Articles | Volume 14, issue 22
https://doi.org/10.5194/bg-14-5171-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-14-5171-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
20 Nov 2017
Research article |
| 20 Nov 2017
| 20 Nov 2017
Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia
Rebecca Elizabeth Cooper
Aquatic Geomicrobiology, Friedrich Schiller University, 07743 Jena, Germany
Karin Eusterhues
Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University, 07743 Jena, Germany
Carl-Eric Wegner
Aquatic Geomicrobiology, Friedrich Schiller University, 07743 Jena, Germany
Kai Uwe Totsche
Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University, 07743 Jena, Germany
Kirsten Küsel
CORRESPONDING AUTHOR
Aquatic Geomicrobiology, Friedrich Schiller University, 07743 Jena, Germany
The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 07743 Leipzig, Germany
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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
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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.
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
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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.
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
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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.
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
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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
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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
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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.
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
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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.
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
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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.
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
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
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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.
Valérie F. Schwab, Martina Herrmann, Vanessa-Nina Roth, Gerd Gleixner, Robert Lehmann, Georg Pohnert, Susan Trumbore, Kirsten Küsel, and Kai U. Totsche
Biogeosciences, 14, 2697–2714, https://doi.org/10.5194/bg-14-2697-2017, https://doi.org/10.5194/bg-14-2697-2017, 2017
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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.
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
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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.
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
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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.
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
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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
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
Related subject area
Biodiversity and Ecosystem Function: Microbial Ecology & Geomicrobiology
The geothermal gradient shapes microbial diversity and processes in natural-gas-bearing sedimentary aquifers
Microbial methane formation in deep aquifers associated with the sediment burial history at a coastal site
Impact of metabolism and temperature on 2H ∕ 1H fractionation in lipids of the marine bacterium Shewanella piezotolerans WP3
Maximum summer temperatures predict the temperature adaptation of Arctic soil bacterial communities
Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China's estuarine and coastal areas
Aqueous system-level processes and prokaryote assemblages in the ferruginous and sulfate-rich bottom waters of a post-mining lake
Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonia compared to neighbouring oceans and Northern Hemisphere fjords
Determining the hierarchical order by which the variables of sampling period, dust outbreak occurrence, and sampling location can shape the airborne bacterial communities in the Mediterranean basin
The water column of the Yamal tundra lakes as a microbial filter preventing methane emission
Bioerosion and fungal colonization of the invasive foraminiferan Amphistegina lobifera in a Mediterranean seagrass meadow
Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove
Deep maxima of phytoplankton biomass, primary production and bacterial production in the Mediterranean Sea
Haplo-diplontic life cycle expands coccolithophore niche
The composition of endolithic communities in gypcrete is determined by the specific microhabitat architecture
Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences
Cryptic roles of tetrathionate in the sulfur cycle of marine sediments: microbial drivers and indicators
Lake mixing regime selects apparent methane oxidation kinetics of the methanotroph assemblage
The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)
The pH-based ecological coherence of active canonical methanotrophs in paddy soils
Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum
Microbial community composition and abundance after millennia of submarine permafrost warming
Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge
Ecophysiological characteristics of red, green, and brown strains of the Baltic picocyanobacterium Synechococcus sp. – a laboratory study
Factors controlling the community structure of picoplankton in contrasting marine environments
Community composition and seasonal changes of archaea in coarse and fine air particulate matter
Microbial community structure in the western tropical South Pacific
Ecophysiological characterization of early successional biological soil crusts in heavily human-impacted areas
Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)
Plant n-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan
Revisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods
Divergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradient
Uncovering biological soil crusts: carbon content and structure of intact Arctic, Antarctic and alpine biological soil crusts
Antagonistic effects of drought and sand burial enable the survival of the biocrust moss Bryum argenteum in an arid sandy desert
Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea
Effects of temperature on the composition and diversity of bacterial communities in bamboo soils at different elevations
Development of bacterial communities in biological soil crusts along a revegetation chronosequence in the Tengger Desert, northwest China
Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments
Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico)
Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea
Mechanisms of Trichodesmium demise within the New Caledonian lagoon during the VAHINE mesocosm experiment
Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids
Effect of light on photosynthetic efficiency of sequestered chloroplasts in intertidal benthic foraminifera (Haynesina germanica and Ammonia tepida)
Seasonal and size-dependent variations in the phytoplankton growth and microzooplankton grazing in the southern South China Sea under the influence of the East Asian monsoon
Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest
Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China
Redox regime shifts in microbially mediated biogeochemical cycles
Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs
Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota
Diversity and seasonal dynamics of airborne archaea
Methanotrophic activity and diversity of methanotrophs in volcanic geothermal soils at Pantelleria (Italy)
Taiki Katayama, Hideyoshi Yoshioka, Toshiro Yamanaka, Susumu Sakata, and Yasuaki Hanamura
Biogeosciences, 21, 4273–4283, https://doi.org/10.5194/bg-21-4273-2024, https://doi.org/10.5194/bg-21-4273-2024, 2024
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To understand microbial processes in deep sedimentary environments where the majority of Earth’s prokaryotes are found, we investigated the microbial communities in microbial natural-gas-bearing aquifers at temperatures of 38–81°C, situated above nonmicrobial oil-bearing sediments. Our results indicate that microbial carbon and sulfur cycling is driven by geothermal heating, showing previously overlooked geothermal-heat-driven geochemical and microbiological processes in the deep biosphere.
Taiki Katayama, Reo Ikawa, Masaru Koshigai, and Susumu Sakata
Biogeosciences, 20, 5199–5210, https://doi.org/10.5194/bg-20-5199-2023, https://doi.org/10.5194/bg-20-5199-2023, 2023
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Methane produced by microorganisms in subsurface environments may account for a large fraction of global natural gas reserves. To understand how microbial methane is produced during sediment burial history, we examined methane-bearing aquifers in which temperature and salinity increase with depth. Geochemical and microbiological analyses showed that microbial methane is produced at depth, where microbial activity is stimulated by the increased temperature, and subsequently migrates upwards.
Xin Chen, Weishu Zhao, Liang Dong, Huahua Jian, Lewen Liang, Jing Wang, and Fengping Wang
Biogeosciences, 20, 1491–1504, https://doi.org/10.5194/bg-20-1491-2023, https://doi.org/10.5194/bg-20-1491-2023, 2023
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Here, we studied the effects of metabolism and growth temperature on 2H/1H fractionation between fatty acids and growth water (εFA/water) by Shewanella piezotolerans WP3. Our results show that the εFA/water values display considerable variations for cultures grown on different substrates. Combined with metabolic model analysis, our results indicate that the central metabolic pathways exert a fundamental effect on the hydrogen isotope composition of lipids in heterotrophs.
Ruud Rijkers, Mark Dekker, Rien Aerts, and James T. Weedon
Biogeosciences, 20, 767–780, https://doi.org/10.5194/bg-20-767-2023, https://doi.org/10.5194/bg-20-767-2023, 2023
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Bacterial communities in the soils of the Arctic region decompose soil organic matter to CO2 from a large carbon pool. The amount of CO2 released is likely to increase under future climate conditions. Here, we study how temperature sensitive the growth of soil bacterial communties is for 12 sampling sites in the sub to high Arctic. We show that the optimal growth temperature varies between 23 and 34 °C and is influenced by the summer temperature.
Xiaofeng Dai, Mingming Chen, Xianhui Wan, Ehui Tan, Jialing Zeng, Nengwang Chen, Shuh-Ji Kao, and Yao Zhang
Biogeosciences, 19, 3757–3773, https://doi.org/10.5194/bg-19-3757-2022, https://doi.org/10.5194/bg-19-3757-2022, 2022
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This study revealed the distinct distribution patterns of six key microbial functional genes and transcripts related to N2O sources and sinks in four estuaries spanning the Chinese coastline, which were significantly constrained by nitrogen and oxygen concentrations, salinity, temperature, and pH. The community structure of the nosZ clade II was distinctly different from those in the soil and marine OMZs. Denitrification may principally control the N2O emissions patterns across the estuaries.
Daniel A. Petrash, Ingrid M. Steenbergen, Astolfo Valero, Travis B. Meador, Tomáš Pačes, and Christophe Thomazo
Biogeosciences, 19, 1723–1751, https://doi.org/10.5194/bg-19-1723-2022, https://doi.org/10.5194/bg-19-1723-2022, 2022
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We spectroscopically evaluated the gradients of dissolved C, N, S, Fe and Mn in a newly formed redox-stratified lake. The lake features an intermediate redox state between nitrogenous and euxinic conditions that encompasses vigorous open sulfur cycling fuelled by the reducible Fe and Mn stocks of the anoxic sediments. This results in substantial bottom water loads of dissolved iron and sulfate. Observations made in this ecosystem have relevance for deep-time paleoceanographic reconstructions.
Francisco Díaz-Rosas, Catharina Alves-de-Souza, Emilio Alarcón, Eduardo Menschel, Humberto E. González, Rodrigo Torres, and Peter von Dassow
Biogeosciences, 18, 5465–5489, https://doi.org/10.5194/bg-18-5465-2021, https://doi.org/10.5194/bg-18-5465-2021, 2021
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Coccolithophores are important unicellular algae with a calcium carbonate covering that might be affected by ongoing changes in the ocean due to absorption of CO2, warming, and melting of glaciers. We used the southern Patagonian fjords as a natural laboratory, where chemical conditions are naturally highly variable. One variant of a widespread coccolithophore species can tolerate these conditions, suggesting it is highly adaptable, while others were excluded, suggesting they are less adaptable.
Riccardo Rosselli, Maura Fiamma, Massimo Deligios, Gabriella Pintus, Grazia Pellizzaro, Annalisa Canu, Pierpaolo Duce, Andrea Squartini, Rosella Muresu, and Pietro Cappuccinelli
Biogeosciences, 18, 4351–4367, https://doi.org/10.5194/bg-18-4351-2021, https://doi.org/10.5194/bg-18-4351-2021, 2021
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The bacteria carried by winds over the island of Sardinia in the Mediterranean Sea were collected, and their identities were investigated by reading DNA sequences. The sampling period was the factor that most determined the airborne species composition as its role was stronger than that of dust-carrying storms and of the geographical position of the sampling station. The bacteria found when the sampling was performed in September had more species variety than those collected in May.
Alexander Savvichev, Igor Rusanov, Yury Dvornikov, Vitaly Kadnikov, Anna Kallistova, Elena Veslopolova, Antonina Chetverova, Marina Leibman, Pavel A. Sigalevich, Nikolay Pimenov, Nikolai Ravin, and Artem Khomutov
Biogeosciences, 18, 2791–2807, https://doi.org/10.5194/bg-18-2791-2021, https://doi.org/10.5194/bg-18-2791-2021, 2021
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Microbial processes of the methane cycle were studied in four lakes of the central part of the Yamal Peninsula in an area of continuous permafrost: two large, deep lakes and two small and shallow ones. It was found that only small, shallow lakes contributed significantly to the overall diffusive methane emissions from the water surface during the warm summer season. The water column of large, deep lakes on Yamal acted as a microbial filter preventing methane emissions into the atmosphere.
Martin Vohník
Biogeosciences, 18, 2777–2790, https://doi.org/10.5194/bg-18-2777-2021, https://doi.org/10.5194/bg-18-2777-2021, 2021
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Amphistegina lobifera (Foraminifera) has colonized the Mediterranean through the Suez Canal, often forming thick sediments altering the invaded environments. Little is known about postmortem fate of its shells, so I investigated their turnover in the rhizosphere of the dominant Mediterranean seagrass. Most were bioeroded, likely by cyanobacteria and algae but not fungi occurring in the seagrass roots. Bioerosion may counterbalance accumulation of A. lobifera shells in the seabed substrate.
Carolina Oliveira de Santana, Pieter Spealman, Vânia Maria Maciel Melo, David Gresham, Taíse Bomfim de Jesus, and Fabio Alexandre Chinalia
Biogeosciences, 18, 2259–2273, https://doi.org/10.5194/bg-18-2259-2021, https://doi.org/10.5194/bg-18-2259-2021, 2021
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This study highlights the influence of
tidal zonationon the prokaryotic sediment communities of a pristine mangrove forest. We observed that the variability in environmental factors between tidal zones results in differences in structure, diversity, and the potential function of prokaryotic populations. This suggests that further work is needed in determining the role tidal microhabitat biodiversity has in mangroves.
Emilio Marañón, France Van Wambeke, Julia Uitz, Emmanuel S. Boss, Céline Dimier, Julie Dinasquet, Anja Engel, Nils Haëntjens, María Pérez-Lorenzo, Vincent Taillandier, and Birthe Zäncker
Biogeosciences, 18, 1749–1767, https://doi.org/10.5194/bg-18-1749-2021, https://doi.org/10.5194/bg-18-1749-2021, 2021
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The concentration of chlorophyll is commonly used as an indicator of the abundance of photosynthetic plankton (phytoplankton) in lakes and oceans. Our study investigates why a deep chlorophyll maximum, located near the bottom of the upper, illuminated layer develops in the Mediterranean Sea. We find that the acclimation of cells to low light is the main mechanism involved and that this deep maximum represents also a maximum in the biomass and carbon fixation activity of phytoplankton.
Joost de Vries, Fanny Monteiro, Glen Wheeler, Alex Poulton, Jelena Godrijan, Federica Cerino, Elisa Malinverno, Gerald Langer, and Colin Brownlee
Biogeosciences, 18, 1161–1184, https://doi.org/10.5194/bg-18-1161-2021, https://doi.org/10.5194/bg-18-1161-2021, 2021
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Coccolithophores are important calcifying phytoplankton with an overlooked life cycle. We compile a global dataset of marine coccolithophore abundance to investigate the environmental characteristics of each life cycle phase. We find that both phases contribute to coccolithophore abundance and that their different environmental preference increases coccolithophore habitat. Accounting for the life cycle of coccolithophores is thus crucial for understanding their ecology and biogeochemical impact.
María Cristina Casero, Victoria Meslier, Jocelyne DiRuggiero, Antonio Quesada, Carmen Ascaso, Octavio Artieda, Tomasz Kowaluk, and Jacek Wierzchos
Biogeosciences, 18, 993–1007, https://doi.org/10.5194/bg-18-993-2021, https://doi.org/10.5194/bg-18-993-2021, 2021
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Endolithic microhabitats have been described as the last refuge for life in arid and hyper-arid deserts where life has to deal with harsh environmental conditions, such as those in the Atacama Desert. In this work, three different endolithic microhabitats occurring in gypcrete rocks of the Atacama Desert are characterized, using both microscopy and molecular techniques, to show if the architecture of each microhabitat has an influence on the microbial communities inhabiting each of them.
Jeffrey M. Dick, Miao Yu, and Jingqiang Tan
Biogeosciences, 17, 6145–6162, https://doi.org/10.5194/bg-17-6145-2020, https://doi.org/10.5194/bg-17-6145-2020, 2020
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Many natural environments differ in their range of salt concentration (salinity). We developed a metric for the number of water molecules in formation reactions of different proteins and found that it decreases between freshwater and marine systems and also in laboratory experiments with increasing salinity. These results demonstrate a new type of link between geochemical conditions and the chemical composition of microbial communities that can be useful for models of microbial adaptation.
Subhrangshu Mandal, Sabyasachi Bhattacharya, Chayan Roy, Moidu Jameela Rameez, Jagannath Sarkar, Tarunendu Mapder, Svetlana Fernandes, Aditya Peketi, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 17, 4611–4631, https://doi.org/10.5194/bg-17-4611-2020, https://doi.org/10.5194/bg-17-4611-2020, 2020
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Potential roles of polythionates as key sulfur cycle intermediates are less appreciated, apparently because, in most of the natural environments, they do not accumulate to easily detectable levels. Our exploration of the eastern Arabian Sea sediment horizons revealed microbe-mediated production and redox transformations of tetrathionate to be important modules of the in situ sulfur cycle, even as high biotic and abiotic reactivity of this polythionate keeps it hidden from geochemical detection.
Magdalena J. Mayr, Matthias Zimmermann, Jason Dey, Bernhard Wehrli, and Helmut Bürgmann
Biogeosciences, 17, 4247–4259, https://doi.org/10.5194/bg-17-4247-2020, https://doi.org/10.5194/bg-17-4247-2020, 2020
Massimiliano Molari, Felix Janssen, Tobias R. Vonnahme, Frank Wenzhöfer, and Antje Boetius
Biogeosciences, 17, 3203–3222, https://doi.org/10.5194/bg-17-3203-2020, https://doi.org/10.5194/bg-17-3203-2020, 2020
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Industrial-scale mining of deep-sea polymetallic nodules will remove nodules in large areas of the sea floor. We describe community composition of microbes associated with nodules of the Peru Basin. Our results show that nodules provide a unique ecological niche, playing an important role in shaping the diversity of the benthic deep-sea microbiome and potentially in element fluxes. We believe that our findings are highly relevant to expanding our knowledge of the impact associated with mining.
Jun Zhao, Yuanfeng Cai, and Zhongjun Jia
Biogeosciences, 17, 1451–1462, https://doi.org/10.5194/bg-17-1451-2020, https://doi.org/10.5194/bg-17-1451-2020, 2020
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We show that soil pH is a key factor in selecting distinct phylotypes of methanotrophs in paddy soils. Type II methanotrophs dominated the methane oxidation in low-pH soils, while type I methanotrophs were more active in high-pH soils. This pH-based niche differentiation of active methanotrophs appeared to be independent of nitrogen fertilization, but the inhibition of type II methanotrophic rate in low-pH soils by the fertilization might aggravate the emission of methane from paddy soils.
Edwin Sien Aun Sia, Zhuoyi Zhu, Jing Zhang, Wee Cheah, Shan Jiang, Faddrine Holt Jang, Aazani Mujahid, Fuh-Kwo Shiah, and Moritz Müller
Biogeosciences, 16, 4243–4260, https://doi.org/10.5194/bg-16-4243-2019, https://doi.org/10.5194/bg-16-4243-2019, 2019
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Microbial community composition and diversity in freshwater habitats are much less studied compared to marine and soil communities. This study presents the first assessment of microbial communities of the Rajang River, the longest river in Malaysia, expanding our knowledge of microbial ecology in tropical regions. Areas surrounded by oil palm plantations showed the lowest diversity and other signs of anthropogenic impacts included the presence of CFB groups as well as probable algal blooms.
Julia Mitzscherling, Fabian Horn, Maria Winterfeld, Linda Mahler, Jens Kallmeyer, Pier P. Overduin, Lutz Schirrmeister, Matthias Winkel, Mikhail N. Grigoriev, Dirk Wagner, and Susanne Liebner
Biogeosciences, 16, 3941–3958, https://doi.org/10.5194/bg-16-3941-2019, https://doi.org/10.5194/bg-16-3941-2019, 2019
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Permafrost temperatures increased substantially at a global scale, potentially altering microbial assemblages involved in carbon mobilization before permafrost thaws. We used Arctic Shelf submarine permafrost as a natural laboratory to investigate the microbial response to long-term permafrost warming. Our work shows that millennia after permafrost warming by > 10 °C, microbial community composition and population size reflect the paleoenvironment rather than a direct effect through warming.
Blanca Rincón-Tomás, Jan-Peter Duda, Luis Somoza, Francisco Javier González, Dominik Schneider, Teresa Medialdea, Esther Santofimia, Enrique López-Pamo, Pedro Madureira, Michael Hoppert, and Joachim Reitner
Biogeosciences, 16, 1607–1627, https://doi.org/10.5194/bg-16-1607-2019, https://doi.org/10.5194/bg-16-1607-2019, 2019
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Cold-water corals were found at active sites in Pompeia Province (Gulf of Cádiz). Since seeped fluids are harmful for the corals, we approached the environmental conditions that allow corals to colonize carbonates while seepage occurs. As a result, we propose that chemosynthetic microorganisms (i.e. sulfide-oxidizing bacteria and AOM-related microorganisms) play an important role in the colonization of the corals at these sites by feeding on the seeped fluids and avoiding coral damage.
Sylwia Śliwińska-Wilczewska, Agata Cieszyńska, Jakub Maculewicz, and Adam Latała
Biogeosciences, 15, 6257–6276, https://doi.org/10.5194/bg-15-6257-2018, https://doi.org/10.5194/bg-15-6257-2018, 2018
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The present study describes responses of picocyanobacteria (PCY) physiology to different environmental conditions. The cultures were grown under 64 combinations of temperature, irradiance in a photosynthetically active spectrum (PAR), and salinity. The results show that each strain of Baltic Synechococcus sp. behaves differently in respective environmental scenarios. The study develops the knowledge on bloom-forming PCY and reasons further research on the smallest size fraction of phytoplankton.
Jose Luis Otero-Ferrer, Pedro Cermeño, Antonio Bode, Bieito Fernández-Castro, Josep M. Gasol, Xosé Anxelu G. Morán, Emilio Marañon, Victor Moreira-Coello, Marta M. Varela, Marina Villamaña, and Beatriz Mouriño-Carballido
Biogeosciences, 15, 6199–6220, https://doi.org/10.5194/bg-15-6199-2018, https://doi.org/10.5194/bg-15-6199-2018, 2018
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The effect of inorganic nutrients on planktonic assemblages has been traditionally assessed by looking at concentrations rather than fluxes of nutrient supply. However, in near-steady-state systems such as subtropical gyres, nitrate concentrations are kept close to the detection limit due to phytoplankton uptake. Our results, based on direct measurements of nitrate diffusive fluxes, support the key role of nitrate supply in controlling the structure of marine picoplankton communities.
Jörn Wehking, Daniel A. Pickersgill, Robert M. Bowers, David Teschner, Ulrich Pöschl, Janine Fröhlich-Nowoisky, and Viviane R. Després
Biogeosciences, 15, 4205–4214, https://doi.org/10.5194/bg-15-4205-2018, https://doi.org/10.5194/bg-15-4205-2018, 2018
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Archaea as a third domain of life play an important role in soils and marine environments. Although archaea have been found in air as a part of the atmospheric bioaerosol, little is known about their atmospheric dynamics due to their low number and challenging analysis.
Here we present a DNA-based study of airborne archaea, show seasonal dynamics, and discuss anthropogenic influences on the diversity, composition, and abundances of airborne archaea.
Nicholas Bock, France Van Wambeke, Moïra Dion, and Solange Duhamel
Biogeosciences, 15, 3909–3925, https://doi.org/10.5194/bg-15-3909-2018, https://doi.org/10.5194/bg-15-3909-2018, 2018
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We report the distribution of major nano- and pico-plankton groups in the western tropical South Pacific. We found microbial community structure to be typical of highly stratified regions of the open ocean, with significant contributions to total biomass by picophytoeukaryotes, and N2 fixation playing a central role in regulating ecosystem processes. Our results also suggest a reduction in the importance of predation in regulating bacteria populations under nutrient-limited conditions.
Michelle Szyja, Burkhard Büdel, and Claudia Colesie
Biogeosciences, 15, 1919–1931, https://doi.org/10.5194/bg-15-1919-2018, https://doi.org/10.5194/bg-15-1919-2018, 2018
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Ongoing human impact transforms habitats into surfaces lacking higher vegetation. Here, biological soil crusts (BSCs) provide ecosystem services like soil creation and carbon uptake. To understand the functioning of these areas, we examined the physiological capability of early successional BSCs. We found features enabling BSCs to cope with varying climatic stresses. BSCs are important carbon fixers independent of the dominating organism. We provide baseline data for modeling carbon fluxes.
Petr Kotas, Hana Šantrůčková, Josef Elster, and Eva Kaštovská
Biogeosciences, 15, 1879–1894, https://doi.org/10.5194/bg-15-1879-2018, https://doi.org/10.5194/bg-15-1879-2018, 2018
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The soil microbial properties were investigated along altitudinal gradients in the Arctic. Systematic altitudinal shift in MCS resulting in high F / B ratios at the most elevated sites was observed. The changes in composition, size and activity of microbial communities were mainly controlled through the effect of vegetation on edaphic properties and by bedrock chemistry. The upward migration of vegetation due to global warming will likely diminish the spatial variability in microbial properties.
Tung-Yi Huang, Bing-Mu Hsu, Wei-Chun Chao, and Cheng-Wei Fan
Biogeosciences, 15, 1815–1826, https://doi.org/10.5194/bg-15-1815-2018, https://doi.org/10.5194/bg-15-1815-2018, 2018
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The n-alkane in litterfall and the microbial community in litter layer in different habitats of lowland subtropical rainforest were studied. We revealed that the plant vegetation of forest not only dominated the n-alkane input of habitats but also governed the diversity of microbial community of litter layer. In this study, we found that the habitat which had high n-alkane input induced a shift of relative abundance toward phylum of Actinobacteria and the growth of alkB gene contained bacteria.
Jennifer Caesar, Alexandra Tamm, Nina Ruckteschler, Anna Lena Leifke, and Bettina Weber
Biogeosciences, 15, 1415–1424, https://doi.org/10.5194/bg-15-1415-2018, https://doi.org/10.5194/bg-15-1415-2018, 2018
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In our study we analyzed the efficiency of different chlorophyll extraction solvents and investigated the effect of different preparatory steps to determine the optimal extraction method for biological soil crusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest to insert an intermediate shaking step for complete chlorophyll extraction.
Zhiwei Xu, Guirui Yu, Xinyu Zhang, Nianpeng He, Qiufeng Wang, Shengzhong Wang, Xiaofeng Xu, Ruili Wang, and Ning Zhao
Biogeosciences, 15, 1217–1228, https://doi.org/10.5194/bg-15-1217-2018, https://doi.org/10.5194/bg-15-1217-2018, 2018
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Forest types with specific soil conditions supported the development of distinct soil microbial communities with variable functions. Our results indicate that the main controls on soil microbes and functions vary across forest ecosystems in different climatic zones. This information will add value to the modeling of microbial processes and will contribute to carbon cycling on a large scale.
Patrick Jung, Laura Briegel-Williams, Anika Simon, Anne Thyssen, and Burkhard Büdel
Biogeosciences, 15, 1149–1160, https://doi.org/10.5194/bg-15-1149-2018, https://doi.org/10.5194/bg-15-1149-2018, 2018
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Arctic, Antarctic and alpine biological soil crusts (BSCs) are formed by adhesion of soil particles to cyanobacteria. BSCs influence ecosystems services like soil erodibility and chemical cycles. In cold environments degradation rates are low and BSCs increase soil organic carbon through photosynthesis, whereby these soils are considered as CO2 sinks. This work provides a novel method to visualize BSCs with a focus on cyanobacteria and their contribution to soil organic carbon.
Rongliang Jia, Yun Zhao, Yanhong Gao, Rong Hui, Haotian Yang, Zenru Wang, and Yixuan Li
Biogeosciences, 15, 1161–1172, https://doi.org/10.5194/bg-15-1161-2018, https://doi.org/10.5194/bg-15-1161-2018, 2018
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Why can biocrust moss survive and flourish in these habitats when stressed simultaneously by drought and sand burial? A field experiment was conducted to assess the combined effects of the two stressors on Bryum argenteum within biocrust. The two stressors did not exacerbate the single negative effects; their mutually antagonistic effect on the physiological vigor of B. argenteum was found, and it provided an opportunity for it to overcome the two co-occurring stressors in arid sandy ecosystems.
Johanna Maltby, Lea Steinle, Carolin R. Löscher, Hermann W. Bange, Martin A. Fischer, Mark Schmidt, and Tina Treude
Biogeosciences, 15, 137–157, https://doi.org/10.5194/bg-15-137-2018, https://doi.org/10.5194/bg-15-137-2018, 2018
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The activity and environmental controls of methanogenesis (MG) within the sulfate-reducing zone (0–30 cm below the seafloor) were investigated in organic-rich sediments of the seasonally hypoxic Eckernförde Bay, SW Baltic Sea. MG activity was mostly linked to non-competitive substrates. The major controls identified were organic matter availability, C / N, temperature, and O2 in the water column, revealing higher rates in warm, stratified, hypoxic seasons compared to colder, oxygenated seasons.
Yu-Te Lin, Zhongjun Jia, Dongmei Wang, and Chih-Yu Chiu
Biogeosciences, 14, 4879–4889, https://doi.org/10.5194/bg-14-4879-2017, https://doi.org/10.5194/bg-14-4879-2017, 2017
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We evaluated the bacterial composition and diversity of bamboo soils sampled at different elevations and incubated at different temperatures. Soil respiration was greater at higher elevation and temperature. Soil bacterial structure and diversity showed variable under different incubation times and temperatures. Increases in temperature increased soil respiration and consumption of soil soluble carbon and nitrogen, thus influencing the bacterial diversity and structure at different elevations.
Lichao Liu, Yubing Liu, Peng Zhang, Guang Song, Rong Hui, Zengru Wang, and Jin Wang
Biogeosciences, 14, 3801–3814, https://doi.org/10.5194/bg-14-3801-2017, https://doi.org/10.5194/bg-14-3801-2017, 2017
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We studied the development process of bacterial community structure of biological soil crusts (BSCs) along a revegetation chronosequence by Illumina MiSeq sequencing in the Tengger Desert. Our results indicated (1) a shift of bacterial composition related to their function in the crust development process; (2) bacterial diversity and richness consistent with the recovery phase of soil properties; and (3) bacteria as key contributors to the BSC succession process.
Sophie L. Nixon, Jon P. Telling, Jemma L. Wadham, and Charles S. Cockell
Biogeosciences, 14, 1445–1455, https://doi.org/10.5194/bg-14-1445-2017, https://doi.org/10.5194/bg-14-1445-2017, 2017
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Despite their permanently cold and dark characteristics, subglacial environments (glacier ice–sediment interface) are known to harbour active microbial communities. However, the role of microbial iron cycling in these environments is poorly understood. Here we show that subglacial sediments harbour active iron-reducing microorganisms, and they appear to be cold-adapted. These results may have important implications for global biogeochemical iron cycling and export to marine ecosystems.
Estelle Couradeau, Daniel Roush, Brandon Scott Guida, and Ferran Garcia-Pichel
Biogeosciences, 14, 311–324, https://doi.org/10.5194/bg-14-311-2017, https://doi.org/10.5194/bg-14-311-2017, 2017
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Endoliths are a prominent bioerosive component of intertidal marine habitats, traditionally thought to be formed by a few cyanobacteria, algae and fungi. Using molecular techniques, however, we found that endoliths from Mona Island, Puerto Rico, were of high diversity, well beyond that reported in traditional studies. We also found evidence for substrate specialization, in that closely related cyanobacteria seem to have diversified to specialize recurrently to excavate various mineral substrates
Yong Wang, Tie Gang Li, Meng Ying Wang, Qi Liang Lai, Jiang Tao Li, Zhao Ming Gao, Zong Ze Shao, and Pei-Yuan Qian
Biogeosciences, 13, 6405–6417, https://doi.org/10.5194/bg-13-6405-2016, https://doi.org/10.5194/bg-13-6405-2016, 2016
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Mild eruption of hydrothermal solutions on deep-sea benthic floor can produce anhydrite crystal layers, where microbes are trapped and preserved for a long period of time. These embedded original inhabitants will be biomarkers for the environment when the hydrothermal eruption occurred. This study discovered a thick anhydrite layer in a deep-sea brine pool in the Red Sea. Oil-degrading bacteria were revealed in the crystals with genomic and microscopic evidence.
Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank
Biogeosciences, 13, 4187–4203, https://doi.org/10.5194/bg-13-4187-2016, https://doi.org/10.5194/bg-13-4187-2016, 2016
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The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.
Lotta Purkamo, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse Ahonen, Ilmo Kukkonen, and Merja Itävaara
Biogeosciences, 13, 3091–3108, https://doi.org/10.5194/bg-13-3091-2016, https://doi.org/10.5194/bg-13-3091-2016, 2016
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The microbial communities of up to 2.3 km depth of Precambrian crystalline bedrock fractures share features with serpenization-driven microbial communities in alkaline springs and subsurface aquifers. This study suggests that phylotypes belonging to Burkholderiales and Clostridia are possible "keystone microbial species" in Outokumpu deep biosphere. Many of the keystone species belong to the rare biosphere with low abundance but a wide range of carbon substrates and a capacity for H2 oxidation.
Thierry Jauffrais, Bruno Jesus, Edouard Metzger, Jean-Luc Mouget, Frans Jorissen, and Emmanuelle Geslin
Biogeosciences, 13, 2715–2726, https://doi.org/10.5194/bg-13-2715-2016, https://doi.org/10.5194/bg-13-2715-2016, 2016
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Some benthic foraminifera can incorporate chloroplasts from microalgae. We investigated chloroplast functionality of two benthic foraminifera (Haynesina germanica & Ammonia tepida) exposed to different light levels. Only H. germanica was capable of using the kleptoplasts, showing net oxygen production. Chloroplast functionality time was longer in darkness (2 weeks) than at high light (1 week). Kleptoplasts are unlikely to be completely functional, thus requiring continuous chloroplast resupply.
L. Zhou, Y. Tan, L. Huang, Z. Hu, and Z. Ke
Biogeosciences, 12, 6809–6822, https://doi.org/10.5194/bg-12-6809-2015, https://doi.org/10.5194/bg-12-6809-2015, 2015
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We observed that phytoplankton biomass and growth rate (μ), microzooplankton grazing rate (m), and coupling (correlation) between the μ and m significantly varied between the summer and winter, and microzooplankton selectively grazed more on the larger-sized phytoplankton, and a low grazing impact on phytoplankton (m/μ < 50%) in the SSCS. The salient seasonal variations in μ and m, and their coupling were closely related to environmental variables under the influence of the East Asian monsoon.
A. M. Womack, P. E. Artaxo, F. Y. Ishida, R. C. Mueller, S. R. Saleska, K. T. Wiedemann, B. J. M. Bohannan, and J. L. Green
Biogeosciences, 12, 6337–6349, https://doi.org/10.5194/bg-12-6337-2015, https://doi.org/10.5194/bg-12-6337-2015, 2015
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Fungi in the atmosphere can affect precipitation by nucleating the formation of clouds and ice. This process is important over the Amazon rainforest where precipitation is limited by the types and amount of airborne particles. We found that the total and metabolically active fungi communities were dominated by different taxonomic groups, and the active community unexpectedly contained many lichen fungi, which are effective at nucleating ice.
W. Y. Dong, X. Y. Zhang, X. Y. Liu, X. L. Fu, F. S. Chen, H. M. Wang, X. M. Sun, and X. F. Wen
Biogeosciences, 12, 5537–5546, https://doi.org/10.5194/bg-12-5537-2015, https://doi.org/10.5194/bg-12-5537-2015, 2015
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We examined how N and P addition influenced soil microbial community composition and enzyme activities in subtropical China. The results showed that C and N cycling enzymes were more sensitive to nutrient additions than P cycling enzymes and Gram-positive bacteria were most closely related to soil nutrient cycling enzymes. Combined additions of N and P fertilizer are recommended to promote soil fertility and microbial activity in this kind of plantation.
T. Bush, I. B. Butler, A. Free, and R. J. Allen
Biogeosciences, 12, 3713–3724, https://doi.org/10.5194/bg-12-3713-2015, https://doi.org/10.5194/bg-12-3713-2015, 2015
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Despite their global importance, redox reactions mediated by microorganisms are often crudely represented in biogeochemical models. We show that including the dynamics of microbial growth in such a model can cause sudden shifts between redox states in response to an environmental change. We identify the conditions required for these redox regime shifts, and predict that they are likely in the modern day sulfur and nitrogen cycles, and potentially the iron cycle in the ancient ocean.
P. K. Gao, G. Q. Li, H. M. Tian, Y. S. Wang, H. W. Sun, and T. Ma
Biogeosciences, 12, 3403–3414, https://doi.org/10.5194/bg-12-3403-2015, https://doi.org/10.5194/bg-12-3403-2015, 2015
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Microbial communities in injected water are expected to have a significant influence on those of reservoir strata in long-term water-flooding petroleum reservoirs. We thereby investigated the similarities and differences in microbial communities in water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous reservoir and a heterogeneous reservoir using high-throughput sequencing.
V. Marteinsson, A. Klonowski, E. Reynisson, P. Vannier, B. D. Sigurdsson, and M. Ólafsson
Biogeosciences, 12, 1191–1203, https://doi.org/10.5194/bg-12-1191-2015, https://doi.org/10.5194/bg-12-1191-2015, 2015
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Colonization of life on Surtsey has been observed systematically since the formation of the island. Microbial colonization and the influence of associate vegetation and birds on viable counts of environmental bacteria at the surface of the Surtsey was explored for the first time in diverse surface soils. Also, hot subsurface samples deep in the centre of this volcanic island were collected. Both uncultivated bacteria and archaea were found in the subsurface samples collected below 145 m.
J. Fröhlich-Nowoisky, C. Ruzene Nespoli, D. A. Pickersgill, P. E. Galand, I. Müller-Germann, T. Nunes, J. Gomes Cardoso, S. M. Almeida, C. Pio, M. O. Andreae, R. Conrad, U. Pöschl, and V. R. Després
Biogeosciences, 11, 6067–6079, https://doi.org/10.5194/bg-11-6067-2014, https://doi.org/10.5194/bg-11-6067-2014, 2014
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We have investigated the presence of archaea as well as their amoA gene diversity in aerosol particles collected over 1 year in central Europe and found that, within the 16S and amoA gene, Thaumarchaeota prevail and experience a diversity peak in fall, while only few Euryarchaeota were detected primarily in spring. We also compared the results with airborne archaea from Cape Verde and observe that the proportions of Euryarchaeota seem to be enhanced in coastal air compared to continental air.
A. L. Gagliano, W. D'Alessandro, M. Tagliavia, F. Parello, and P. Quatrini
Biogeosciences, 11, 5865–5875, https://doi.org/10.5194/bg-11-5865-2014, https://doi.org/10.5194/bg-11-5865-2014, 2014
Cited articles
Adhikari, D., Zhao, Q., Das, K., Mejia, J., Huang, R., Wang, X., Poulson, S. R., Tang, Y., Roden, E. E., and Yang, Y.: Dynamics of ferrihydrite-bound organic carbon during microbial Fe reduction, Geochim. Cosmochim. Ac., 212, 221–233, https://doi.org/10.1016/j.gca.2017.06.017, 2017.
Alves, M. N., Fernandes, A. P., Salgueiro, C. A., and Paquete, C. M.: Unraveling the electron transfer processes of a nanowire protein from Geobacter sulfurreducens, BBA-Bioenerg., 1857, 7–13, https://doi.org/10.1016/j.bbabio.2015.09.010, 2016.
Amstaetter, K., Borch, T., and Kappler, A.: Influence of humic acid imposed changes of ferrihydrite aggregation on microbial Fe(III) reduction, Geochim. Cosmochim. Ac., 85, 326–341, https://doi.org/10.1016/j.gca.2012.02.003, 2012.
Benjamini, Y. and Hochberg, Y.: Controlling the false discovery rate: A Practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B, 57, 289–300, 1995.
Bigham, J. M., Fitzpatrick, R. W., and Schulze, D. G.: Iron oxides in: Soil Mineralology with Environmental Applications, in: SSSA Book Set No. 7, edited by: Dixon, D. G. and Schulze, J. B., Soil Science Society of America, Madison, WI, 2002.
Blodau, C., Basiliko, N., and Moore, T. R.: Carbon turnover in peatland mesocosms exposed to different water table levels, Biogeochemistry, 67, 331–351, https://doi.org/10.1023/B:BIOG.0000015788.30164.e2, 2004.
Boesen, T. and Nielsen, L. P.: Molecular dissection of bacterial nanowires, MBio, 4, e00270-13, https://doi.org/10.1128/mBio.00270-13, 2013.
Borch, T., Kretzschmar, R., Kappler, A., Van Cappellen, P., Ginder-Vogel, M., Voegelin, A., and Campbell, K.: Biogeochemical Redox Processes and their Impact on Contaminant Dynamics, Environ. Sci. Technol., 44, 15–23, https://doi.org/10.1021/es9026248, 2010.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R.: QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335–336, https://doi.org/10.1038/nmeth.f.303, 2010.
Chao, A.: Nonparametric estimation of the number of classes in a population, Source Scand. J. Stat., 11, 265–270, 1984.
Cismasu, A. C., Michel, F. M., Tcaciuc, A. P., Tyliszczak, T., and Brown Jr., G. E.: Composition and structural aspects of naturally occurring ferrihydrite, C. R. Geosci., 343, 210–218, https://doi.org/10.1016/j.crte.2010.11.001, 2011.
Coates, J. D., Cole, K. A., Chakraborty, R., O 'connor, S. M., and Achenbach, L. A.: Diversity and Ubiquity of Bacteria Capable of Utilizing Humic Substances as Electron Donors for Anaerobic Respiration, Appl. Environ. Microb., 68, 2445–2452, https://doi.org/10.1128/AEM.68.5.2445-2452.2002, 2002.
Cooper, R. E., Goff, J. L., Reed, B. C., Sekar, R., and Di Christina, T. J.: Breathing Iron: Molecular Mechanism of Microbial Iron Reduction by Shewanella oneidensis, in: Manual of Environmental Microbiology, 4th edition, 5.2.1-1–5.2.1-13, American Society of Microbiology, 2016.
Cornell, R. M. and Schwertmann, U.: The Iron Oxides, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG, 1–664, 2003.
Daims, H., Brühl, A., Amann, R., Schleifer, K.-H., and Wagner, M.: The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set, Syst. Appl. Microbiol., 22, 434–444, https://doi.org/10.1016/S0723-2020(99)80053-8, 1999.
Davison, W.: Iron and manganese in lakes, Earth-Sci. Rev., 34, 119–163, https://doi.org/10.1016/0012-8252(93)90029-7, 1993.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460–2461, https://doi.org/10.1093/bioinformatics/btq461, 2010.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R.: UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194, https://doi.org/10.1093/bioinformatics/btr381, 2011.
El-Naggar, M. Y., Wanger, G., Leung, K. M., Yuzvinsky, T. D., Southam, G., Yang, J., Lau, W. M., Nealson, K. H., and Gorby, Y. A.: Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1, P. Natl. Acad. Sci. USA, 107, 18127–18131, https://doi.org/10.1073/pnas.1004880107, 2010.
Eusterhues, K., Rumpel, C., and Kogel-Knabner, I.: Organo-mineral associations in sandy acid forest soils: importance of specific surface area, iron oxides and micropores, Eur. J. Soil Sci., 56, 753–763, https://doi.org/10.1111/j.1365-2389.2005.00710.x, 2005.
Eusterhues, K., Wagner, F. E., Häusler, W., Hanzlik, M., Knicker, H., Totsche, K. U., Kögel-Knabner, I., and Schwertmann, U.: Characterization of ferrihydrite-soil organic matter coprecipitates by X-ray diffraction and Mössbauer spectroscopy, Environ. Sci. Technol., 42, 7891–7897, 2008.
Eusterhues, K., Hädrich, A., Neidhardt, J., Küsel, K., Keller, T. F., Jandt, K. D., and Totsche, K. U.: Reduction of ferrihydrite with adsorbed and coprecipitated organic matter: microbial reduction by Geobacter bremensis vs. abiotic reduction by Na-dithionite, Biogeosciences, 11, 4953–4966, https://doi.org/10.5194/bg-11-4953-2014, 2014.
Gorby, Y. A., Yanina, S., McLean, J. S., Rosso, K. M., Moyles, D., Dohnalkova, A., Beveridge, T. J., Chang, I. S., Kim, B. H., Kim, K. S., Culley, D. E., Reed, S. B., Romine, M. F., Saffarini, D. A., Hill, E. A., Shi, L., Elias, D. A., Kennedy, D. W., Pinchuk, G., Watanabe, K., Ishii, S., Logan, B., Nealson, K. H., and Fredrickson, J. K.: Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms, P. Natl. Acad. Sci. USA, 103, 11358–11363, https://doi.org/10.1073/pnas.0604517103, 2006.
Hansel, C. M., Benner, S. G., Nico, P., and Fendorf, S.: Structural constraints of ferric (hydr)oxides on dissimilatory iron reduction and the fate of Fe(II), Geochim. Cosmochim. Ac., 68, 3217–3229, https://doi.org/10.1016/j.gca.2003.10.041, 2004.
Hausmann, B., Knorr, K.-H., Schreck, K., Tringe, S. G., Glavina del Rio, T., Loy, A., and Pester, M.: Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms, ISME J., 10, 2365–2375, https://doi.org/10.1038/ismej.2016.42, 2016.
Henneberry, Y. K., Kraus, T. E. C., Nico, P. S., and Horwath, W. R.: Structural stability of coprecipitated natural organic matter and ferric iron under reducing conditions, Org. Geochem., 48, 81–89, https://doi.org/10.1016/j.orggeochem.2012.04.005, 2012.
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.
Himmelheber, D. W., Thomas, S. H., Löffler, F. E., Taillefert, M., and Hughes, J. B.: Microbial Colonization of an In Situ Sediment Cap and Correlation to Stratified Redox Zones, Environ. Sci. Technol., 43, 66–74, https://doi.org/10.1021/es801834e, 2009.
Hori, T., Müller, A., Igarashi, Y., Conrad, R., and Friedrich, M. W.: Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing, ISME J., 4, 267–278, https://doi.org/10.1038/ismej.2009.100, 2010.
Hori, T., Aoyagi, T., Itoh, H., Narihiro, T., Oikawa, A., Suzuki, K., Ogata, A., Friedrich, M. W., Conrad, R., and Kamagata, Y.: Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments, Front. Microbiol., 6, 386, https://doi.org/10.3389/fmicb.2015.00386, 2015.
International Centre for Diffraction Data (ICDD): PDF-4/Organics 2011 (Database), edited by: Dr. Soorya Kabekkodu, Newtown Square, PA, USA, 2010.
Jambor, J. L. and Dutrizac, J. E.: Occurrence and Constitution of Natural and Synthetic Ferrihydrite, a Widespread Iron Oxyhydroxide, Chem. Rev., 98, 2549–2586, https://doi.org/10.1021/CR970105T, 1998.
Jiang, J. and Kappler, A.: Kinetics of Microbial and Chemical Reduction of Humic Substances: Implications for Electron Shuttling, Environ. Sci. Technol., 42, 3563–3569, https://doi.org/10.1021/es7023803, 2008.
Jones, A. M., Collins, R. N., Rose, J., and Waite, T. D.: The effect of silica and natural organic matter on the Fe(II)-catalysed transformation and reactivity of Fe(III) minerals, Geochim. Cosmochim. Ac., 73, 4409–4422, https://doi.org/10.1016/j.gca.2009.04.025, 2009.
Kaiser, K. and Zech, W.: Dissolved organic matter sorption by mineral constituents of subsoil clay fractions, J. Plant Nutr. Soil Sci., 163, 531–535, https://doi.org/10.1002/1522-2624(200010)163:5<531::AID-JPLN531>3.0.CO;2-N, 2000.
Kappler, A., Benz, M., Schink, B., and Brune, A.: Electron shuttling via humic acids in microbial iron(III) reduction in a freshwater sediment, FEMS Microbiol. Ecol., 47, 85–92, https://doi.org/10.1016/S0168-6496(03)00245-9, 2004.
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., and Glöckner, F. O.: Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucleic Acids Res., 41, e1, https://doi.org/10.1093/nar/gks808, 2013.
Klüpfel, L., Piepenbrock, A., Kappler, A., and Sander, M.: Humic substances as fully regenerable electron acceptors in recurrently anoxic environments, Nat. Geosci., 7, 195–200, https://doi.org/10.1038/ngeo2084, 2014.
Knorr, K.-H. and Blodau, C.: Impact of experimental drought and rewetting on redox transformations and methanogenesis in mesocosms of a northern fen soil, Soil Biol. Biochem., 41, 1187–1198, https://doi.org/10.1016/j.soilbio.2009.02.030, 2009.
Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., and Ley, R. E.: A Guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets, edited by: Eisen, J. A., PLoS Comput. Biol., 9, 1–16, https://doi.org/10.1371/journal.pcbi.1002863, 2013.
Kotloski, N. J. and Gralnick, J. A.: Flavin Electron Shuttles Dominate Extracellular Electron Transfer by Shewanella oneidensis, mBio, 4, e00553-12, https://doi.org/10.1128/mBio.00553-12, 2013.
Kraemer, S. M.: Iron oxide dissolution and solubility in the presence of siderophores, Aquat. Sci., 6604, 3–18, https://doi.org/10.1007/s00027-003-0690-5, 2004.
Küsel, K., Blöthe, M., Schulz, D., Reiche, M., and Drake, H. L.: Microbial reduction of iron and porewater biogeochemistry in acidic peatlands, Biogeosciences, 5, 1537–1549, https://doi.org/10.5194/bg-5-1537-2008, 2008.
Lalonde, K., Mucci, A., Ouellet, A., and Gélinas, Y.: Preservation of organic matter in sediments promoted by iron, Nature, 483, 198–200, https://doi.org/10.1038/nature10855, 2012.
Lehmann, J. and Kleber, M.: The contentious nature of soil organic matter, Nature, 528, 60–68, https://doi.org/10.1038/nature16069, 2015.
Lentini, C. J., Wankel, S. D., and Hansel, C. M.: Enriched iron(III)-reducing bacterial communities are shaped by carbon substrate and iron oxide mineralogy, Front. Microbiol., 3, 1–19, https://doi.org/10.3389/fmicb.2012.00404, 2012.
Love, M. I., Huber, W., and Anders, S.: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, https://doi.org/10.1186/s13059-014-0550-8, 2014.
Lovley, D. R., Woodward, J. C., and Chapelle, F. H.: Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands, Nature, 370, 128–131, https://doi.org/10.1038/370128a0, 1994.
Lovley, D. R., Coates, J. D., Blunt-Harris, E. L., Phillips, E. J. P., and Woodward, J. C.: Humic substances as electron acceptors for microbial respiration, Nature, 382, 445–448, https://doi.org/10.1038/382445a0, 1996.
Lovley, D. R., Fraga, J. L., Coates, J. D., and Blunt-Harris, E. L.: Humics as an electron donor for anaerobic respiration, Environ. Microbiol., 1, 89–98, https://doi.org/10.1046/j.1462-2920.1999.00009.x, 1999.
Loy, A., Lehner, A., Lee, N., Adamczyk, J., Meier, H., Ernst, J., Schleifer, K.-H., and Wagner, M.: Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment, Appl. Environ. Microb., 68, 5064–5081, 2002.
Loy, A., Küsel, K., Lehner, A., Drake, H. L., and Wagner, M.: Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages, Appl. Environ. Microb., 70, 6998–7009, https://doi.org/10.1128/AEM.70.12.6998-7009.2004, 2004.
Malvankar, N. S., Vargas, M., Nevin, K. P., Franks, A. E., Leang, C., Kim, B.-C., Inoue, K., Mester, T., Covalla, S. F., Johnson, J. P., Rotello, V. M., Tuominen, M. T., and Lovley, D. R.: Tunable metallic-like conductivity in microbial nanowire networks, Nat. Nanotechnol., 6, 573–579, https://doi.org/10.1038/NNANO.2011.119, 2011.
Marsili, E., Baron, D. B., Shikhare, I. D., Coursolle, D., Gralnick, J. A., and Bond, D. R.: Shewanella secretes flavins that mediate extracellular electron transfer, P. Natl. Acad. Sci. USA, 105, 3968–3973, https://doi.org/10.1073/pnas.0710525105, 2008.
Martin, M.: Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, 17, 10–12, https://doi.org/10.14806/ej.17.1.200, 2011.
McMurdie, P. J. and Holmes, S.: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible, PLoS Comput. Biol., available from: http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003531&type=printable (last access: 1 September 2017), 2014.
McMurdie, P. J., Holmes, S., Kindt, R., Legendre, P., and O'Hara, R.: phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data, edited by: Watson, M., PLoS One, 8, e61217, https://doi.org/10.1371/journal.pone.0061217, 2013.
Melton, E. D., Swanner, E. D., Behrens, S., Schmidt, C., and Kappler, A.: The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle, Nat. Rev. Microbiol., 12, 797–808, https://doi.org/10.1038/nrmicro3347, 2014.
Mikutta, C., Mikutta, R., Bonneville, S., Wagner, F., Voegelin, A., Christl, I., and Kretzschmar, R.: Synthetic coprecipitates of exopolysaccharides and ferrihydrite. Part I: Characterization, Geochim. Cosmochim. Ac., 72, 1111–1127, https://doi.org/10.1016/j.gca.2007.11.035, 2008.
Myers, C. R. and Nealson, K. H.: Bacterial Manganese Reduction and Growth with Manganese Oxide as the Sole Electron Acceptor, Science, 240, 1319–1321, https://doi.org/10.1126/science.240.4857.1319, 1988.
Myers, C. R. and Nealson, K. H.: Respiration-linked proton translocation coupled to anaerobic reduction of manganese(IV) and iron(III) in Shewanella putrefaciens MR-1, J. Bacteriol., 172, 6232–6238, 1990.
Narvekar, S. P., Ritschel, T., and Totsche, K. U.: Colloidal stability and mobility of extracellular polymeric substance amended hematite nanoparticles, Vadose Zone J., 16, 8, https://doi.org/10.2136/vzj2017.03.0063, 2017.
Nevin, K. P. and Lovley, D. R.: Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens., Appl. Environ. Microb., 66, 2248–2251, https://doi.org/10.1128/AEM.66.5.2248-2251.2000, 2000.
Nevin, K. P. and Lovley, D. R.: Mechanisms for Fe(III) Oxide Reduction in Sedimentary Environments, Geomicrobiol. J., 19, 141–159, https://doi.org/10.1080/01490450252864253, 2002.
Newman, D. K. and Kolter, R.: A role for excreted quinones in extracellular electron transfer, Nature, 405, 94–97, https://doi.org/10.1038/35011098, 2000.
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P., Stevens, H., Szöcs, E., and Wagner, H. H.: vegan: Community Ecology Package. Ordination methods, diversity analysis and other functions for community and vegetation ecologists, Version 2.4-3, 1–293, 2017.
Pédrot, M., Boudec, A. Le, Davranche, M., Dia, A., and Henin, O.: How does organic matter constrain the nature, size and availability of Fe nanoparticles for biological reduction?, J. Colloid Interf. Sci., 359, 75–85, https://doi.org/10.1016/j.jcis.2011.03.067, 2011.
Pester, M., Bittner, N., Deevong, P., Wagner, M., and Loy, A.: A “rare biosphere” microorganism contributes to sulfate reduction in a peatland, ISME J., 4, 1591–1602, https://doi.org/10.1038/ismej.2010.75, 2010.
Pester, M., Knorr, K.-H., Friedrich, M. W., Wagner, M., and Loy, A.: Sulfate-reducing microorganisms in wetlands – fameless actors in carbon cycling and climate change, Front. Microbiol., 3, 72, https://doi.org/10.3389/fmicb.2012.00072, 2012.
Piepenbrock, A., Schröder, C., and Kappler, A.: Electron Transfer from Humic Substances to Biogenic and Abiogenic Fe(III) Oxyhydroxide Minerals, Environ. Sci. Technol., 48, 1656–1664, https://doi.org/10.1021/es404497h, 2014.
Poggenburg, C., Mikutta, R., Sander, M., Schippers, A., Marchanka, A., Dohrmann, R., and Guggenberger, G.: Microbial reduction of ferrihydrite-organic matter coprecipitates by Shewanella putrefaciens and Geobacter metallireducens in comparison to mediated electrochemical reduction, Chem. Geol., 447, 133–147, https://doi.org/10.1016/j.chemgeo.2016.09.031, 2016.
R Development Core Team: R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, available at: http://www.r-project.org (last access: 16 November 2017), 2008.
Reguera, G., McCarthy, K. D., Mehta, T., Nicoll, J. S., Tuominen, M. T., and Lovley, D. R.: Extracellular electron transfer via microbial nanowires, Nature, 435, 1098–1101, https://doi.org/10.1038/nature03661, 2005.
Reiche, M., Torburg, G., and Küsel, K.: Competition of Fe(III) reduction and methanogenesis in an acidic fen, FEMS Microbiol. Ecol., 65, 88–101, https://doi.org/10.1111/j.1574-6941.2008.00523.x, 2008.
Roden, E. E., Kappler, A., Bauer, I., Jiang, J., Paul, A., Stoesser, R., Konishi, H., and Xu, H.: Extracellular electron transfer through microbial reduction of solid-phase humic substances, Nat. Geosci., 3, 417–421, https://doi.org/10.1038/ngeo870, 2010.
Rognes, T., Flouri, T., Nichols, B., Quince, C., and Mahé, F.: VSEARCH: a versatile open source tool for metagenomics, Peer J., 4, e2584, https://doi.org/10.7717/peerj.2584, 2016.
Royer, R. A., Burgos, W. D., Fisher, A. S., Jeon, B.-H., Unz, R. F., and Dempsey, B. A.: Enhancement of Hematite Bioreduction by Natural Organic Matter, Environ. Sci. Technol., 36, 2897–2904, https://doi.org/10.1021/ES015735Y, 2002.
Schmieder, R. and Edwards, R.: Quality control and preprocessing of metagenomic datasets, Bioinformatics, 27, 863–864, https://doi.org/10.1093/bioinformatics/btr026, 2011.
Schwertmann, U., Wagner, F., and Knicker, H.: Ferrihydrite–Humic Associations, Soil Sci. Soc. Am. J., 69, 1009, https://doi.org/10.2136/sssaj2004.0274, 2005.
Scott, D. T., McKnight, D. M., Blunt-Harris, E. L., Kolesar, S. E., and Lovley, D. R.: Quinone Moieties Act as Electron Acceptors in the Reduction of Humic Substances by Humics-Reducing Microorganisms, 32, 2986–2989, https://doi.org/10.1021/ES980272Q, 1998.
Shannon, C. E.: A Mathematical theory of communication, Bell Syst. Tech. J., 27, 379–423, https://doi.org/10.1002/j.1538-7305.1948.tb01338.x, 1948.
Shelobolina, E. S., Nevin, K. P., Blakeney-Hayward, J. D., Johnsen, C. V., Plaia, T. W., Krader, P., Woodard, T., Holmes, D. E., Van Praagh, C. G., and Lovley, D. R.: Geobacter pickeringii sp. nov., Geobacter argillaceus sp. nov. and Pelosinus fermentans gen. nov., sp. nov., isolated from subsurface kaolin lenses, Int. J. Syst. Evol. Microbiol., 57, 126–135, https://doi.org/10.1099/ijs.0.64221-0, 2007.
Shi, L., Rosso, K. M., Clarke, T. A., Richardson, D. J., Zachara, J. M., and Fredrickson, J. K.: Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella Oneidensis MR-1, Front. Microbiol., 3, 50, https://doi.org/10.3389/fmicb.2012.00050, 2012.
Shimizu, M., Zhou, J., Schröder, C., Obst, M., Kappler, A., and Borch, T.: Dissimilatory Reduction and Transformation of Ferrihydrite-Humic Acid Coprecipitates, Environ. Sci. Technol., 47, 13375–13384, https://doi.org/10.1021/es402812j, 2013.
Stumm, W. and Sulzberger, B.: The cycling of iron in natural environments: Considerations based on laboratory studies of heterogeneous redox processes, Geochim. Cosmochim. Ac., 56, 3233–3257, https://doi.org/10.1016/0016-7037(92)90301-X, 1992.
Tamura, H., Goto, K., Yotsuyanagi, T., and Nagayama, M.: Spectrophotometric determination of iron(II) with 1,10-phenanthroline in the presence of large amounts of iron(III), Talanta, 21, 314–318, https://doi.org/10.1016/0039-9140(74)80012-3, 1974.
Torn, M. S., Trumbore, S. E., Chadwick, O. A., Vitousek, P. M., and Hendricks, D. M.: Mineral control of soil organic carbon storage and turnover, Nature, 389, 170–173, https://doi.org/10.1038/38260, 1997.
Venkateswaran, K., Moser, D. P., Dollhopf, M. E., Lies, D. P., Saffarini, D. A., MacGregor, B. J., Ringelberg, D. B., White, D. C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K. H.: Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov., Int. J. Syst. Bacteriol., 49, 705–724, https://doi.org/10.1099/00207713-49-2-705, 1999.
Vindedahl, A. M., Strehlau, J. H., Arnold, W. A., and Penn, R. L.: Organic matter and iron oxide nanoparticles: aggregation, interactions, and reactivity, Environ. Sci. Nano, 3, 494–505, https://doi.org/10.1039/C5EN00215J, 2016.
von Canstein, H., Ogawa, J., Shimizu, S., and Lloyd, J. R.: Secretion of flavins by Shewanella species and their role in extracellular electron transfer, Appl. Environ. Microb., 74, 615–623, https://doi.org/10.1128/AEM.01387-07, 2008.
Weber, K. A., Urrutia, M. M., Churchill, P. F., Kukkadapu, R. K., and Roden, E. E.: Anaerobic redox cycling of iron by freshwater sediment microorganisms, Environ. Microbiol., 8, 100–113, https://doi.org/10.1111/j.1462-2920.2005.00873.x, 2006a.
Weber, K. A., Achenbach, L. A., and Coates, J. D.: Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction, Nat. Rev. Microbiol., 4, 752–764, https://doi.org/10.1038/nrmicro1490, 2006b.
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.
In this study we show increasing organic matter (OM) content on ferrihydrite surfaces enhances...
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