-12-5277-2015, https://doi.org/10.5194/bg-12-5277-2015, 2015
Short summary
Short summary
We studied filamentous macroscopic algae growing in metal-rich stream water that leaked from a former uranium-mining district. These algae were encrusted with Fe-deposits that were associated with microbes, mainly Gallionella-related Fe-oxidizing bacteria, and extracellular polymeric substances. Algae with a lower number of chloroplasts often exhibited discontinuous series of precipitates, likely due to the intercalary growth of algae which allowed them to avoid detrimental encrustation.
K. Eusterhues, A. Hädrich, J. Neidhardt, K. Küsel, T. F. Keller, K. D. Jandt, and K. U. Totsche
Biogeosciences, 11, 4953–4966, https://doi.org/10.5194/bg-11-4953-2014, https://doi.org/10.5194/bg-11-4953-2014, 2014
C. A. Sierra, M. Müller, and S. E. Trumbore
Geosci. Model Dev., 7, 1919–1931, https://doi.org/10.5194/gmd-7-1919-2014, https://doi.org/10.5194/gmd-7-1919-2014, 2014
R. Kretschmer, C. Gerbig, U. Karstens, G. Biavati, A. Vermeulen, F. Vogel, S. Hammer, and K. U. Totsche
Atmos. Chem. Phys., 14, 7149–7172, https://doi.org/10.5194/acp-14-7149-2014, https://doi.org/10.5194/acp-14-7149-2014, 2014
M. Zech, R. Zech, K. Rozanski, A. Hemp, G. Gleixner, and W. Zech
Biogeosciences Discuss., https://doi.org/10.5194/bgd-11-7823-2014, https://doi.org/10.5194/bgd-11-7823-2014, 2014
Preprint withdrawn
B. Ahrens, M. Reichstein, W. Borken, J. Muhr, S. E. Trumbore, and T. Wutzler
Biogeosciences, 11, 2147–2168, https://doi.org/10.5194/bg-11-2147-2014, https://doi.org/10.5194/bg-11-2147-2014, 2014
M. S. Torn, M. Kleber, E. S. Zavaleta, B. Zhu, C. B. Field, and S. E. Trumbore
Biogeosciences, 10, 8067–8081, https://doi.org/10.5194/bg-10-8067-2013, https://doi.org/10.5194/bg-10-8067-2013, 2013
E. Solly, I. Schöning, S. Boch, J. Müller, S. A. Socher, S. E. Trumbore, and M. Schrumpf
Biogeosciences, 10, 4833–4843, https://doi.org/10.5194/bg-10-4833-2013, https://doi.org/10.5194/bg-10-4833-2013, 2013
Related subject area
Biogeochemistry: Groundwater
Small-scale hydrological patterns in a Siberian permafrost ecosystem affected by drainage
Predicting the impact of spatial heterogeneity on microbially mediated nutrient cycling in the subsurface
Conversion of tropical forests to smallholder rubber and oil palm plantations impacts nutrient leaching losses and nutrient retention efficiency in highly weathered soils
Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization
Tracking the direct impact of rainfall on groundwater at Mt. Fuji by multiple analyses including microbial DNA
Biogeochemical constraints on the origin of methane in an alluvial aquifer: evidence for the upward migration of methane from underlying coal measures
Ash leachates from some recent eruptions of Mount Etna (Italy) and Popocatépetl (Mexico) volcanoes and their impact on amphibian living freshwater organisms
Predicting the denitrification capacity of sandy aquifers from in situ measurements using push–pull 15N tracer tests
Biomass uptake and fire as controls on groundwater solute evolution on a southeast Australian granite: aboriginal land management hypothesis
17O excess traces atmospheric nitrate in paleo-groundwater of the Saharan desert
Interactions of local climatic, biotic and hydrogeochemical processes facilitate phosphorus dynamics along an Everglades forest-marsh gradient
Predicting the denitrification capacity of sandy aquifers from shorter-term incubation experiments and sediment properties
Management, regulation and environmental impacts of nitrogen fertilization in northwestern Europe under the Nitrates Directive; a benchmark study
Regional analysis of groundwater nitrate concentrations and trends in Denmark in regard to agricultural influence
Denitrification and inference of nitrogen sources in the karstic Floridan Aquifer
Characterization of broom fibers for PRB in the remediation of aquifers contaminated by heavy metals
Sandra Raab, Karel Castro-Morales, Anke Hildebrandt, Martin Heimann, Jorien Elisabeth Vonk, Nikita Zimov, and Mathias Goeckede
Biogeosciences, 21, 2571–2597, https://doi.org/10.5194/bg-21-2571-2024, https://doi.org/10.5194/bg-21-2571-2024, 2024
Short summary
Short summary
Water status is an important control factor on sustainability of Arctic permafrost soils, including production and transport of carbon. We compared a drained permafrost ecosystem with a natural control area, investigating water levels, thaw depths, and lateral water flows. We found that shifts in water levels following drainage affected soil water availability and that lateral transport patterns were of major relevance. Understanding these shifts is crucial for future carbon budget studies.
Swamini Khurana, Falk Heße, Anke Hildebrandt, and Martin Thullner
Biogeosciences, 19, 665–688, https://doi.org/10.5194/bg-19-665-2022, https://doi.org/10.5194/bg-19-665-2022, 2022
Short summary
Short summary
In this study, we concluded that the residence times of solutes and the Damköhler number (Da) of the biogeochemical reactions in the domain are governing factors for evaluating the impact of spatial heterogeneity of the domain on chemical (such as carbon and nitrogen compounds) removal. We thus proposed a relationship to scale this impact governed by Da. This relationship may be applied in larger domains, thereby resulting in more accurate modelling outcomes of nutrient removal in groundwater.
Syahrul Kurniawan, Marife D. Corre, Amanda L. Matson, Hubert Schulte-Bisping, Sri Rahayu Utami, Oliver van Straaten, and Edzo Veldkamp
Biogeosciences, 15, 5131–5154, https://doi.org/10.5194/bg-15-5131-2018, https://doi.org/10.5194/bg-15-5131-2018, 2018
Short summary
Short summary
Our study generates information to aid policies and improve soil management practices for minimizing the negative impacts of forest conversion to rubber and oil palm plantations while maintaining production. Compared to forests, the fertilized areas of oil palm plantations had higher leaching of N, organic C, and base cations, whereas the unfertilized rubber plantations showed lower leaching of dissolved P and organic C. These signaled a decrease in extant soil fertility and groundwater quality.
Lara E. Pracht, Malak M. Tfaily, Robert J. Ardissono, and Rebecca B. Neumann
Biogeosciences, 15, 1733–1747, https://doi.org/10.5194/bg-15-1733-2018, https://doi.org/10.5194/bg-15-1733-2018, 2018
Short summary
Short summary
Organic carbon in aquifer recharge waters and sediments can fuel microbial reactions that affect groundwater quality. We used high-resolution mass spectrometry to molecularly characterize organic carbon mobilized off sediment collected from a Bangladeshi aquifer, to reference its composition against dissolved organic carbon in aquifer recharge water, to track compositional changes during incubation, and to advance understanding of microbial processing of organic carbon in anaerobic environments.
Ayumi Sugiyama, Suguru Masuda, Kazuyo Nagaosa, Maki Tsujimura, and Kenji Kato
Biogeosciences, 15, 721–732, https://doi.org/10.5194/bg-15-721-2018, https://doi.org/10.5194/bg-15-721-2018, 2018
Short summary
Short summary
The direct impact of rainfall on groundwater at Mt. Fuji, the largest volcanic mountain in Japan, was elucidated by multiple analyses including microbial DNA. Bacterial abundance and DNA not only supported the findings on the movement of groundwater obtained from chemical analyses but also elucidated chemically unseen flow. Evidence of piston flow in deep groundwater was first shown through changes in archaeal density and diversity. Microbial analysis extends our understanding of groundwater.
Charlotte P. Iverach, Sabrina Beckmann, Dioni I. Cendón, Mike Manefield, and Bryce F. J. Kelly
Biogeosciences, 14, 215–228, https://doi.org/10.5194/bg-14-215-2017, https://doi.org/10.5194/bg-14-215-2017, 2017
Short summary
Short summary
This research characterised the biogeochemical constraints on the origin of methane in an alluvial aquifer, concluding that the most likely source was the upward migration from a directly underlying coal seam. This research was undertaken due to concerns about the effect of coal seam gas production on groundwater quality in the study area. The implications include the fact that no methane is being produced in the aquifer (in situ) and that there is local natural connectivity in the study area.
M. D'Addabbo, R. Sulpizio, M. Guidi, G. Capitani, P. Mantecca, and G. Zanchetta
Biogeosciences, 12, 7087–7106, https://doi.org/10.5194/bg-12-7087-2015, https://doi.org/10.5194/bg-12-7087-2015, 2015
Short summary
Short summary
Leaching experiments were carried out on fresh ash samples from the 2012 Popocatépetl, and 2011/12 Etna eruptions, in order to investigate the release of compounds in water. Results were discussed in the light of changing pH and release of compounds for the different leachates. They were used for toxicity experiments on living biota (Xenopus laevis). They are mildly toxic, and no significant differences exist between the toxic profiles of the two leachates.
W. Eschenbach, R. Well, and W. Walther
Biogeosciences, 12, 2327–2346, https://doi.org/10.5194/bg-12-2327-2015, https://doi.org/10.5194/bg-12-2327-2015, 2015
J. F. Dean, J. A. Webb, G. E. Jacobsen, R. Chisari, and P. E. Dresel
Biogeosciences, 11, 4099–4114, https://doi.org/10.5194/bg-11-4099-2014, https://doi.org/10.5194/bg-11-4099-2014, 2014
M. Dietzel, A. Leis, R. Abdalla, J. Savarino, S. Morin, M. E. Böttcher, and S. Köhler
Biogeosciences, 11, 3149–3161, https://doi.org/10.5194/bg-11-3149-2014, https://doi.org/10.5194/bg-11-3149-2014, 2014
T. G. Troxler, C. Coronado-Molina, D. N. Rondeau, S. Krupa, S. Newman, M. Manna, R. M. Price, and F. H. Sklar
Biogeosciences, 11, 899–914, https://doi.org/10.5194/bg-11-899-2014, https://doi.org/10.5194/bg-11-899-2014, 2014
W. Eschenbach and R. Well
Biogeosciences, 10, 1013–1035, https://doi.org/10.5194/bg-10-1013-2013, https://doi.org/10.5194/bg-10-1013-2013, 2013
H. J. M. van Grinsven, H. F. M. ten Berge, T. Dalgaard, B. Fraters, P. Durand, A. Hart, G. Hofman, B. H. Jacobsen, S. T. J. Lalor, J. P. Lesschen, B. Osterburg, K. G. Richards, A.-K. Techen, F. Vertès, J. Webb, and W. J. Willems
Biogeosciences, 9, 5143–5160, https://doi.org/10.5194/bg-9-5143-2012, https://doi.org/10.5194/bg-9-5143-2012, 2012
B. Hansen, T. Dalgaard, L. Thorling, B. Sørensen, and M. Erlandsen
Biogeosciences, 9, 3277–3286, https://doi.org/10.5194/bg-9-3277-2012, https://doi.org/10.5194/bg-9-3277-2012, 2012
J. B. Heffernan, A. R. Albertin, M. L. Fork, B. G. Katz, and M. J. Cohen
Biogeosciences, 9, 1671–1690, https://doi.org/10.5194/bg-9-1671-2012, https://doi.org/10.5194/bg-9-1671-2012, 2012
C. Fallico, S. Troisi, A. Molinari, and M. F. Rivera
Biogeosciences, 7, 2545–2556, https://doi.org/10.5194/bg-7-2545-2010, https://doi.org/10.5194/bg-7-2545-2010, 2010
Cited articles
Akob, D. M. and Küsel, K.: Where microorganisms meet rocks in the Earth's Critical Zone, Biogeosciences, 8, 3531–3543, https://doi.org/10.5194/bg-8-3531-2011, 2011.
American Public Health Association: Standard methods for the examination of water and wastewater: selected analytical methods approved and cited by the United States Environmental Protection Agency, 1981.
Arrieta, L. and Grez, R.: Solubilization of iron-containing minerals by soil microorganisms, Appl. Microbiol., 22, 487–490, 1971.
Arts, M. T., Ackman, R. G., and Holub, B. J.: “Essential fatty acids” in aquatic ecosystems: a crucial link between diet and human health and evolution, Can. J. Fish. Aquat. Sci., 58, 122–137, https://doi.org/10.1139/f00-224, 2001.
Bååth, E. and Anderson, T.-H.: Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques, Soil Biol. Biochem., 35, 955–963, https://doi.org/10.1016/S0038-0717(03)00154-8, 2003.
Bååth, E., Frostegård, Å., Pennanen, T., and Fritze, H.: Microbial community structure and pH response in relation to soil organic matter quality in wood-ash fertilized, clear-cut or burned coniferous forest soils, Soil Biol. Biochem., 27, 229–240, https://doi.org/10.1016/0038-0717(94)00140-V, 1995.
Balkwill, D. L., Murphy, E. M., Fair, D. M., Ringelberg, D. B., and White, D. C.: Microbial communities in high and low recharge environments:implications for microbial transport in the vadose zone, Microbiol. Ecol., 35, 156–171, https://doi.org/10.1007/s002489900070, 1998.
Benner, S. G., Smart, E. W., and Moore, J. N.: Metal behavior during surface-groundwater interaction, Silver Bow Creek, Montana, Environ. Sci. Technol., 29, 1789–1795, https://doi.org/10.1021/es00007a015, 1995.
Blair, N., Leu, A., Muñoz, E., Olsen, J., Kwong, E., and Des Marais, D.: Carbon isotopic fractionation in heterotrophic microbial metabolism, Appl. Environ. Microbiol., 50, 996–1001, 1985.
Blazewicz, S. J., Barnard, R. L., Daly, R. A., and Firestone, M. K.: Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses, ISME J., 7, 2061–2068, https://doi.org/10.1038/ismej.2013.102, 2013.
Bligh, E. G. and Dyer, W. J.: A rapid method of total lipid extraction and purification, Can. J. Biochem. Physiol., 37, 911–917, https://doi.org/10.1139/o59-099, 1959.
Bossio, D. A. and Scow, K. M.: Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns, Microbiol. Ecol., 35, 265–278, https://doi.org/10.1007/s002489900082, 1998.
Brad, T., Braster, M., van Breukelen, B. M., van Straalen, N. M., and Röling, W. F. M.: Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate, Appl. Environ. Microbiol., 74, 3959–3968, https://doi.org/10.1128/AEM.02820-07, 2008.
Burgin, A. and Hamilton, S. K.: NO3−-driven SO42− production in freshwater ecosystems: implications for N and S cycling, Ecosystems, 11, 908–922, https://doi.org/10.1007/s10021-008-9169-5, 2008.
Burgin, A. J. and Hamilton, S. K.: Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways, Front. Ecol. Environ., 5, 89–96, https://doi.org/10.1890/1540-9295(2007)5[89:HWOTRO]2.0.CO;2, 2007.
Canfield, D. E., Stewart, F. J., Thamdrup, B., Brabandere, L. D., Dalsgaard, T., Delong, E. F., Revsbech, N. P., and Ulloa, O.: A cryptic sulfur cycle in oxygen-minimum-zone waters of the chilean coast, Science, 330, 1375–1378, https://doi.org/10.1126/science.1196889, 2010.
Chapelle, F. H.: Ground-water microbiology and geochemistry, John Wiley & Sons, 2001.
Chapelle, F. H. and Lovley, D. R.: Competitive exclusion of sulfate reduction by Fe(lll)-reducing bacteria: A mechanism for producing discrete zones of high-iron ground water, Groundwater, 30, 29–36, https://doi.org/10.1111/j.1745-6584.1992.tb00808.x, 1992.
Coleman, M. L., Hedrick, D. B., Lovley, D. R., White, D. C., and Pye, K.: Reduction of Fe(III) in sediments by sulphate-reducing bacteria, Nature, 361, 436–438, https://doi.org/10.1038/361436a0, 1993.
Dalsgaard, T. and Thamdrup, B.: Factors controlling anaerobic ammonium oxidation with nitrite in marine sediments, Appl. Environ. Microbiol., 68, 3802–3808, https://doi.org/10.1128/AEM.68.8.3802-3808.2002, 2002.
Dalsgaard, T., Canfield, D. E., Petersen, J., Thamdrup, B., and Acuña-González, J.: N2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica, Nature, 422, 606–608, https://doi.org/10.1038/nature01526, 2003.
Dibbern, D., Schmalwasser, A., Lueders, T., and Totsche, K. U.: Selective transport of plant root-associated bacterial populations in agricultural soils upon snowmelt, Soil Biol. Biochem., 69, 187–196, https://doi.org/10.1016/j.soilbio.2013.10.040, 2014.
DIN 38409-7: Deutsche Einheitsverfahren zur Wasser-, Abwasser- und Schlammuntersuchung – Summarische Wirkungs- und Stoffkenngrößen (Gruppe H) – Teil 7: Bestimmung der Säure- und Basekapazität (H7), in: Normung, D.D.I.f., Beuth Verlag GmbH, Berlin, 2005.
DIN EN 1484: Wasseranalytik – Anleitungen zur Bestimmung des gesamten organischen Kohlenstoffs (TOC) und des gelösten organischen Kohlenstoffs (DOC), in: Normung, D.D.I.f., Beuth Verlag GmbH, Berlin, 1997.
DIN EN ISO 10304-1: Wasserbeschaffenheit – Bestimmung von gelösten Anionen mittels Flüssigkeits-Ionenchromatographie – Teil 1: Bestimmung von Bromid, Chlorid, Fluorid, Nitrat, Nitrit, Phosphat und Sulfat, in: Normung, D.D.I.f., Beuth Verlag GmbH, Berlin, p. 24, 2009.
DIN EN ISO 11885: Wasserbeschaffenheit – Bestimmung von ausgewählten Elementen durch induktiv gekoppelte Plasma-Atom-Emissionsspektrometrie (ICP-OES), in: Normung, D.D.I.f., Beuth Verlag GmbH, Berlin, 2009.
Dowling, N. J. E., Widdel, F., and White, D. C.: Phospholipid ester-linked fatty acid biomarkers of acetate-oxidizing sulphate-reducers and other sulphide-forming bacteria, Microbiol., 132, 1815–1825, https://doi.org/10.1099/00221287-132-7-1815, 1986.
Edlund, A., Nichols, P. D., Roffey, R., and White, D. C.: Extractable and lipopolysaccharide fatty acid and hydroxy acid profiles from Desulfovibrio species, J. Lipid Res., 26, 982–988, 1985.
Edwards, K. J., Becker, K., and Colwell, F.: The deep, dark energy biosphere: intraterrestrial life on earth, Annu. Rev. Earth Pl. Sc., 40, 551–568, https://doi.org/10.1146/annurev-earth-042711-105500, 2012.
Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W., and Bock, E.: A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship, Arch. Microbiol., 164, 16–23, https://doi.org/10.1007/BF02568729, 1995.
Emerson, J. B., Thomas, B. C., Alvarez, W., and Banfield, J. F.: Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla, Environ. Microbiol., 18, 1462–2920, https://doi.org/10.1111/1462-2920.12817, 2015.
Etingoff, K.: Organic agricultural practices: Alternatives to conventional agricultural systems, CRC Press, Toronto, Canada, 2014.
Filion, G., Laflamme, C., Turgeon, N., Ho, J., and Duchaine, C.: Permeabilization and hybridization protocols for rapid detection of Bacillus spores using fluorescence in situ hybridization, J. Microbiol. Meth., 77, 29–36, https://doi.org/10.1016/j.mimet.2008.12.009, 2009.
Frostegård, A. and Bååth, E.: The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil, Biol. Fertil. Soils, 22, 59–65, https://doi.org/10.1007/BF00384433, 1996.
Frostegård, Å., Tunlid, A., and Bååth, E.: Use and misuse of PLFA measurements in soils, Soil Biol. Biochem., 43, 1621–1625, https://doi.org/10.1016/j.soilbio.2010.11.021, 2011.
Gadd, G. M.: Metals, minerals and microbes: geomicrobiology and bioremediation, Microbiology, 156, 609–643, https://doi.org/10.1099/mic.0.037143-0, 2010.
Green, C. T. and Scow, K. M.: Analysis of phospholipid fatty acids (PLFA) to characterize microbial communities in aquifers, Hydrogeol. J., 8, 126–141, https://doi.org/10.1007/s100400050013, 2000.
Hamman, S. T., Burke, I. C., and Stromberger, M. E.: Relationships between microbial community structure and soil environmental conditions in a recently burned system, Soil Biol. Biochem., 39, 1703–1711, https://doi.org/10.1016/j.soilbio.2007.01.018, 2007.
Harwood, D. L. and Russell, N. J.: Lipids in plants and microbes, George Allen and Unwin, London, 1984.
Hedrick, D. B., Peacock, A. D., Lovley, D. R., Woodard, T. L., Nevin, K. P., Long, P. E., and White, D. C.: Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor, J. Ind. Microbiol. Biot., 36, 205–209, https://doi.org/10.1007/s10295-008-0486-7, 2009.
Heikkinen, R. K., Luoto, M., Virkkala, R., and Rainio, K.: Effects of habitat cover, landscape structure and spatial variables on the abundance of birds in an agricultural–forest mosaic, J. Appl. Ecol., 41, 824–835, https://doi.org/10.1111/j.0021-8901.2004.00938.x, 2004.
Heinzelmann, S. M., Bale, N. J., Hopmans, E. C., Sinninghe Damsté, J. S., Schouten, S., and van der Meer, M. T. J.: Critical Assessment of glyco- and phospholipid separation by using silica chromatography, Appl. Environ. Microbiol., 80, 360–365, https://doi.org/10.1128/AEM.02817-13, 2014.
Herlemann, D. P., Labrenz, M., Jürgens, K., Bertilsson, S., Waniek, J. J., and Andersson, A. F.: Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea, ISME J., 5, 1571–1579, https://doi.org/10.1038/ismej.2011.41, 2011.
Herrmann, M., Hädrich, A., and Küsel, K.: Predominance of thaumarchaeal ammonia oxidizer abundance and transcriptional activity in an acidic fen, Environ. Microbiol., 14, 3013–3025, https://doi.org/10.1111/j.1462-2920.2012.02882.x, 2012.
Herrmann, M., Rusznyák, A., Akob, D. M., Schulze, I., Opitz, S., Totsche, K. U., and Küsel, K.: Large Fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds, Appl. Environ. Microbiol., 81, 2384–2394, https://doi.org/10.1128/AEM.03269-14, 2015.
Holmes, D. E., Bond, D. R., and Lovley, D. R.: Electron Transfer by Desulfobulbus propionicus to Fe(III) and Graphite Electrodes, Appl. Environ. Microbiol., 70, 1234–1237, https://doi.org/10.1128/AEM.70.2.1234-1237.2004, 2004.
Hu, B. L., Shen, L. D., Xu, X. Y., and Zheng, P.: Anaerobic ammonium oxidation (anammox) in different natural ecosystems, Biochem. Soc. Trans., 39, 1811–1816, https://doi.org/10.1042/BST20110711, 2011.
Humbert, S., Tarnawski, S., Fromin, N., Mallet, M.-P., Aragno, M., and Zopfi, J.: Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity, ISME J., 4, 450–454, https://doi.org/10.1038/ismej.2009.125, 2009.
Jaeschke, A., Rooks, C., Trimmer, M., Nicholls, J. C., Hopmans, E. C., Schouten, S., and Sinninghe Damsté, J. S.: Comparison of ladderane phospholipid and core lipids as indicators for anaerobic ammonium oxidation (anammox) in marine sediments, Geochim. Cosmochim. Ac., 73, 2077–2088, https://doi.org/10.1016/j.gca.2009.01.013, 2009.
Kaiser, C., Frank, A., Wild, B., Koranda, M., and Richter, A.: Negligible contribution from roots to soil-borne phospholipid fatty acid fungal biomarkers 18:2ω6,9 and 18:1ω9, Soil Biol. Biochem., 42, 1650–1652, https://doi.org/10.1016/j.soilbio.2010.05.019, 2010.
Kalbus, E., Reinstorf, F., and Schirmer, M.: Measuring methods for groundwater – surface water interactions: a review, Hydrol. Earth Syst. Sci., 10, 873–887, https://doi.org/10.5194/hess-10-873-2006, 2006.
Kalvelage, T., Jensen, M. M., Contreras, S., Revsbech, N. P., Lam, P., Günter, M., LaRoche, J., Lavik, G., and Kuypers, M. M. M.: Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones, PLos ONE, 6, e29299, https://doi.org/10.1371/journal.pone.0029299, 2011.
Kandeler, E.: Physiological and biochemical methods for studying soil biota and their function, in: Soil Microbiology, Ecology, and Biochemistry, edited by: Eldor, A. P., Academic Press Elesvier, 53–83, 2007.
Kartal, B., Kuypers, M. M. M., Lavik, G., Schalk, J., Op den Camp, H. J. M., Jetten, M. S. M., and Strous, M.: Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium, Environ. Microbiol., 9, 635–642, https://doi.org/10.1111/j.1462-2920.2006.01183.x, 2007.
Kaur, A., Chaudhary, A., Kaur, A., Choudhary, R., and Kaushik, R.: Phospholipid fatty acid-A bioindicator of environment monitoring and assessment in soil ecosystem, Curr. Sci., 89, 1103–1112, 2005.
Kennedy, M., Reader, S., and Davies, R.: Fatty acid production characteristics of fungi with particular emphasis on gamma linolenic acid production, Biotechnol. and Bioeng., 42, 625–634, https://doi.org/10.1002/bit.260420511, 1993.
Kerger, B. D., Nichols, P. D., Antworth, C. P., Sand, W., Bock, E., Cox, J. C., Langworthy, T. A., and White, D. C.: Signature fatty acids in the polar lipids of acid-producing Thiobacillus spp.: methoxy, cyclopropyl, alpha-hydroxycyclopropyl and branched and normal monoenoic fatty acids, FEMS Microbiol. Ecol., 38, 67–78, https://doi.org/10.1016/0378-1097(86)90144-8, 1986.
Kerger, B. D., Nichols, P. D., Sand, W., Bock, E., and White, D. C.: Association of acid-producing thiobacilli with degradation of concrete: analysis by “signature” fatty acids from the polar lipids and lipopolysaccharide, J. Ind. Microbiol., 2, 63–70, https://doi.org/10.1007/BF01569504, 1987.
Koeve, W. and Kähler, P.: Heterotrophic denitrification vs. autotrophic anammox – quantifying collateral effects on the oceanic carbon cycle, Biogeosciences, 7, 2327–2337, https://doi.org/10.5194/bg-7-2327-2010, 2010.
Kohlhepp, B., Lehmann, R., Seeber, P., Küsel, K., Trumbore, S. E., and Totsche, K. U.: Pedological and hydrogeological setting and subsurface flow structure of the carbonate-rock CZE Hainich in western Thuringia, Germany, Hydrol. Earth Syst. Sci. Discuss., https://doi.org/10.5194/hess-2016-374, in review, 2016.
Kohring, L. L., Ringelberg, D. B., Devereux, R., Stahl, D. A., Mittelman, M. W., and White, D. C.: Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria, FEMS Microbiol. Lett., 119, 303–308, https://doi.org/10.1111/j.1574-6968.1994.tb06905.x, 1994.
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., and Schloss, P. D.: Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform, Appl. Environ. Microbiol., 79, 5112–5120, https://doi.org/10.1128/AEM.01043-13, 2013.
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.
Küsel, K., Totsche, K. U., Trumbore, S. E., Lehmann, R., Steinhäuser, C., and Herrmann, M.: How deep can surface signals be traced in the critical zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape, Front. Earth Sci., 4, 32, https://doi.org/10.3389/feart.2016.00032, 2016.
Kuypers, M. M. M., Sliekers, A. O., Lavik, G., Schmid, M., Jorgensen, B. B., Kuenen, J. G., Sinninghe Damsté, J. S., Strous, M., and Jetten, M. S. M.: Anaerobic ammonium oxidation by anammox bacteria in the Black Sea, Nature, 422, 608–611, https://doi.org/10.1038/nature01472, 2003.
Landeweert, R., Hoffland, E., Finlay, R. D., Kuyper, T. W., and van Breemen, N.: Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals, Trends Ecol. Evol., 16, 248–254, https://doi.org/10.1016/S0169-5347(01)02122-X, 2001.
Landmeyer, J. E., Vroblesky, D. A., and Chapelle, F. H.: Stable carbon isotope evidence of biodegradation zonation in a shallow jet-fuel contaminated aquifer, Environ. Sci. Technol., 30, 1120–1128, https://doi.org/10.1021/es950325t, 1996.
Lipski, A., Spieck, E., Makolla, A., and Altendorf, K.: Fatty acid profiles of nitrite-oxidizing bacteria reflect their phylogenetic heterogeneity, Syst. Appl. Microbiol., 24, 377–384, https://doi.org/10.1078/0723-2020-00049, 2001.
Londry, K. L., Jahnke, L. L., and Des Marais, D. J.: Stable carbon isotope ratios of lipid biomarkers of sulfate-reducing bacteria, Appl. Environ. Microbiol., 70, 745–751, https://doi.org/10.1128/AEM.70.2.745-751.2004, 2004.
Lovley, D. R., Giovannoni, S. J., White, D. C., Champine, J. E., Phillips, E., Gorby, Y. A., and Goodwin, S.: Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals, Arch. Microbiol., 159, 336–344, https://doi.org/10.1007/BF00290916, 1993.
Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., Rattei, T., Sinninghe Damsté, J. S., Spieck, E., Le Paslier, D., and Daims, H.: A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria, P. Natl. Acad. Sci. USA., 107, 13479–13484, https://doi.org/10.1073/pnas.1003860107, 2010.
Ludvigsen, L., Albrechtsen, H. J., Holst, H., and Christensen, T. H.: Correlating phospholipid fatty acids (PLFA) in a landfill leachate polluted aquifer with biogeochemical factors by multivariate statistical methods, FEMS Microbiol. Rev., 20, 447–460, https://doi.org/10.1111/j.1574-6976.1997.tb00329.x, 1997.
Macalady, J., Mack, E., Nelson, D., and Scow, K.: Sediment microbial community structure and mercury methylation in mercury-polluted Clear Lake, California, Appl. Environ. Microbiol., 66, 1479–1488, https://doi.org/10.1128/AEM.66.4.1479-1488.2000, 2000.
Mills, C. T., Dias, R. F., Graham, D., and Mandernack, K. W.: Determination of phospholipid fatty acid structures and stable carbon isotope compositions of deep-sea sediments of the Northwest Pacific, ODP site 1179, Mar. Chem., 98, 197–209, https://doi.org/10.1016/j.marchem.2005.10.001, 2006.
Morgenroth, E., Obermayer, A., Arnold, E., Brühl, A., Wagner, M., and Wilderer, P.: Effect of long-term idle periods on the performance of sequencing batch reactors, Water Sci. Technol., 41, 105–113, 2000.
Myers, R. T., Zak, D. R., White, D. C., and Peacock, A.: Landscape-level patterns of microbial community composition and substrate use in upland forest ecosystems, Soil Sci. Soc. Am. J., 65, 359–367, https://doi.org/10.2136/sssaj2001.652359x, 2001.
Nawaz, A., Purahong, W., Lehmann, R., Herrmann, M., Küsel, K., Totsche, K. U., Buscot, F., and Wubet, T.: Superimposed pristine limestone aquifers with marked hydrochemical differences exhibit distinct fungal communities, Front. Microbiol., 7, 666, https://doi.org/10.3389/fmicb.2016.00666, 2016.
Olsson, P.: Signature fatty acids provide tools for determination of the distribution and interactions of mycorrhizal fungi in soil, FEMS Microbiol. Ecol., 29, 303–310, https://doi.org/10.1016/S0168-6496(99)00021-5, 1999.
O'Neil, R. A., Holmes, D. E., Coppi, M. V., Adams, L. A., Larrahondo, M. J., Ward, J. E., Nevin, K. P., Woodard, T. L., Vrionis, H. A., N'Guessan, A. L., and Lovley, D. R.: Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation, Environ. Microbiol., 10, 1218–1230, https://doi.org/10.1111/j.1462-2920.2007.01537.x, 2008.
Parkes, R. J. and Graham Calder, A.: The cellular fatty acids of three strains of Desulfobulbus, a propionate-utilising sulphate-reducing bacterium, FEMS Microbiol. Lett., 31, 361–363, https://doi.org/0.1016/0378-1097(85)90032-1, 1985.
Pinto, A. J., Marcus, D. N., Ijaz, U. Z., Bautista-de lose Santos, Q. M., Dick, G. J., and Raskin, L.: Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in a drinking water system, mSphere, 1, https://doi.org/10.1128/mSphere.00054-15, 2016.
Prokopenko, M. G., Hirst, M. B., De Brabandere, L., Lawrence, D. J. P., Berelson, W. M., Granger, J., Chang, B. X., Dawson, S., Crane Iii, E. J., Chong, L., Thamdrup, B., Townsend-Small, A., and Sigman, D. M.: Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia, Nature, 500, 194–198, https://doi.org/10.1038/nature12365, 2013.
Qi, B., Fraser, T., Mugford, S., Dobson, G., Sayanova, O., Butler, J., Napier, J. A., Stobart, A. K., and Lazarus, C. M.: Production of very long chain polyunsaturated omega-3 and omega-6 fatty acids in plants, Nat. Biotech., 22, 739–745, https://doi.org/10.1038/nbt972, 2004.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F. O.: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res., 41, D590–D596, https://doi.org/10.1093/nar/gks1219, 2013.
Reardon, J., Foreman, J., and Searcy, R.: New reactants for the colorimetric determination of ammonia, Clin. Chim. Acta, 14, 203–205, https://doi.org/10.1016/0009-8981(66)90120-3, 1966.
Risse-Buhl, U., Herrmann, M., Lange, P., Akob, D. M., Pizani, N., Schönborn, W., Totsche, K. U., and Küsel, K.: Phagotrophic protist diversity in the groundwater of a karstified aquifer–morphological and molecular analysis, J. Eukaryot. Microbiol., 60, 467–479, https://doi.org/10.1111/jeu.12054, 2013.
Roth, V.-N., Dittmar, T., Gaupp, R., and Gleixner, G.: The molecular composition of dissolved organic matter in forest soils as a function of pH and temperature, PLos ONE, 10, e0119188, https://doi.org/10.1371/journal.pone.0119188, 2015.
Ruzicka, S., Edgerton, D., Norman, M., and Hill, T.: The utility of ergosterol as a bioindicator of fungi in temperate soils, Soil Biol. Biochem., 32, 989–1005, https://doi.org/10.1016/S0038-0717(00)00009-2, 2000.
Satoh, H., Nakamura, Y., Ono, H., and Okabe, S.: Effect of oxygen concentration on nitrification and denitrification in single activated sludge flocs, Biotechnol. Bioeng., 83, 604–607, https://doi.org/10.1002/bit.10717, 2003.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., and Weber, C. F.: Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 75, 7537–7541, https://doi.org/10.1128/AEM.01541-09, 2009.
Schneider, T., Keiblinger, K. M., Schmid, E., Sterflinger-Gleixner, K., Ellersdorfer, G., Roschitzki, B., Richter, A., Eberl, L., Zechmeister-Boltenstern, S., and Riedel, K.: Who is who in litter decomposition and quest; metaproteomics reveals major microbial players and their biogeochemical functions, ISME J., 6, 1749–1762, https://doi.org/10.1038/ismej.2012.1, 2012.
Schouten, S., Strous, M., Kuypers, M. M. M., Rijpstra, W. I. C., Baas, M., Schubert, C. J., Jetten, M. S. M., and Sinninghe Damsté, J. S.: Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria, Appl. Environ. Microbiol., 70, 3785–3788, https://doi.org/10.1128/AEM.70.6.3785-3788.2004, 2004.
Seifert, A.-G., Trumbore, S., Xu, X., Zhang, D., and Gleixner, G.: Variable effects of plant colonization on black slate uptake into microbial PLFAs, Geochim. Cosmochim. Ac., 106, 391–403, https://doi.org/10.1016/j.gca.2012.12.011, 2013.
Shinmen, Y., Shimizu, S., Akimoto, K., Kawashima, H., and Yamada, H.: Production of arachidonic acid by Mortierella fungi, Appl. Microbiol. Biotechnol., 31, 11–16, https://doi.org/10.1007/BF02932833, 1989.
Sinninghe Damsté, J. S., Strous, M., Rijpstra, W. I. C., Hopmans, E. C., Geenevasen, J. A. J., van Duin, A. C. T., van Niftrik, L. A., and Jetten, M. S. M.: Linearly concatenated cyclobutane lipids form a dense bacterial membrane, Nature, 419, 708–712, https://doi.org/10.1038/nature01128, 2002.
Sinninghe Damsté, J. S., Rijpstra, W. I. C., Geenevasen, J. A. J., Strous, M., and Jetten, M. S. M.: Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox), FEBS J., 272, 4270–4283, https://doi.org/10.1111/j.1742-4658.2005.04842.x, 2005.
Šmilauer, P. and Lepš, J.: Multivariate analysis of ecological data using CANOCO 5, Cambridge University Press, 2014.
Stevens, T. O. and McKinley, J. P.: Lithoautotrophic microbial ecosystems in deep basalt aquifers, Science, 270, 450, https://doi.org/10.1126/science.270.5235.450, 1995.
Sukenik, A., Kaplan-Levy, R. N., Welch, J. M., and Post, A. F.: Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria), ISME J., 6, 670–679, https://doi.org/10.1038/ismej.2011, 2012.
Teece, M. A., Fogel, M. L., Dollhopf, M. E., and Nealson, K. H.: Isotopic fractionation associated with biosynthesis of fatty acids by a marine bacterium under oxic and anoxic conditions, Org. Geochem., 30, 1571–1579, https://doi.org/10.1016/S0146-6380(99)00108-4, 1999.
Torsvik, V. and Øvreås, L.: Microbial diversity and function in soil: from genes to ecosystems, Curr. Opin. Microbiol., 5, 240–245, https://doi.org/10.1016/S1369-5274(02)00324-7, 2002.
Vainshtein, M., Hippe, H., and Kroppenstedt, R. M.: Cellular fatty acid composition of Desulfovibrio species and its use in classification of sulfate-reducing bacteria, Syst. Appl. Microbiol., 15, 554–566, https://doi.org/10.1016/S0723-2020(11)80115-3, 1992.
van der Meer, M. T. J., Schouten, S., and Sinninghe Damsté, J. S.: The effect of the reversed tricarboxylic acid cycle on the 13C contents of bacterial lipids, Org. Geochem., 28, 527–533, https://doi.org/10.1016/S0146-6380(98)00024-2, 1998.
van der Meer, M. T. J., Schouten, S., van Dongen, B. E., Rijpstra, W. I. C., Fuchs, G., Sinninghe Damsté, J. S., de Leeuw, J. W., and Ward, D. M.: Biosynthetic controls on the 13C contents of organic components in the photoautotrophic bacterium chloroflexus aurantiacus, J. Biol. Chem., 276, 10971–10976, https://doi.org/10.1074/jbc.M009701200, 2001.
van Kessel, M. A. H. J., Speth, D. R., Albertsen, M., Nielsen, P. H., Op den Camp, H. J. M., Kartal, B., Jetten, M. S. M., and Lücker, S.: Complete nitrification by a single microorganism, Nature, 528, 555–559, https://doi.org/10.1038/nature16459, 2015.
van Schöll, L., Kuyper, T., Smits, M., Landeweert, R., Hoffland, E., and Breemen, N.: Rock-eating mycorrhizas: their role in plant nutrition and biogeochemical cycles, Plant Soil, 303, 35–47, https://doi.org/10.1007/s11104-007-9513-0, 2008.
Volkman, J. K., Jeffrey, S. W., Nichols, P. D., Rogers, G. I., and Garland, C. D.: Fatty acid and lipid composition of 10 species of microalgae used in mariculture, J. Exp. Mar. Biol. Ecol., 128, 219–240, https://doi.org/10.1016/0022-0981(89)90029-4, 1989.
Wenk, C. B., Blees, J., Zopfi, J., Veronesi, M., Bourbonnais, A., Schubert, C. J., Niemann, H., and Lehmann, M. F.: Anaerobic ammonium oxidation (anammox) bacteria and sulfide-dependent denitrifiers coexist in the water column of a meromictic south-alpine lake, ASLO, 58, 1–12, https://doi.org/10.4319/lo.2013.58.1.0001, 2013.
White, D. C.: Validation of quantitative analysis for microbial biomass, community structure, and metabolic activity, Adv. Limnol., 31, 1–18, 1988.
White, D. C., Davis, W. M., Nickels, J. S., King, J. D., and Robbie, R. J.: Determination of the seddimentary microbial biomass by extractible lipid phosphate, Oecologia, 40, 51–52, https://doi.org/10.1007/BF00388810, 1979.
Wilkinson, S. G.: Gram-negative bacteria, in: Microbial lipids, edited by: Ratledge, C. and Wilkinson, S. G., Vol. 1. Academic Press, London, 299–488, 1988.
Wisotzky, F.: Angewandte Grundwasserchemie, Hydrogeologie und hydrogeochemische Modellierung, Springer, Berlin, 2011.
Yoshinaga, I., Amano, T., Yamagishi, T., Okada, K., Ueda, S., Sako, Y., and Suwa, Y.: Distribution and diversity of anaerobic ammonium oxidation (Anammox) bacteria in the sediment of a eutrophic freshwater lake, Lake Kitaura, Japan, Microbiol. Environ., 26, 189–197, https://doi.org/10.1264/jsme2.ME10184, 2011.
Zelles, L., Palojärvi, A., Kandeler, E., von Lützow, M., Winter, K., and Bai, Q. Y.: Changes in soil microbial properties and phospholipid fatty acid fractions after chloroform fumigation, Soil Biol. Biochem., 29, 1325–1336, https://doi.org/10.1016/S0038-0717(97)00062-X, 1997.
Zhang, C. L., Li, Y., Ye, Q., Fong, J., Peacock, A. D., Blunt, E., Fang, J., Lovley, D. R., and White, D. C.: Carbon isotope signatures of fatty acids in Geobacter metallireducens and Shewanella algae, Chem. Geol., 195, 17–28, https://doi.org/10.1016/S0009-2541(02)00386-8, 2003.
Zogg, G. P., Zak, D. R., Ringelberg, D. B., White, D. C., MacDonald, N. W., and Pregitzer, K. S.: Compositional and functional shifts in microbial communities due to soil warming, Soil Sci. Soc. Am. J., 61, 475–481, https://doi.org/10.2136/sssaj1997.03615995006100020015x, 1997.
Short summary
We used phospholipid fatty acids (PLFAs) to link specific microbial markers to the spatio-temporal changes of groundwater physico-chemistry. PLFA-based functional groups were directly supported by DNA/RNA results. O2 resulted in increased eukaryotic biomass and abundance of nitrite-oxidizing bacteria but impeded anammox, sulphate-reducing and iron-reducing bacteria. Our study demonstrates the power of PLFA-based approaches to study the nature and activity of microorganisms in pristine aquifers.
We used phospholipid fatty acids (PLFAs) to link specific microbial markers to the...
Altmetrics
Final-revised paper
Preprint