Articles | Volume 10, issue 10
Research article 25 Oct 2013
Research article | 25 Oct 2013
Nitrous Oxide (N2O) production in axenic Chlorella vulgaris microalgae cultures: evidence, putative pathways, and potential environmental impacts
B. Guieysse et al.
Related subject area
Biogeochemistry: Environmental MicrobiologyPotential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteriaMicrobial functional signature in the atmospheric boundary layerNew insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystemMetagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret sedimentsImpact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamicsBiotic and abiotic transformation of amino acids in cloud water: Experimental studies and atmospheric implicationsReviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pumpSalinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)On giant shoulders: how a seamount affects the microbial community composition of seawater and spongesSpatial variations in sedimentary N-transformation rates in the North Sea (German Bight)Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic RidgeCo-occurrence of Fe and P stress in natural populations of the marine diazotroph TrichodesmiumSenescence as the main driver of iodide release from a diverse range of marine phytoplanktonReviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scaleDeep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic spongesInducing the attachment of cable bacteria on oxidizing electrodesBacterial degradation activity in the eastern tropical South Pacific oxygen minimum zoneMacromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processingEffects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime AntarcticaComprehensive characterization of an aspen (Populus tremuloides) leaf litter sample that maintained ice nucleation activity for 48 yearsThe origin and role of biological rock crusts in rocky desert weatheringPyrite oxidization accelerates bacterial carbon sequestration in copper mine tailingsBiogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort SeaFiltration artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assaysPredominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissionsTrichodesmium physiological ecology and phosphate reduction in the western tropical South PacificPotential for phenol biodegradation in cloud watersColony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistryIn-depth characterization of diazotroph activity across the western tropical South Pacific hotspot of N2 fixation (OUTPACE cruise)Programmed cell death in diazotrophs and the fate of organic matter in the western tropical South Pacific Ocean during the OUTPACE cruiseRapid mineralization of biogenic volatile organic compounds in temperate and Arctic soilsA three-dimensional niche comparison of Emiliania huxleyi and Gephyrocapsa oceanica: reconciling observations with projectionsDistribution and drivers of symbiotic and free-living diazotrophic cyanobacteria in the western tropical South PacificVirus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplanktonEnvironmental controls on the elemental composition of a Southern Hemisphere strain of the coccolithophore Emiliania huxleyiCalcium carbonates: induced biomineralization with controlled macromorphologyContrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical ChinaEffects of ultraviolet radiation on photosynthetic performance and N2 fixation in Trichodesmium erythraeum IMS 101Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation historyAlterations in microbial community composition with increasing fCO2: a mesocosm study in the eastern Baltic SeaLong-distance electron transport occurs globally in marine sedimentsVertical profiles of sediment methanogenic potential and communities in two plateau freshwater lakesAnnual variability and regulation of methane and sulfate fluxes in Baltic Sea estuarine sedimentsOcean acidification impacts bacteria–phytoplankton coupling at low-nutrient conditionsSeasonal changes in the D / H ratio of fatty acids of pelagic microorganisms in the coastal North SeaThe role of coccoliths in protecting Emiliania huxleyi against stressful light and UV radiationBiogeochemical and biological impacts of diazotroph blooms in a low-nutrient, low-chlorophyll ecosystem: synthesis from the VAHINE mesocosm experiment (New Caledonia)Nitrogen fixation in sediments along a depth transect through the Peruvian oxygen minimum zoneTransfer of diazotroph-derived nitrogen towards non-diazotrophic planktonic communities: a comparative study between Trichodesmium erythraeum, Crocosphaera watsonii and Cyanothece sp.Cell-free extracellular enzymatic activity is linked to seasonal temperature changes: a case study in the Baltic Sea
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285,
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095,Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032,Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Revised manuscript accepted for BG
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374,Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Revised manuscript accepted for BGShort summary
Our study is of interest to atmospheric scientists and environmental microbiologists as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition to chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778,Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732,Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486,Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851,Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519,Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551,Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471,Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533,Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245,Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607,Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230,Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659,Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128,Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683,Short summary
Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145,Short summary
In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583,Short summary
This paper contributes to the study of bacterial carbon sequestration in mine tailings. Previous studies focused on carbonate mineral precipitation, while the role of autotrophs in carbon sequestration has been neglected. Carbon sequestration in two mine tailings treated with FeS2 was analyzed using 13C isotope labeling, pyrosequencing, and DNA SIP to identify carbon fixers. This paper is the first to investigate carbon sequestration by autotrophic groups in mine tailings.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433,Short summary
In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154,Short summary
Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536,Short summary
Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778,Short summary
Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744,Short summary
The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 15, 4923–4942,Short summary
Phaeocystis antarctica is an important phytoplankter of the Antarctic coastal environment where it dominates the early season bloom after sea ice retreat. Iron nutrition was found to be an important factor that results in Phaeocystis colony formation and a large restructuring of the proteome, including changes associated with the flagellate to colonial transition and adaptive responses to iron scarcity. Analysis of Phaeocystis proteins from the Ross Sea revealed the presence of both cell types.
Sophie Bonnet, Mathieu Caffin, Hugo Berthelot, Olivier Grosso, Mar Benavides, Sandra Helias-Nunige, Cécile Guieu, Marcus Stenegren, and Rachel Ann Foster
Biogeosciences, 15, 4215–4232,
Dina Spungin, Natalia Belkin, Rachel A. Foster, Marcus Stenegren, Andrea Caputo, Mireille Pujo-Pay, Nathalie Leblond, Cécile Dupouy, Sophie Bonnet, and Ilana Berman-Frank
Biogeosciences, 15, 3893–3908,Short summary
The way marine organisms die can determine the fate of organic matter (OM) in the ocean. We investigated whether a form of auto-induced programmed cell death (PCD) influenced phytoplankton mortality and fate of OM. Our results from high biomass blooms of the cyanobacterium Trichodesmium show evidence for PCD and high production of sticky carbon material termed transparent exopolymeric particles (TEP) that facilitates cellular aggregation and enhances the vertical flux of OM to depth.
Christian Nyrop Albers, Magnus Kramshøj, and Riikka Rinnan
Biogeosciences, 15, 3591–3601,
Natasha A. Gafar and Kai G. Schulz
Biogeosciences, 15, 3541–3560,Short summary
Emiliania huxleyi and Gephyrocapsa oceanica are the most prolific calcifying phytoplankton in today's oceans. We compare their sensitivity to combined anthropogenic stressors of temperature, light and CO2. For the future, we project a niche contraction for G. oceanica. Furthermore, there was good correlation of our new metric, the CaCO3 production potential, with satellite-derived concentrations in the modern ocean, indicating means of assessing overall coccolithophorid success in the future.
Marcus Stenegren, Andrea Caputo, Carlo Berg, Sophie Bonnet, and Rachel A. Foster
Biogeosciences, 15, 1559–1578,Short summary
We successfully performed quantitative PCR at sea. The qPCR data were procured within 3 h and used in decisions on further sampling on site. We designed and applied a new primer and probe set for quantifying the UCYN-A1 host and observed discrepancies between host and symbiont, which contradict previous studies. Lastly, we observed a clear vertical separation between a subsurface group (UCYN-A with hosts) and a surface group (remaining diazotrophs), mainly separated by temperature.
Emma J. Shelford and Curtis A. Suttle
Biogeosciences, 15, 809–819,Short summary
This work demonstrates that lysis by viruses facilitates the transfer of nitrogen to phytoplankton in the ocean, and thus viruses are key players in nitrogen cycling in the oceans and in maintaining oxygen production by marine primary producers.
Yuanyuan Feng, Michael Y. Roleda, Evelyn Armstrong, Cliff S. Law, Philip W. Boyd, and Catriona L. Hurd
Biogeosciences, 15, 581–595,Short summary
We conducted a series of incubation experiments to understand how the changes in five environmental drivers will affect the elemental composition of the calcifying phytoplankton species Emiliania huxleyi. These findings provide new diagnostic information to aid our understanding of how the physiology and the related marine biogeochemistry of the ecologically important species Emiliania huxleyi will respond to changes in different environmental drivers in the global climate change scenario.
Aileen Meier, Anne Kastner, Dennis Harries, Maria Wierzbicka-Wieczorek, Juraj Majzlan, Georg Büchel, and Erika Kothe
Biogeosciences, 14, 4867–4878,Short summary
Biomineralization of (magnesium) calcite and vaterite by bacterial isolates was observed using isolates from limestone associated groundwater, rock and soil. More than 92 % of isolates could form carbonates with different crystal macromorphologies. Using different conditions like varying temperature, pH or media components but also cocultivation to test for collaborative effects of sympatric bacteria, mechanisms of calcium carbonate formation were studied.
Chuang Zhang, Xin-Yu Zhang, Hong-Tao Zou, Liang Kou, Yang Yang, Xue-Fa Wen, Sheng-Gong Li, Hui-Min Wang, and Xiao-Min Sun
Biogeosciences, 14, 4815–4827,Short summary
Ammonium additions had stronger inhibition effects on soil microbial biomass of different communities than nitrate addition. However, inhibition effects of nitrate additions on P hydrolase were stronger than ammonium additions, but not on C- and N-hydrolase and oxidase. Ammonium additions decreased N-acquisition specific enzyme activities normalized by total microbial biomass, but increased P-acquisition specific enzyme activities. Different effects on soil pH may explain the different effects.
Xiaoni Cai, David A. Hutchins, Feixue Fu, and Kunshan Gao
Biogeosciences, 14, 4455–4466,Short summary
Trichodesmium is significant marine N2 fixer. We conducted short- and long-term UV exposure experiment to investigate how UV affects this organism. Our results showed N2 fixation and carbon fixation rates were significantly reduced under UV radiation. As a defense strategy, Trichodesmium is able to synthesize UV-absorbing compounds to protect from UV damage. Our results suggest that shipboard experiments in UV-opaque containers may have substantially overestimated in situ N2 fixation rate.
Amy E. Goldman, Emily B. Graham, Alex R. Crump, David W. Kennedy, Elvira B. Romero, Carolyn G. Anderson, Karl L. Dana, Charles T. Resch, Jim K. Fredrickson, and James C. Stegen
Biogeosciences, 14, 4229–4241,Short summary
The history of river inundation influences shoreline sediment biogeochemical cycling and microbial dynamics. Sediment exhibited a binary respiration response to rewetting, in which respiration from less recently saturated sediment was suppressed relative to more recently saturated sediment, likely due to inhibition of fungal metabolic activity. River shorelines should likely be integrated as a distinct environment into hydrobiogeochemical models to predict watershed biogeochemical function.
Katharine J. Crawfurd, Santiago Alvarez-Fernandez, Kristina D. A. Mojica, Ulf Riebesell, and Corina P. D. Brussaard
Biogeosciences, 14, 3831–3849,Short summary
Carbon dioxide (CO2) is increasing in the atmosphere and oceans. To simulate future conditions we manipulated CO2 concentrations of natural Baltic seawater in 55 m3 bags in situ. We saw increased growth rates and abundances of the smallest-sized eukaryotic phytoplankton and reduced abundances of other phytoplankton with increased CO2. Viral and bacterial abundances were also affected. This would lead to more carbon recycling in the surface water and affect marine food webs and the carbon cycle.
Laurine D. W. Burdorf, Anton Tramper, Dorina Seitaj, Lorenz Meire, Silvia Hidalgo-Martinez, Eva-Maria Zetsche, Henricus T. S. Boschker, and Filip J. R. Meysman
Biogeosciences, 14, 683–701,Short summary
Recently, long filamentous bacteria have been reported to conduct electrons over centimetre distances in marine sediments. These so-called cable bacteria have an
electricity-based metabolism, effectively turning the seafloor into a natural battery. In this study we demonstrate a global occurrence of these cable bacteria in marine sediments, spanning a large range of climate zones (off Greenland, the USA, Australia, the Netherlands) and a large range of coastal habitats.
Yuyin Yang, Ningning Li, Wei Wang, Bingxin Li, Shuguang Xie, and Yong Liu
Biogeosciences, 14, 341–351,Short summary
The present study investigated the vertical profiles of sediment methanogenic potential and communities in two plateau freshwater lakes. Hydrogenotrophic methanogenesis was the major methane production pathway in the freshwater lakes. Lake trophic status was found to influence sediment methanogen community and activity. This work could provide some new insights into methane production in freshwater sediment ecosystem.
Joanna E. Sawicka and Volker Brüchert
Biogeosciences, 14, 325–339,Short summary
The biogeochemistry of methane was studied in high-latitude fjord-type estuarine sediment in the Baltic Sea from April 2012 to April 2013. A large variability in methane-producing and methane-oxidizing processes was observed over the year. Oxygen was the most important regulator for the methane flux. In addition to eutrophication effects, free gas movement is suggested as a factor controlling methane concentrations.
Thomas Hornick, Lennart T. Bach, Katharine J. Crawfurd, Kristian Spilling, Eric P. Achterberg, Jason N. Woodhouse, Kai G. Schulz, Corina P. D. Brussaard, Ulf Riebesell, and Hans-Peter Grossart
Biogeosciences, 14, 1–15,
Sandra Mariam Heinzelmann, Nicole Jane Bale, Laura Villanueva, Danielle Sinke-Schoen, Catharina Johanna Maria Philippart, Jaap Smede Sinninghe Damsté, Stefan Schouten, and Marcel Teunis Jan van der Meer
Biogeosciences, 13, 5527–5539,Short summary
In order to understand microbial communities in the environment it is necessary to assess their metabolic potential. The hydrogen isotopic composition of fatty acids has been shown to be promising tool to study the general metabolism of microorganisms in pure culture. Here we showed that it is possible to study seasonal changes in the general metabolism of the whole community by studying the hydrogen isotopic composition of fatty acids.
Juntian Xu, Lennart T. Bach, Kai G. Schulz, Wenyan Zhao, Kunshan Gao, and Ulf Riebesell
Biogeosciences, 13, 4637–4643,
Sophie Bonnet, Melika Baklouti, Audrey Gimenez, Hugo Berthelot, and Ilana Berman-Frank
Biogeosciences, 13, 4461–4479,
Jessica Gier, Stefan Sommer, Carolin R. Löscher, Andrew W. Dale, Ruth A. Schmitz, and Tina Treude
Biogeosciences, 13, 4065–4080,Short summary
Benthic nitrogen fixation and sulfate reduction were investigated in the Peruvian oxygen minimum zone. The data suggest a coupling of both activities to a large extent, but that also sulfide and organic matter availability are controlling the benthic diazotrophy in this area. The molecular analysis confirms the presence of heterotrophic diazotrophs. This work improves our understanding of N cycling in OMZ sediments and the understanding of N sources in the marine environment.
Hugo Berthelot, Sophie Bonnet, Olivier Grosso, Véronique Cornet, and Aude Barani
Biogeosciences, 13, 4005–4021,
Federico Baltar, Catherine Legrand, and Jarone Pinhassi
Biogeosciences, 13, 2815–2821,Short summary
This work deals with one of the central topics in biogeochemistry, the factors controlling the degradation of organic matter. We found the contribution of dissolved (cell-free) to the total extracellular enzymatic activities follows a strong seasonal pattern, with the largest proportions during cold periods. Our results suggest that temperature changes can have strong implications in the hydrolysis of organic matter, suggesting a link between global warming and the degradation of organic matter.
Andersen, R. A.: Algal culturing techniques, Elsevier Academic press, Singapore, 2005.
Arnelle, D. R. and Stamler, J. S.: NO+, NO·, and NO- donation by S-nitrosothiols: Implications for regulation of physiological functions by S-nitrosylation and acceleration of disulfide formation, Arch. Biochem. Biophys, 318, 279–285, 1995.
Batan, L., Quinn, J., Willson, B., and Bradley, T.: Net energy and greenhouse gas emission evaluation of biodiesel derived from microalgae, Environ. Sci. Technol, 44, 7975–7980, 2010.
Béchet, Q., Muñoz, R., Shilton, A., and Guieysse, B.: Outdoor cultivation of temperature-tolerant Chlorella sorokiniana in a column photobioreactor under low power-input, Biotechnol. Bioeng, 110, 118–126, 2013.
Beckman, J. S. and Koppenol, W. H.: Nitric oxide, superoxide, and peroxynitrite: the good, the bad, and ugly, Am. J. Physiol, 271, C1424–1437, 1996.
Bell, L. C. and Ferguson, S. J.: Nitric and nitrous oxide reductases are active under aerobic conditions in cells of Thiosphaera pantotropha, Biochem. J., 273, 423–427, 1991.
Blanc, G., Duncan, G., Agarkova, I., Borodovsky, M., Gurnon, J., Kuo, A., Lindquist, E., Lucas, S., Pangilinan, J., Polle, J., Salamov, A., Terry, A., Yamada, T., Dunigan, D. D., Grigoriev, I. V., Claverie, J. M., and Van Etten, J. L.: The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex, Plant cell, 22, 2943–2955, 2010.
Büsch, A., Friedrich, B., and Cramm, R.: Characterisation of the norB Gene encoding nitric oxide reductase, in the nondenitrifying cyanobacterium Synechocystis sp. Strain PCC6803, Appl. Environ. Microbiol, 68, 668–672, 2002.
Codispoti, L. A.: Interesting times for marine N2O, Science, 327, 1339–1340, 2010.
Cohen, Y. and Gordon, L. I.: Nitrous oxide in the oxygen minimum of the eastern tropical North Pacific: evidence for its consumption during denitrification and possible mechanisms for its production, Deep-Sea Res., 25, 509–524, 1978.
Croft, M. T., Lawrence, A. D., Raux-Deery, E., Warren, M. J., and Smith, A. G.: Algae acquire vitamin B12 through a symbiotic relationship with bacteria, Nature, 438, 90–93, 2005.
Deng, M., Moureaux, T., and Caboche, M.: Tungstate, a molybdate analog inactivating nitrate reductase, deregulates the expression of the nitrate reductase structural gene, Plant Physiol, 91, 304–309, 1989.
Fagerstone, K. D., Quinn, J. C., Bradley, T. H., De Long, S. K., and Marchese, A. J.: Quantitative measurement of direct nitrous oxide emissions from microalgae cultivation, Environ. Sci. Technol, 45, 9449–9456, 2011.
Ferrón, S., Ho, D. T., Johnson, Z. I., and Huntley, M. E.: Air–water fluxes of N2O and CH4 during microalgae (Staurosira sp.) cultivation in an open raceway pond, Environ. Sci. Technol, 46, 10842–10848, 2012.
Florez-Leiva, L., Tarifeño, E., Cornejo, M., Kiene, R., and Farías, L.: High production of nitrous oxide (N2O), methane (CH4) and dimethylsulphoniopropionate (DMSP) in a massive marine phytoplankton culture, Biogeosciences Discuss., 7, 6705–6723, https://doi.org/10.5194/bgd-7-6705-2010, 2010.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B. B.: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean, Proc. Natl. Acad. Sci. USA, 102, 14683–14688, 2005.
Fukuto, J. M., Switzer, C. H., Miranda, K. M., and Wink, D. A.: Nitroxyl (HNO), Chemistry, Biochemistry, and Pharmacology, Annu. Rev. Pharmacol. Toxicol, 45, 335–355, 2005.
Gantner, S., Andersson, A. F., Alonso-Sáez, L., and Bertislon, S.: Novel primers for 16S rRNA-based archaeal community analysis in environmental samples, J. Microbiol. Methods, 84, 12–18, 2011.
Giovannoni, S. J.: Nucleic acid techniques in bacterial systematics, in: The Polymerase Chain Reaction, edited by: Stackerbrandt, E. and Goodfellow, M., John Wiley and Sons. Chichester, 177–203, 1991.
Goshima, N., Mukai, T., Suemori, M., Takakashi, M., Caboche, M., and Morikawa, H.: Emission of nitrous oxide (N2O) from transgenic tobacco expressing antisense NiR mRNA, The Plant J., 19, 75–80, 1999.
Guieysse, B., Béchet. Q., and Shilton, A.: Variability and uncertainty in water demand and water footprint assessments of fresh algae cultivation based on case studies from five climatic regions, Bioresour. Technol, 128, 317–323, 2013.
Gupta, K. J., Fernie, A. R., Kaiser, W. M., and van Dongen, J. T.: On the origins of nitric oxide, Trends Plant. Sci., 16, 160–168, 2011.
Harter, T., Bossier, P., Verreth, J., Bodé, S., Van der Ha, D., Debeer, A. E., Boon, N., Boeckx, P., Vyverman, W., and Nevejan, N.: Carbon and nitrogen mass balance during flue gas treatment with Dunaliella salina cultures, J. Appl. Phycol., 25, 359–368, 2013.
Hasebe, M., Omori, T., Nakazawa, M., Sano, T., Kato, M., and Iwatzuki, K.: rbcL gene sequences provide evidence for the evolutionary lineages of Leptosporangiate ferns, Proc. Natl. Acad. Sci. USA, 91, 5730–5734, 1994.
Hatzenpichler, R.: Diversity, physiology and niche differentition of ammonia-oxidizing archaea, Appl. Environ. Microbiol, 78, 7501–7510, 2012.
Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Fukumori, Y., Muratam T., Iwata, S., and Shiro, Y.: Structural basis of biological N2O generation by bacterial nitric oxide reductase, Science, 330, 1666–1670, 2010.
Ishimura, Y., Gao, Y. T., Panda, S. P., Roman, L. J., Masters, B. S. S., and Weintraub, S. T.: Detection of nitrous oxide in the neuronal nitric oxide synthase reaction by gas chromatography – mass spectrometry, Biochem. Biophys. Res. Commun, 338, 543–549, 2005.
Kay, R. A.: Microalgae as food and supplement, Crit. Rev. Food Sci. Nutr., 30, 555–573, 1991.
Lane, J. and Lant, P.: Including N2O in ozone depletion models for LCA, Int. J. Life Cy. Assess, 17, 252–257, 2012.
Law, C. S., Rees, A. P., and Owens, N. J. P.: Nitrous oxide production by estuarine epiphyton, Limnol. Oceanogr, 38, 435–441, 1993.
Li, B. and Bishop, P. L.: Micro-profiles of activated sludge floc determined using microelectrodes, Water Res, 38, 1248–1258, 2004.
Löscher, C. R., Kock, A., Könneke, M., LaRoche, J., Bange, H. W., and Schmitz, R. A.: Production of oceanic nitrous oxide by ammonia-oxidizing archaea, Biogeosciences, 9, 2419–2429, https://doi.org/10.5194/bg-9-2419-2012, 2012.
Mengis, M., Gachterm R., and Wehrli, B.: Sources and sinks of nitrous oxide (N2O) in deep lakes, Biogeochem, 38, 281–301, 1997.
Miranda, K. M.: The chemistry of nitroxyl (HNO) and implications in biology, Coord. Chem. Rev, 249, 433–455, 2005.
Miranda, K. M., Paolocci, N., Katori, T., Thomas, D. D., Ford, E., Bartberger, M. D., Espey, M. G., Kass, D. A., Feelisch, M., Fukuto, J. M., and Wink, D. A.: A biochemical rationale for the discrete behavior of nitroxyl and nitric oxide in the cardiovascular system, Proc. Nat. Acad. Sci. USA, 100, 9196–9201, 2003.
Morell, J. M., Capella, J., Mercado, A., Bauzá, J., and Corredor, J. E.: Nitrous oxide fluxes in the Caribbean and tropical Atlantic waters: evidence for near surface production, Mar. Chem, 74, 131–143, 2001.
Morley, N., Baggs, E. M., Dörsch, P., and Bakken, L.: Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2- and O2 concentrations, FEMS Microbiol. Ecol, 65, 102–112, 2008.
Ni, W. Z. and Zhu, Z. L.: Gaseous nitrogen losses and nitrous oxide emission from a flooded paddy soil affected by illumination and copper addition, Biol. Fertil. Soils, 34, 460–462, 2001.
Oudot, C., Andrie, C., and Montel, Y.: Nitrous oxide production in the tropical Atlantic ocean, Deep-Sea Res, 37, 183–202, 1990.
Paz-Yepes, J., Herrero, A., and Flores, E.: The NtcA-regulated amtB gene is necessary for full methylammonium uptake activity in the cyanobacterium synechococcus elongates, J. Bacteriol, 189, 7791–7798, 2007.
Pienkos, P. T. and Darzins, A.: The promise and challenges of microalgal-derived biofuels, Biofuels Bioprod, Biorefining, 3, 431–440, 2009.
Planchet, E. and Kaiser, W. M.: Nitric oxide production in plants, Plant Signaling Behav, 1, 46–51, 2006.
Qian, H., Li, J., Pan, X., Sun, Z., Ye, C., Jin, G., and Fu, Z.: Effects of streptomycin on growth of algae Chlorella vulgaris and Microcystis aeruginosa, Environ. Toxicol., 27, 229–237, 2012.
Ravishankara, A. R., Daniel, J. S., and Portmann, R. W.: Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century, Science, 326, 123–125, 2009.
Revell, L. E., Bodeker, G. E., Huck, P. E., and Williamson, B. E.: Impacts of the production and consumption of biofuels on stratospheric ozone, Geophys. Res. Lett, 39, L10804, https://doi.org/10.1029/2012GL051546, 2012.
Ricard, J. and Cornish-Bowden, A.: Co-operative and allosteric enzymes: 20 years on, Eur. J. Biochem, 166, 255–272, 1987.
Richmond, A.: Handbook of microalgal culture: biotechnology and applied phycology, Blackwell Publishing, UK, 2004.
Sakihama, Y., Nakamura, S., and Yamasaki, H.: Nitric oxide production mediated by nitrate reductase in the green alga Chlamydomonas reinhardtii: an alternative NO production pathway in photosynthetic organisms, Plant Cell Physiol., 43, 290–297, 2002.
Santoro, A. E., Buchwald, C., McIlvin, M. R., and Casciotti, K. L.: Isotopic signature of N2O produced by marine ammonia-oxidizing archaea, Science, 333, 1282–1285, 2011.
Schmidt, H. H. H. W., Hofmann, H., Schindler, U., Shutenko, Z., Cunningham, D. D., and Feelisch, M.: No \textbullet NO from NO synthase, Proc. Natl. Acad. Sci. USA, 94, 14492–14497, 1996.
Schreiber, F., Loeffler, B., Polerecky, L., Kuypers, M. M., and de Beer, D.: Mechanisms of transient nitric oxide and nitrous oxide production in a complex biofilm, ISME J., 3, 1301–1313, 2009.
Sharpe, M. A and Cooper, C. E.: Reactions of nitric oxide with mitochondrial cytochrome c: a novel mechanism for the formation of nitroxyl anion and peroxynitrite, Biochem. J., 332, 9–19, 1998.
Smeets, E. M. W., Bouwman, L. F., Stehfest, E., van Vuuren, D. P., and Posthuma, A.: Contribution of N2O to the greenhouse gas balance of first-generation biofuels, Glob. Change Biol, 15, 1–23, 2009.
Spolaore, P., Joannis-Cassan, C., Duran, E., and Isambert, A.: Commercial applications of microalgae, J. Biosci. Bioeng, 101, 87–96, 2006.
Stolz, J. F. and Basu, P.: Evolution of nitrate reductases: molecular and structural variations on a common function, Chem. Bio. Chem., 3, 198–206, 2002.
Takaya, N. and Shoun, H.: Nitric oxide reduction, the last step in denitrification by Fusarium oxysporum, is obligatory mediated by cytochrom P450nor, Mol. Gen. Genet, 263, 342–348, 2000.
Tischner, R., Planchet, E., and Kaiser, W. M.: Mitochondrial electron transport as a source for nitric oxide in the unicellular green algae Chlorella sorokiniana, FEBS Lett, 576, 151–155, 2004.
Twining, B. S., Mylon, S. E., and Benoit, G.: Potential role of copper availability in nitrous oxide accumulation in a temperate lake, Limnol. Oceanogr, 52, 1354–1366, 2007.
US EPA: Methane and nitrous oxide emissions from natural sources, US EPA, 430-R-10-001, 2010.
Vajrala, N., Martens-Habbena, W., Sayavedra-Sota, L. A., Schauer, A., Bottomley, P. J., Stahl, D. A., and Arp, D. J.: Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea, Proc. Natl. Aca. Sci. USA, 110, 1006–1011, 2013.
Vega, J. M., Herrera, J., Aparicio, P. J., Paneque, A., and Losada, M.: Role of molybdenum in nitrate reduction by Chlorella, Plant. Physiol., 48, 294–299, 1971.
Wang, H., Wang, W., Yin, C., Wang, Y., and Lu, J.: Littoral zones as the hotspots of nitrous oxide (N2O) emission in a hyper-eutrophic lake in China, Atmos. Environ., 40, 5522–5527, 2006.
Wang, S., Yeager, K. M., Wan, G., Liu, C., Tao, F., and Fan, C.: Short term field observation of nitrous oxide saturations in Lake Taihu, China: The need for high temporal resolution studies, J. Environ. Qual, 39, 1858–1863, 2010.
Weathers, P. J.: N2O evolution by green algae, Appl. Environ. Microbiol., 48, 1251–1253, 1984.
Weathers, P. J. and Niedzielski, J. J.: Nitrous oxide production by cyanobacteria, Arch. Microbiol, 146, 204–206, 1986.
Wijffels, R. H. and Barbosa, M. J.: An outlook on microalgal biofuels. Science, 329, 796–799, 2010.
Williams, J. and Crutzen, P. J.: Nitrous Oxide from aquaculture, Nat. Geosci, 3, 143 pp., 2010.
Wrage, N., Velthof, G. L., van Beusichem, M. L., and Oenema, O.: Role of nitrifier denitrification in the production of nitrous oxide, Soil Biol. Biochem, 33, 1723–1732, 2001.
Xiong, J., Fu, G., Yang, Y., Zhu, C., and Tao, L.: Tungstate: is it really a specific nitrate reductase inhibitor in plant nitric oxide research?, J. Exp. Biol, 63, 33–41, 2012.