38 results on '"Phyllis Lam"'
Search Results
2. Sampling and Processing Methods Impact Microbial Community Structure and Potential Activity in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia
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Mónica Torres-Beltrán, Andreas Mueller, Melanie Scofield, Maria G. Pachiadaki, Craig Taylor, Kateryna Tyshchenko, Céline Michiels, Phyllis Lam, Osvaldo Ulloa, Klaus Jürgens, Jung-Ho Hyun, Virginia P. Edgcomb, Sean A. Crowe, and Steven J. Hallam
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microbial ecology ,oxygen minimum zone ,standards of practice ,filtration methods ,amplicon sequencing ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 Microbial Community Responses to Ocean Deoxygenation workshop held in Vancouver, B.C on July 2014 had the primary objective of initiating a process to standardize operating procedures for compatible process rate and multi-omic (DNA, RNA, protein, and metabolite) data collection in marine oxygen minimum zones and other oxygen depleted waters. Workshop attendees participated in practical sampling and experimental activities in Saanich Inlet, British Columbia, a seasonally anoxic fjord. Experiments were designed to compare and cross-calibrate in situ versus bottle sampling methods to determine effects on microbial community structure and potential activity when using different filter combinations, filtration methods, and sample volumes. Resulting biomass was preserved for small subunit ribosomal RNA (SSU or 16S rRNA) and SSU rRNA gene (rDNA) amplicon sequencing followed by downstream statistical and visual analyses. Results from these analyses showed that significant community shifts occurred between in situ versus on ship processed samples. For example, Bacteroidetes, Alphaproteobacteria, and Opisthokonta associated with on-ship filtration onto 0.4 μm filters increased fivefold compared to on-ship in-line 0.22 μm filters or 0.4 μm filters processed and preserved in situ. In contrast, Planctomycetes associated with 0.4 μm in situ filters increased fivefold compared to on-ship filtration onto 0.4 μm filters and on-ship in-line 0.22 μm filters. In addition, candidate divisions and Chloroflexi were primarily recovered when filtered onto 0.4 μm filters in situ. Results based on rRNA:rDNA ratios for microbial indicator groups revealed previously unrecognized roles of candidate divisions, Desulfarculales, and Desulfuromandales in sulfur cycling, carbon fixation and fermentation within anoxic basin waters. Taken together, filter size and in situ versus on-ship filtration had the largest impact on recovery of microbial groups with the potential to influence downstream metabolic reconstruction and process rate measurements. These observations highlight the need for establishing standardized and reproducible techniques that facilitate cross-scale comparisons and more accurately assess in situ activities of microbial communities.
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- 2019
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3. Controls over Ocean Mesopelagic Interior Carbon Storage (COMICS): fieldwork, synthesis and modelling efforts
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Richard John Sanders, Stephanie Henson, Adrian Martin, Tom Anderson, Raffaele Bernardello, Peter Enderlein, Sophie Fielding, Sarah L. C Giering, Manuela Hartmann, Morten Iversen, Samar Khatiwala, Phyllis Lam, Richard Lampitt, Daniel Mayor, Mark Moore, Eugene Murphy, Stuart Painter, Alex James Poulton, Kevin Saw, Gabriele Stowasser, Geraint Tarling, Sinhue Torres-Valdes, Mark Trimmer, George Wolff, Andrew Yool, and Mike Zubkov
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biological carbon pump ,field campaign ,ocean carbon cycle ,Biogeochemical model ,Science plan ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
The ocean’s biological carbon pump plays a central role in regulating atmospheric CO2 levels. In particular, the depth at which sinking organic carbon is broken down and respired in the mesopelagic zone is critical, with deeper remineralisation resulting in greater carbon storage. Until recently, however, a balanced budget of the supply and consumption of organic carbon in the mesopelagic had not been constructed in any region of the ocean, and the processes controlling organic carbon turnover are still poorly understood. Large-scale data syntheses suggest that a wide range of factors can influence remineralisation depth including upper-ocean ecological interactions, and interior dissolved oxygen concentration and temperature. However these analyses do not provide a mechanistic understanding of remineralisation, which increases the challenge of appropriately modelling the mesopelagic carbon dynamics. In light of this, the UK Natural Environment Research Council has funded a programme with this mechanistic understanding as its aim, drawing targeted fieldwork right through to implementation of a new parameterisation for mesopelagic remineralisation within an IPCC class global biogeochemical model. The Controls over Ocean Mesopelagic Interior Carbon Storage (COMICS) programme will deliver new insights into the processes of carbon cycling in the mesopelagic zone and how these influence ocean carbon storage. Here we outline the programme’s rationale, its goals, planned fieldwork and modelling activities, with the aim of stimulating international collaboration.
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- 2016
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4. 16S rRNA gene-based molecular analysis of mat-forming and accompanying bacteria covering organically-enriched marine sediments underlying a salmon farm in Southern Chile (Calbuco Island) Análisis molecular basado en secuencias del gen ARNr 16s en bacterias formadoras de tapete y bacterias acompañantes en sedimentos marinos enriquecidos orgánicamente por una instalación de cultivo de salmones en el sur de Chile (isla Calbuco)
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Carlos Aranda, Javier Paredes, Cristian Valenzuela, Phyllis Lam, and Laure Guillou
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Ciclo de azufre ,genes 16S rARN ,salmonicultura ,sedimentos ,tapete de Beggiatoa ,16S rRNA genes ,Beggiatoa mat ,salmon farming sediments ,sulphur cycle ,Oceanography ,GC1-1581 ,Zoology ,QL1-991 - Abstract
The mat forming bacteria covering organic matter-enriched and anoxic marine sediments underlying a salmon farm in Southern Chile, were examined using 16S rRNA gene phylogenies. This mat was absent in the sea bed outside the direct influence of the farm (360 m outside fish cages). Based on nearly complete 16S rRNA gene sequences (-1500 bp), mat-forming filamentous cells were settled as the sulphur-oxidizing and putatively dissimilative nitrate-reducing Beggiatoa spp., being closely related (up to 97% sequence identity) to Beggiatoa spp. identified in eutrophic shallow sediments in northern Europe (Danish Limfjorden and German Dangast inlets). Their phylogenetic affiliation was consistent with their morphology as vacuolated and sulphur-containing cells arranged on tandem along trichomes (18 to 28 μm diameter). Additionally, deltaproteobacterial sulphate reducers, Sulfurospirillum, Sulfurovum and Fusibacter were detected according to partial 16S rRNA gene sequences (-500 bp). Their concurrence with Beggiatoa suggested an intense and complex sulphur cycle within the surface of these aquaculture-affected sediments, which may have important implications for the necessity of more efficient benthic-bioremediation of finfish aquaculture in Chile and worldwide.Las bacterias formadoras de tapete sobre sedimentos anóxicos enriquecidos orgánicamente por residuos de una instalación de cultivo intensivo de salmones en el sur de Chile fueron examinadas a partir de sus secuencias del gen ARNr 16S. Este tapete está ausente en el lecho marino que está fuera de la influencia directa de la instalación de cultivo (360 m alejado de las balsas jaula). Según el análisis de secuencias casi completas de este gen (-1500 bp), las células filamentosas formadoras de tapete fueron identificadas como sulfuro-oxidantes Beggiatoa spp., del tipo vacuolado y putativamente capaces de reducir desasimilatoriamente nitrato en amonio, siendo estrechamente relacionadas (hasta 97% de homología) con Beggiaota spp. identificadas en sedimentos de baja profundidad en mares interiores eutroficados de Dinamarca (Limfjorden) y el norte de Alemania (Dangast). Esta afiliación filogenética fue consistente con la morfología caracterizadora, es decir, presencia de células discoidales con vacuolas y granulos de azufre, dispuestas a lo largo de un tren o tricoma de 18 a 28 μm de diámetro. Adicionalmente, deltaproteobacterias reductoras de sulfato, Sulfurospirillum, Sulfurovum y Fusibacter fueron también detectados de acuerdo a sus secuencias parciales del gen ARNr 16S (-500 bp). La concurrencia de estas células con los filamentos de Beggiatoa sugieren el funcionamiento de un ciclo de azufre intenso y complejo ocurriendo en la superficie de estos sedimentos afectados por el cultivo de salmones, ciclo que puede aportar importantes consideraciones biológicas a la necesidad de un biocontrol y/o biorrermediaición del impacto bentónico por la acuicultura de peces marinos en Chile y el mundo.
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- 2010
5. Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones.
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Tim Kalvelage, Marlene M Jensen, Sergio Contreras, Niels Peter Revsbech, Phyllis Lam, Marcel Günter, Julie LaRoche, Gaute Lavik, and Marcel M M Kuypers
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Medicine ,Science - Abstract
Nutrient measurements indicate that 30-50% of the total nitrogen (N) loss in the ocean occurs in oxygen minimum zones (OMZs). This pelagic N-removal takes place within only ~0.1% of the ocean volume, hence moderate variations in the extent of OMZs due to global warming may have a large impact on the global N-cycle. We examined the effect of oxygen (O(2)) on anammox, NH(3) oxidation and NO(3)(-) reduction in (15)N-labeling experiments with varying O(2) concentrations (0-25 µmol L(-1)) in the Namibian and Peruvian OMZs. Our results show that O(2) is a major controlling factor for anammox activity in OMZ waters. Based on our O(2) assays we estimate the upper limit for anammox to be ~20 µmol L(-1). In contrast, NH(3) oxidation to NO(2)(-) and NO(3)(-) reduction to NO(2)(-) as the main NH(4)(+) and NO(2)(-) sources for anammox were only moderately affected by changing O(2) concentrations. Intriguingly, aerobic NH(3) oxidation was active at non-detectable concentrations of O(2), while anaerobic NO(3)(-) reduction was fully active up to at least 25 µmol L(-1) O(2). Hence, aerobic and anaerobic N-cycle pathways in OMZs can co-occur over a larger range of O(2) concentrations than previously assumed. The zone where N-loss can occur is primarily controlled by the O(2)-sensitivity of anammox itself, and not by any effects of O(2) on the tightly coupled pathways of aerobic NH(3) oxidation and NO(3)(-) reduction. With anammox bacteria in the marine environment being active at O(2) levels ~20 times higher than those known to inhibit their cultured counterparts, the oceanic volume potentially acting as a N-sink increases tenfold. The predicted expansion of OMZs may enlarge this volume even further. Our study provides the first robust estimates of O(2) sensitivities for processes directly and indirectly connected with N-loss. These are essential to assess the effects of ocean de-oxygenation on oceanic N-cycling.
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- 2011
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6. Pathways of Nitrous Oxide Production in the Eastern Tropical South Pacific Oxygen Minimum Zone
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Daniel McCoy, Pierre Damien, Daniel J Clements, Simon Yang, Daniele Bianchi, Annie Bourbonnais, Laura Bristow, Pearse Buchanan, Phyllis Lam, Andrew Babbin, Emily Zakem, and Colette Kelly
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Oceanic emissions of nitrous oxide (N2O) account for roughly one-third of all natural sources to the atmosphere. Hot-spots of N2O outgassing occur over oxygen minimum zones (OMZs), where the presence of steep oxygen gradients surrounding anoxic waters leads to enhanced N2O production from both nitrification and denitrification. However, the relative contributions from these pathways to N2O production and outgassing in these regions remains poorly constrained, in part due to shared intermediary nitrogen tracers, and the tight coupling of denitrification sources and sinks. To shed light on this problem, we embed a new, mechanistic model of the OMZ nitrogen cycle within a three-dimensional eddy-resolving physical-biogeochemical model of the ETSP, tracking contributions from remote advection, atmospheric exchange, and local nitrification and denitrification. Our results indicate that net N2O production from denitrification is approximately one order of magnitude greater than nitrification within the ETSP OMZ. However, only ~30% of denitrification-derived N2O production ultimately outgasses to the atmosphere in this region (contributing ~34% of the air-sea N2O flux on an annual basis), while the remaining is exported out of the domain. Instead, remotely-produced N2O advected into the OMZ region accounts for roughly half (~56%) of the total N2O outgassing, with smaller contributions from nitrification (~7%). Our results suggests that, together with enhanced production by denitrification, upwelling of remotely-derived N2O (likely produced via nitrification in the oxygenated ocean) contributes the most to N2O outgassing over the ETSP OMZ.
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- 2022
7. Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles
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Phyllis Lam, Richard S. Lampitt, and Manon T. Duret
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Oceanography ,chemistry ,fungi ,Environmental science ,chemistry.chemical_element ,Aquatic Science ,Carbon ,human activities ,DNA sequencing ,Scotia sea ,18S ribosomal RNA - Abstract
Suspended marine particles constitute most of the particulate organic matter pool in the oceans, thereby providing substantial substrates for heterotrophs, especially in the mesopelagic. Conversely, sinking particles are major contributors to carbon fluxes defining the strength of the biological carbon pump (BCP). This study is the first to investigate the differential influence of eukaryotic communities to suspended and sinking particles, using 18S rRNA gene sequencing on particles collected with a marine snow catcher in the mixed layer and upper mesopelagic of the Scotia Sea, Southern Ocean. In the upper mesopelagic, most eukaryotic phytoplankton sequences belonged to chain-forming diatoms in sinking particles and to prymnesiophytes in suspended particles. This suggests that diatom-enriched particles are more efficient in carbon transfer to the upper mesopelagic than those enriched in prymnesiophytes in the Scotia Sea, the latter more easily disintegrating into suspended particles. In the upper mesopelagic, copepods appeared most influential on sinking particles whereas soft-tissue metazoan sequences contributed more to suspended particles. Heterotrophic protists and fungi communities were distinct between mixed layer and upper mesopelagic, implying that few protists ride along sinking particles. Furthermore, differences between predatory flagellates and radiolarians between suspended and sinking particles implied different ecological conditions between the two particles pools, and roles in the BCP. Molecular analyses of sinking and suspended particles constitute powerful diagnostic tools to study the eukaryotic influence on the BCP in a more holistic manner compared to classic carbon export studies focusing on sinking particles.
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- 2020
8. Sediment microbial assemblage structure is modified by marine polychaete gut passage
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Martin Solan, Phyllis Lam, Michael Cunliffe, and Harriet Dale
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0301 basic medicine ,Biogeochemical cycle ,Geologic Sediments ,030106 microbiology ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,Ammonia ,Animals ,Ecosystem ,Nitrogen cycle ,Phylogeny ,Invertebrate ,Polychaete ,Ecology ,Bacteria ,Sediment ,Polychaeta ,Nitrogen Cycle ,biology.organism_classification ,Burrow ,Archaea ,Gastrointestinal Microbiome ,030104 developmental biology ,Hediste diversicolor - Abstract
Invertebrate activities in sediments, predominantly the redistribution of particles and porewater, are well-known to regulate the structure of associated microbial assemblages; however, relatively little attention has been given to the effects of sediment ingestion, gut passage and excretion by deposit-feeding invertebrates. Here, we use high-throughput sequencing and quantitative PCR to examine how passage through the gut of the marine polychaete Hediste diversicolor affects the structure of bacterial and archaeal assemblages and the abundance of nitrogen cycling taxa. We show that the digestive tract of H. diversicolor contains unique transitory microbial assemblages that, during gut passage, become more like the surrounding sediment assemblages. Enrichment of similar microbial taxa in both the hindgut and the burrow wall suggest that these transitory gut assemblages may influence the composition of the local sediment community. The hindgut of H. diversicolor also forms a reservoir for unique ammonia-oxidising archaeal taxa. Furthermore, distinct microbial assemblages on external polychaete surfaces suggest that deposit-feeding invertebrates act as vectors that transport microbes between sediment patches. Collectively, these findings suggest that the passage of sediment and associated microbial assemblages through the gut of deposit feeding invertebrates is likely to play a significant role in regulating sediment microbial assemblages and biogeochemical functioning.
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- 2019
9. Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups
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Martin Solan, Joe D. Taylor, Harriet Dale, Michael Cunliffe, and Phyllis Lam
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0301 basic medicine ,Geologic Sediments ,Nitrogen ,030106 microbiology ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Nitrate ,Ammonia ,Animals ,Ecosystem ,Nitrogen cycle ,Nitrites ,Glycosaminoglycans ,Nitrates ,Bacteria ,Ecology ,Sediment ,Polychaeta ,Nitrogen Cycle ,biology.organism_classification ,Archaea ,Nitrification ,030104 developmental biology ,chemistry ,Microbial population biology ,Environmental chemistry ,Hediste diversicolor ,Oxidation-Reduction - Abstract
Sediment nitrogen cycling is a network of microbially mediated biogeochemical processes that are vital in regulating ecosystem functioning. Mucopolysaccharides (mucus) are produced by many invertebrates and have the potential to be an important source of organic carbon and nitrogen to sediment microorganisms. At present, we have limited understanding of how mucopolysaccharide moderates total sediment microbial communities and specific microbial functional groups that drive nitrogen cycling processes. To start addressing this knowledge gap, sediment slurries were incubated with and without Hediste diversicolor mucus. Changes in dissolved inorganic nitrogen (ammonia, nitrite and nitrate) concentrations and bacterial and archaeal community diversity were assessed. Our results showed that mucopolysaccharide addition supported a more abundant and distinct microbial community. Moreover, mucus stimulated the growth of bacterial and archaeal ammonia oxidisers, with a concomitant increase in nitrite and nitrate. Hediste diversicolor mucopolysaccharide appears to enhance sediment nitrification rates by stimulating and fuelling nitrifying microbial groups. We propose that invertebrate mucopolysaccharide secretion should be considered as a distinct functional trait when assessing invertebrate contributions to sediment ecosystem function. By including this additional trait, we can improve our mechanistic understanding of invertebrate-microbe interactions in nitrogen transformation processes and provide opportunity to generate more accurate models of global nitrogen cycling.
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- 2018
10. Omic Approaches to Microbial Geochemistry
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Phyllis Lam and Gregory J. Dick
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Geochemistry and Petrology ,Earth and Planetary Sciences (miscellaneous) ,Geochemistry ,DECIPHER ,Genomics ,Biology - Abstract
The past two decades have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into genome sequences—the blueprints of life on Earth. Although initially driven by biomedical research, this revolution offers exciting opportunities in Earth sciences. Analyzing genomes and other biomolecules (“omic” methods) within environmental samples provides new vistas of microbial geochemistry. However, the massive amount of data produced can be hard to decipher, and the resources and infrastructure to train and support geoscientists in omics approaches are lacking. This article summarizes some of the opportunities and challenges in the applications of omic approaches to geochemical problems.
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- 2015
11. Methane stimulates massive nitrogen loss from freshwater reservoirs in India
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Marcel M. M. Kuypers, Hema Naik, S. Wajih A. Naqvi, Samir Damare, Amit Sarkar, Siby Kurian, Damodar M. Shenoy, Manon T. Duret, Mangesh Gauns, Phyllis Lam, Gaute Lavik, Gayatree Narvenkar, and Anil Pratihary
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0301 basic medicine ,Multidisciplinary ,Denitrification ,Reactive nitrogen ,Science ,General Physics and Astronomy ,chemistry.chemical_element ,General Chemistry ,Nitrous oxide ,Nitrogen ,Anoxic waters ,Article ,General Biochemistry, Genetics and Molecular Biology ,Methane ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Environmental chemistry ,lcsh:Q ,Hypolimnion ,lcsh:Science ,Eutrophication - Abstract
The fate of the enormous amount of reactive nitrogen released to the environment by human activities in India is unknown. Here we show occurrence of seasonal stratification and generally low concentrations of dissolved inorganic combined nitrogen, and high molecular nitrogen (N2) to argon ratio, thus suggesting seasonal loss to N2 in anoxic hypolimnia of several dam-reservoirs. However, 15N-experiments yielded low rates of denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium—except in the presence of methane (CH4) that caused ~12-fold increase in denitrification. While nitrite-dependent anaerobic methanotrophs belonging to the NC10 phylum were present, previously considered aerobic methanotrophs were far more abundant (up to 13.9%) in anoxic hypolimnion. Methane accumulation in anoxic freshwater systems seems to facilitate rapid loss of reactive nitrogen, with generally low production of nitrous oxide (N2O), through widespread coupling between methanotrophy and denitrification, potentially mitigating eutrophication and emissions of CH4 and N2O to the atmosphere., The fate of anthropogenic nitrogen (N) remains understudied in South Asian water bodies despite its impact on water chemistry and quality. Here the authors show that N loss in Indian freshwater reservoirs is tightly coupled to methanotrophy, which has helped curb eutrophication and greenhouse gas emissions.
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- 2018
12. Prokaryotic niche partitioning between suspended and sinking marine particles
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Manon T. Duret, Phyllis Lam, and Richard S. Lampitt
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Geologic Sediments ,Mesopelagic zone ,Flavobacteriales ,Oceans and Seas ,Heterotroph ,Deep sea ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Organic matter ,Seawater ,Organic Chemicals ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,030304 developmental biology ,Marine snow ,Total organic carbon ,chemistry.chemical_classification ,0303 health sciences ,biology ,Bacteria ,030306 microbiology ,Microbiota ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Archaea ,Rhodobacterales ,Oceanography ,chemistry ,Prokaryotic Cells - Abstract
Suspended particles are major organic carbon substrates for heterotrophic microorganisms in the mesopelagic ocean (100–1000 m). Nonetheless, communities associated with these particles have been overlooked compared with sinking particles, the latter generally considered as main carbon transporters to the deep ocean. This study is the first to differentiate prokaryotic communities associated with suspended and sinking particles, collected with a marine snow catcher at four environmentally distinct stations in the Scotia Sea. Amplicon sequencing of 16S rRNA gene revealed distinct prokaryotic communities associated with the two particle‐types in the mixed‐layer (0–100 m) and upper‐mesopelagic zone (mean dissimilarity 42.5% ± 15.2%). Although common remineralising taxa were present within both particle‐types, gammaproteobacterial Pseudomonadales and Vibrionales, and alphaproteobacterial Rhodobacterales were found enriched in sinking particles up to 32‐fold, while Flavobacteriales (Bacteroidetes) favoured suspended particles. We propose that this niche‐partitioning may be driven by organic matter properties found within both particle‐types: K‐strategists, specialised in the degradation of complex organic compounds, thrived on semi‐labile suspended particles, while generalists r‐strategists were adapted to the transient labile organic contents of sinking particles. Differences between the two particle‐associated communities were more pronounced in the mesopelagic than in the surface ocean, likely resulting from exchanges between particle‐pools enabled by the stronger turbulence.
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- 2017
13. Adaptability as the key to success for the ubiquitous marine nitrite oxidizer
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Jessika, Füssel, Sebastian, Lücker, Pelin, Yilmaz, Boris, Nowka, Maartje A H J, van Kessel, Patric, Bourceau, Philipp F, Hach, Sten, Littmann, Jasmine, Berg, Eva, Spieck, Holger, Daims, Marcel M M, Kuypers, and Phyllis, Lam
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Nitrates ,Oceans and Seas ,fungi ,Environmental Studies ,food and beverages ,SciAdv r-articles ,Nitrogen Cycle ,Sulfides ,equipment and supplies ,Metagenomics ,Ectothiorhodospiraceae ,Oxidation-Reduction ,Nitrites ,Phylogeny ,Research Articles ,Research Article - Abstract
A globally distributed yet previously overlooked marine nitrite oxidizer can reduce nitrate, produce N2O, and oxidize sulfide., Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences.
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- 2017
14. Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa
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Phyllis Lam, Marc Strous, Abdul Sheik, Corina P. D. Brussaard, Marcel M. M. Kuypers, Gaute Lavik, Sten Littmann, Andreas Krupke, Niculina Musat, and Aquatic Microbiology (IBED, FNWI)
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Environmental sciences & ecology [F08] [Life sciences] ,Microbiologie [F11] [Sciences du vivant] ,Aquatic sciences & oceanology [F04] [Life sciences] ,Nitrogen ,Microorganism ,Population ,carbon remineralisation ,nanoSIMS ,Phaeocystis globosa ,pyrosequencing ,marine viruses ,Biochemistry, biophysics & molecular biology [F05] [Life sciences] ,Sciences aquatiques & océanologie [F04] [Sciences du vivant] ,Bacterial Physiological Phenomena ,Microbiology ,Marine bacteriophage ,Microbial ecology ,Algae ,RNA, Ribosomal, 16S ,Botany ,Proteobacteria ,Organic matter ,Microbiology [F11] [Life sciences] ,Seawater ,Biomass ,education ,Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant] ,Ecology, Evolution, Behavior and Systematics ,chemistry.chemical_classification ,education.field_of_study ,Carbon Isotopes ,biology ,Nitrogen Isotopes ,Haptophyta ,Biodiversity ,biology.organism_classification ,Roseobacter ,Carbon ,Alteromonas and Roseobacter ,Sciences de l'environnement & écologie [F08] [Sciences du vivant] ,chemistry ,Original Article ,North Sea ,Alteromonas ,Bacteria ,Virus Physiological Phenomena - Abstract
The release of organic material upon algal cell lyses has a key role in structuring bacterial communities and affects the cycling of biolimiting elements in the marine environment. Here we show that already before cell lysis the leakage or excretion of organic matter by infected yet intact algal cells shaped North Sea bacterial community composition and enhanced bacterial substrate assimilation. Infected algal cultures of Phaeocystis globosa grown in coastal North Sea water contained gamma-and alphaproteobacterial phylotypes that were distinct from those in the non-infected control cultures 5 h after infection. The gammaproteobacterial population at this time mainly consisted of Alteromonas sp. cells that were attached to the infected but still intact host cells. Nano-scale secondary-ion mass spectrometry (nanoSIMS) showed similar to 20% transfer of organic matter derived from the infected C-13- and N-15-labelled P. globosa cells to Alteromonas sp. cells. Subsequent, viral lysis of P. globosa resulted in the formation of aggregates that were densely colonised by bacteria. Aggregate dissolution was observed after 2 days, which we attribute to bacteriophage-induced lysis of the attached bacteria. Isotope mass spectrometry analysis showed that 40% of the particulate C-13-organic carbon from the infected P. globosa culture was remineralized to dissolved inorganic carbon after 7 days. These findings reveal a novel role of viruses in the leakage or excretion of algal biomass upon infection, which provides an additional ecological niche for specific bacterial populations and potentially redirects carbon availability.
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- 2014
15. High rates of denitrification and nitrous oxide emission in arid biological soil crusts from the Sultanate of Oman
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Peter Stief, Dirk de Beer, Phyllis Lam, and Raeid M. M. Abed
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Denitrification ,Lichens ,Oman ,Nitrogen ,Nitrous Oxide ,stable isotopes ,Biology ,Cyanobacteria ,Microbiology ,biological soil crust ,Soil ,Denitrifying bacteria ,Ammonia ,Nitrogen Fixation ,Botany ,nitrogen cycle ,Nitrogen cycle ,Soil Microbiology ,Ecology, Evolution, Behavior and Systematics ,denitrification ,Bacteria ,Biological soil crust ,Genetic Variation ,Gene Expression Regulation, Bacterial ,Anoxic waters ,microsensors ,Anammox ,quantitative PCR ,Nitrogen fixation ,Original Article ,Soil microbiology - Abstract
Using a combination of process rate determination, microsensor profiling and molecular techniques, we demonstrated that denitrification, and not anaerobic ammonium oxidation (anammox), is the major nitrogen loss process in biological soil crusts from Oman. Potential denitrification rates were 584±101 and 58±20 μmol N m -2 h -1 for cyanobacterial and lichen crust, respectively. Complete denitrification to N 2 was further confirmed by an 15 NO 3 - tracer experiment with intact crust pieces that proceeded at rates of 103±19 and 27±8 μmol N m -2 h -1 for cyanobacterial and lichen crust, respectively. Strikingly, N 2 O gas was emitted at very high potential rates of 387±143 and 31±6 μmol N m -2 h -1 from the cyanobacterial and lichen crust, respectively, with N 2 O accounting for 53-66% of the total emission of nitrogenous gases. Microsensor measurements revealed that N 2 O was produced in the anoxic layer and thus apparently originated from incomplete denitrification. Using quantitative PCR, denitrification genes were detected in both the crusts and were expressed either in comparable (nirS) or slightly higher (narG) numbers in the cyanobacterial crusts. Although 99% of the nirS sequences in the cyanobacterial crust were affiliated to an uncultured denitrifying bacterium, 94% of these sequences were most closely affiliated to Paracoccus denitrificans in the lichen crust. Sequences of nosZ gene formed a distinct cluster that did not branch with known denitrifying bacteria. Our results demonstrate that nitrogen loss via denitrification is a dominant process in crusts from Oman, which leads to N 2 O gas emission and potentially reduces desert soil fertility.
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- 2013
16. The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium
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Lina Russ, Kees-Jan Francoijs, Jolein Gloerich, Wim Geerts, Phyllis Lam, Dagmar Woebken, Rudolf Amann, Wouter J. Maalcke, Wendy Pluk, Stefanie A Malfatti, Hans J. C. T. Wessels, Daan R. Speth, Suzanne C. M. Haaijer, Jia Yan, Jack van de Vossenberg, Eva M. Janssen-Megens, Bas E. Dutilh, Mike S. M. Jetten, Marcel M. M. Kuypers, Guus Roeselers, Henk Stunnenberg, Boran Kartal, Erwin van der Biezen, Huub J. M. Op den Camp, and Susannah G. Tringe
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Aquatic Organisms ,Nitrite Reductases ,Oceans and Seas ,Biomedical Innovation ,Oligopeptide transport ,Biology ,Microbiology ,Enrichment culture ,03 medical and health sciences ,Life ,RNA, Ribosomal, 16S ,14. Life underwater ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Research Articles ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Nitrogen Cycle ,biology.organism_classification ,Nitrite reductase ,Quaternary Ammonium Compounds ,Anammoxosome ,Planctomycetales ,MSB - Microbiology and Systems Biology ,Mitochondrial medicine [IGMD 8] ,Biochemistry ,Metagenomics ,Anammox ,Ecological Microbiology ,Candidatus ,Scalindua ,Metagenome ,Energy and redox metabolism Mitochondrial medicine [NCMLS 4] ,EELS - Earth, Environmental and Life Sciences ,Water Microbiology ,Oxidation-Reduction ,Healthy Living ,Genome, Bacterial - Abstract
Contains fulltext : 117292.pdf (Publisher’s version ) (Open Access) Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
- Published
- 2013
17. Controls over Ocean Mesopelagic Interior Carbon Storage (COMICS): fieldwork, synthesis and modelling efforts
- Author
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Geraint A. Tarling, Daniel J. Mayor, Mike Zubkov, Raffaele Bernardello, Peter Enderlein, Sinhue Torres-Valdes, Richard S. Lampitt, Morten Hvitfeldt Iversen, Andrew Yool, Kevin Saw, Richard Sanders, Phyllis Lam, Sarah L. C. Giering, George A. Wolff, Samar Khatiwala, Mark Moore, Sophie Fielding, Alex J. Poulton, Adrian Martin, Manuela Hartmann, Thomas R. Anderson, Stephanie A. Henson, Gabriele Stowasser, Stuart C. Painter, Eugene J. Murphy, and Mark Trimmer
- Subjects
0106 biological sciences ,Biogeochemical model ,lcsh:QH1-199.5 ,010504 meteorology & atmospheric sciences ,Mesopelagic zone ,chemistry.chemical_element ,Ocean Engineering ,lcsh:General. Including nature conservation, geographical distribution ,Aquatic Science ,Oceanography ,01 natural sciences ,Carbon cycle ,Science plan ,Marine Science ,field campaign ,14. Life underwater ,lcsh:Science ,0105 earth and related environmental sciences ,Water Science and Technology ,Total organic carbon ,Global and Planetary Change ,Remineralisation ,010604 marine biology & hydrobiology ,biological carbon pump ,Carbon storage ,chemistry ,13. Climate action ,Environmental science ,lcsh:Q ,Oceanic carbon cycle ,ocean carbon cycle ,Carbon - Abstract
The ocean’s biological carbon pump plays a central role in regulating atmospheric CO2 levels. In particular, the depth at which sinking organic carbon is broken down and respired in the mesopelagic zone is critical, with deeper remineralisation resulting in greater carbon storage. Until recently, however, a balanced budget of the supply and consumption of organic carbon in the mesopelagic had not been constructed in any region of the ocean, and the processes controlling organic carbon turnover are still poorly understood. Large-scale data syntheses suggest that a wide range of factors can influence remineralisation depth including upper-ocean ecological interactions, and interior dissolved oxygen concentration and temperature. However these analyses do not provide a mechanistic understanding of remineralisation, which increases the challenge of appropriately modelling the mesopelagic carbon dynamics. In light of this, the UK Natural Environment Research Council has funded a programme with this mechanistic understanding as its aim, drawing targeted fieldwork right through to implementation of a new parameterisation for mesopelagic remineralisation within an IPCC class global biogeochemical model. The Controls over Ocean Mesopelagic Interior Carbon Storage (COMICS) programme will deliver new insights into the processes of carbon cycling in the mesopelagic zone and how these influence ocean carbon storage. Here we outline the programme’s rationale, its goals, planned fieldwork and modelling activities, with the aim of stimulating international collaboration.
- Published
- 2016
18. GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms
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Rudolf Amann, Phyllis Lam, Cristina Moraru, Marcel M. M. Kuypers, and Bernhard M. Fuchs
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clone (Java method) ,Genetics ,In situ ,Phylogenetic tree ,biology ,medicine.diagnostic_test ,Microorganism ,Computational biology ,Ribosomal RNA ,biology.organism_classification ,Microbiology ,Crenarchaeota ,medicine ,Gene ,Ecology, Evolution, Behavior and Systematics ,Fluorescence in situ hybridization - Abstract
Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH - a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA-targeted catalysed reporter deposition - fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the T(m) of probes, targets and hybrids was estimated based on theoretical calculations and in vitro measurements. It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia.
- Published
- 2010
19. Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland)
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Hannah, Halm, Niculina, Musat, Phyllis, Lam, Rebecca, Langlois, Florin, Musat, Sandro, Peduzzi, Gaute, Lavik, Carsten J, Schubert, Bärbel, Sinha, Bärbel, Singha, Julie, LaRoche, and Marcel M M, Kuypers
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Denitrification ,Chromatium ,Nitrogen ,chemistry.chemical_element ,Fresh Water ,Chlorobium ,Biology ,Chemocline ,Microbiology ,Total inorganic carbon ,Nitrogen Fixation ,RNA, Ribosomal, 16S ,Botany ,Nitrogen cycle ,In Situ Hybridization ,Nitrites ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Carbon Dioxide ,biology.organism_classification ,Quaternary Ammonium Compounds ,Chlorobium tepidum ,chemistry ,Environmental chemistry ,Nitrogen fixation ,Oxidoreductases ,Switzerland - Abstract
The nitrogen cycling of Lake Cadagno was investigated by using a combination of biogeochemical and molecular ecological techniques. In the upper oxic freshwater zone inorganic nitrogen concentrations were low (up to approximately 3.4 microM nitrate at the base of the oxic zone), while in the lower anoxic zone there were high concentrations of ammonium (up to 40 microM). Between these zones, a narrow zone was characterized by no measurable inorganic nitrogen, but high microbial biomass (up to 4 x 10(7) cells ml(-1)). Incubation experiments with (15)N-nitrite revealed nitrogen loss occurring in the chemocline through denitrification (approximately 3 nM N h(-1)). At the same depth, incubations experiments with (15)N(2)- and (13)C(DIC)-labelled bicarbonate, indicated substantial N(2) fixation (31.7-42.1 pM h(-1)) and inorganic carbon assimilation (40-85 nM h(-1)). Catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and sequencing of 16S rRNA genes showed that the microbial community at the chemocline was dominated by the phototrophic green sulfur bacterium Chlorobium clathratiforme. Phylogenetic analyses of the nifH genes expressed as mRNA revealed a high diversity of N(2) fixers, with the highest expression levels right at the chemocline. The majority of N(2) fixers were related to Chlorobium tepidum/C. phaeobacteroides. By using Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS), we could for the first time directly link Chlorobium to N(2) fixation in the environment. Moreover, our results show that N(2) fixation could partly compensate for the N loss and that both processes occur at the same locale at the same time as suggested for the ancient Ocean.
- Published
- 2009
20. Revising the nitrogen cycle in the Peruvian oxygen minimum zone
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Dimitri Gutiérrez, Phyllis Lam, Rudolf Amann, Jack van de Vossenberg, Mike S. M. Jetten, Marlene Mark Jensen, Marcel M. M. Kuypers, Markus Schmid, Dagmar Woebken, and Gaute Lavik
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Biogeochemical cycle ,Denitrification ,Nitrogen ,chemistry.chemical_element ,Oxygen minimum zone ,Nitric Oxide ,chemistry.chemical_compound ,Nitrate ,Peru ,Organic matter ,Nitrogen cycle ,Nitrites ,chemistry.chemical_classification ,Multidisciplinary ,Bacteria ,Chemistry ,Ecology ,Gene Expression Regulation, Bacterial ,Oxygen ,Quaternary Ammonium Compounds ,Anammox ,Environmental chemistry ,Ecological Microbiology ,Commentary ,Oxidation-Reduction - Abstract
The oxygen minimum zone (OMZ) of the Eastern Tropical South Pacific (ETSP) is 1 of the 3 major regions in the world where oceanic nitrogen is lost in the pelagic realm. The recent identification of anammox, instead of denitrification, as the likely prevalent pathway for nitrogen loss in this OMZ raises strong questions about our understanding of nitrogen cycling and organic matter remineralization in these waters. Without detectable denitrification, it is unclear how NH 4 + is remineralized from organic matter and sustains anammox or how secondary NO 2 − maxima arise within the OMZ. Here we show that in the ETSP-OMZ, anammox obtains 67% or more of NO 2 − from nitrate reduction, and 33% or less from aerobic ammonia oxidation, based on stable-isotope pairing experiments corroborated by functional gene expression analyses. Dissimilatory nitrate reduction to ammonium was detected in an open-ocean setting. It occurred throughout the OMZ and could satisfy a substantial part of the NH 4 + requirement for anammox. The remaining NH 4 + came from remineralization via nitrate reduction and probably from microaerobic respiration. Altogether, deep-sea NO 3 − accounted for only ≈50% of the nitrogen loss in the ETSP, rather than 100% as commonly assumed. Because oceanic OMZs seem to be expanding because of global climate change, it is increasingly imperative to incorporate the correct nitrogen-loss pathways in global biogeochemical models to predict more accurately how the nitrogen cycle in our future ocean may respond.
- Published
- 2009
21. Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria
- Author
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Mike S. M. Jetten, Huub J. M. Op den Camp, Alan B. Hooper, Martin G. Klotz, Marcel M. M. Kuypers, Dagmar Woebken, Andreas Pommerening-Roeser, Phyllis Lam, and Markus Schmid
- Subjects
DNA, Bacterial ,Molecular Sequence Data ,Cytochrome c Group ,Hydroxylamine ,Biology ,Microbiology ,Polymerase Chain Reaction ,chemistry.chemical_compound ,Bacterial Proteins ,Oxidoreductase ,Environmental Microbiology ,Amino Acid Sequence ,Hydroxylamine Oxidoreductase ,Gene ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,DNA Primers ,chemistry.chemical_classification ,Sequence Analysis, DNA ,biology.organism_classification ,Hydrazines ,chemistry ,Biochemistry ,Anammox ,Ecological Microbiology ,Scalindua ,Primer (molecular biology) ,Oxidoreductases ,Sequence Alignment ,Bacteria - Abstract
Bacterial aerobic ammonium oxidation and anaerobic ammonium oxidation (anammox) are important processes in the global nitrogen cycle. Key enzymes in both processes are the octahaem cytochrome c (OCC) proteins, hydroxylamine oxidoreductase (HAO) of aerobic ammonium-oxidizing bacteria (AOB), which catalyses the oxidation of hydroxylamine to nitrite, and hydrazine oxidoreductase (HZO) of anammox bacteria, which converts hydrazine to N(2). While the genomes of AOB encode up to three nearly identical copies of hao operons, genome analysis of Candidatus'Kuenenia stuttgartiensis' showed eight highly divergent octahaem protein coding regions as possible candidates for the HZO. Based on their phylogenetic relationship and biochemical characteristics, the sequences of these eight gene products grouped in three clusters. Degenerate primers were designed on the basis of available gene sequences with the aim to detect hao and hzo genes in various ecosystems. The hao primer pairs amplified gene fragments from 738 to 1172 bp and the hzo primer pairs amplified gene fragments from 289 to 876 bp in length, when tested on genomic DNA isolated from a variety of AOB and anammox bacteria. A selection of these primer pairs was also used successfully to amplify and analyse the hao and hzo genes in community DNA isolated from different ecosystems harbouring both AOB and anammox bacteria. We propose that OCC protein-encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium-oxidizing bacteria.
- Published
- 2008
22. Methane oxidation coupled to oxygenic photosynthesis in anoxic waters
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Phyllis Lam, Mathias K. Kirf, Sten Littmann, Andreas Krupke, Jana Milucka, Carsten J. Schubert, Marcel M. M. Kuypers, and Lu Lu
- Subjects
Biogeochemical cycle ,Biology ,Photosynthesis ,Chemocline ,Microbiology ,Methane ,chemistry.chemical_compound ,Algae ,Ecology, Evolution, Behavior and Systematics ,Nitrites ,Carbon Isotopes ,Ecology ,Geomicrobiology ,Atmosphere ,Sulfates ,biology.organism_classification ,Anoxic waters ,Oxygen ,Lakes ,chemistry ,Environmental chemistry ,Anaerobic oxidation of methane ,Original Article ,Water Microbiology ,Oxidation-Reduction ,Gammaproteobacteria - Abstract
Freshwater lakes represent large methane sources that, in contrast to the Ocean, significantly contribute to non-anthropogenic methane emissions to the atmosphere. Particularly mixed lakes are major methane emitters, while permanently and seasonally stratified lakes with anoxic bottom waters are often characterized by strongly reduced methane emissions. The causes for this reduced methane flux from anoxic lake waters are not fully understood. Here we identified the microorganisms and processes responsible for the near complete consumption of methane in the anoxic waters of a permanently stratified lake, Lago di Cadagno. Interestingly, known anaerobic methanotrophs could not be detected in these waters. Instead, we found abundant gamma-proteobacterial aerobic methane-oxidizing bacteria active in the anoxic waters. In vitro incubations revealed that, among all the tested potential electron acceptors, only the addition of oxygen enhanced the rates of methane oxidation. An equally pronounced stimulation was also observed when the anoxic water samples were incubated in the light. Our combined results from molecular, biogeochemical and single-cell analyses indicate that methane removal at the anoxic chemocline of Lago di Cadagno is due to true aerobic oxidation of methane fuelled by in situ oxygen production by photosynthetic algae. A similar mechanism could be active in seasonally stratified lakes and marine basins such as the Black Sea, where light penetrates to the anoxic chemocline. Given the widespread occurrence of seasonally stratified anoxic lakes, aerobic methane oxidation coupled to oxygenic photosynthesis might have an important but so far neglected role in methane emissions from lakes.
- Published
- 2015
23. Autotrophic ammonia oxidation in a deep-sea hydrothermal plume
- Author
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James P. Cowen, Ronald D. Jones, and Phyllis Lam
- Subjects
Chemoautotrophic Growth ,Hot Temperature ,chemistry.chemical_element ,Mineralogy ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,Hydrothermal circulation ,Ammonia ,chemistry.chemical_compound ,Seawater ,Nitrosomonas ,In Situ Hybridization, Fluorescence ,Total organic carbon ,Ecology ,Betaproteobacteria ,biology.organism_classification ,humanities ,Plume ,chemistry ,Environmental chemistry ,Anaerobic oxidation of methane ,Nitrification ,Oxidation-Reduction ,Carbon - Abstract
Direct evidence for autotrophic ammonia oxidation is documented for the first time in a deep-sea hydrothermal plume. Elevated NH(4) (+) concentrations of up to 341+/-136 nM were recorded in the plume core at Main Endeavour Field, Juan de Fuca Ridge. This fueled autotrophic ammonia oxidation rates as high as 91 nM day(-1), or 92% of the total net NH(4) (+) removal. High abundance of ammonia-oxidizing bacteria was detected using fluorescence in situ hybridization. Ammonia-oxidizing bacteria within the plume core (1.0-1.4x10(4) cells ml(-1)) accounted for 7.0-7.5% of the total microbial community, and were at least as abundant as methanotrophs. Ammonia-oxidizing bacteria were a substantial component of the particle-associated communities (up to 51%), with a predominance of the r-strategist Nitrosomonas-like cells. In situ chemolithoautotrophic organic carbon production via ammonia oxidation may yield 3.9-18 mg C m(-2) day(-1) within the plume directly over Main Endeavour Field. This rate was comparable to that determined for methane oxidation in a previous study, or at least four-fold greater than the flux of photosynthetic carbon reaching plume depths measured in another study. Hence, autotrophic ammonia oxidation in the neutrally buoyant hydrothermal plume is significant to both carbon and nitrogen cycling in the deep-sea water column at Endeavour, and represents another important link between seafloor hydrothermal systems and deep-sea biogeochemistry.
- Published
- 2004
24. Processing Deep-Sea Particle-Rich Water Samples for Fluorescence In Situ Hybridization: Consideration of Storage Effects, Preservation, and Sonication
- Author
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James P. Cowen and Phyllis Lam
- Subjects
Polymers ,Sonication ,Preservation, Biological ,Particle (ecology) ,Fractionation ,Biology ,Applied Microbiology and Biotechnology ,law.invention ,law ,Formaldehyde ,Methods ,Seawater ,Particle Size ,In Situ Hybridization, Fluorescence ,Filtration ,Bacteriological Techniques ,Bacteria ,Ecology ,Pelagic zone ,Microbial population biology ,Environmental chemistry ,Particle size ,Food Science ,Biotechnology - Abstract
Particles are often regarded as microniches of enhanced microbial production and activities in the pelagic ocean and are vehicles of vertical material transport from the euphotic zone to the deep sea. Fluorescence in situ hybridization (FISH) can be a useful tool to study the microbial community structures associated with these particles, and thus their ecological significance, yet an appropriate protocol for processing deep-sea particle-rich water samples is lacking. Some sample processing considerations are discussed in the present study, and different combinations of existing procedures for preservation, size fractionation sequential filtration, and sonication were tested in conjunction with FISH. Results from this study show that water samples should be filtered and processed within no more than 10 to 12 h after collection, or else preservation is necessary. The commonly used prefiltration formaldehyde fixation was shown to be inadequate for the rRNA targeted by FISH. However, prefiltration formaldehyde fixation followed by immediate freezing and postfiltration paraformaldehyde fixation yielded highly consistent cell abundance estimates even after 96 days or potentially longer storage. Size fractionation sequential filtration and sonication together enhanced cell abundance estimates by severalfold. Size fractionation sequential filtration effectively separated particle-associated microbial communities from their free-living counterparts, while sonication detached cells from particles or aggregates for more-accurate cell counting using epifluorescence microscopy. Optimization in sonication time is recommended for different specific types of samples. These tested and optimized procedures can be incorporated into a FISH protocol for sampling in deep-sea particle-rich waters.
- Published
- 2004
25. Microbial biomass in the hydrothermal plumes associated with the 1998 Axial Volcano Eruption
- Author
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Donald McGee, Rachel Shackelford, Phyllis Lam, James P. Cowen, Edward T. Baker, and Eric J. Olson
- Subjects
geography ,Biomass (ecology) ,geography.geographical_feature_category ,Mineralogy ,Mid-ocean ridge ,humanities ,Hydrothermal circulation ,Plume ,Geophysics ,Water column ,Volcano ,Panache ,General Earth and Planetary Sciences ,Caldera ,Geology - Abstract
The Axial Response Team (ART-1) documented greatly intensified chronic-style hydrothermal plumes at Axial Volcano following a 1998 eruptive event. Significantly higher numbers of bacteria were found in the plume versus background stations and depths, due largely to 5 samples with high numbers (to 1.8×105 /ml) in far field stations. Highest ratios (0.20) of metal depositing capsuled bacteria to total bacteria were found in the near-field (over caldera) plume. An unusual capsule form (FeCap), that dominated the near field plume capsule populations, was present in all plume samples, but were absent in background samples. Multi-cell filaments, metal-encrusted sheathed clusters and matrix-enmeshed colonies, all uncommon in the water column, were also present in plume samples
- Published
- 1999
26. Nitrogen Cycling Driven By Organic Matter Export In The South Pacific Oxygen Minimum Zone
- Author
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Tim Kalvelage, Lionel Arteaga, Carolin R. Löscher, Lothar Stramma, Phyllis Lam, Gaute Lavik, Aurélien Paulmier, Marcel M. M. Kuypers, Sergio Contreras, Andreas Oschlies, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Large Lakes Observatory, University of Minnesota [Duluth], University of Minnesota System-University of Minnesota System, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Institute for General Microbiology, DYNBIO LEGOS, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Instituto del Mar del Peru (IMARPE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,Denitrification ,010504 meteorology & atmospheric sciences ,CYCLE DE L'AZOTE ,chemistry.chemical_element ,UPWELLING ,Oxygen minimum zone ,NITRIFICATION ,01 natural sciences ,ANAMMOX ,WATERS ,CYCLE BIOGEOCHIMIQUE ,OCEAN ,Organic matter ,14. Life underwater ,Nitrogen cycle ,0105 earth and related environmental sciences ,chemistry.chemical_classification ,[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere ,ARABIAN SEA ,010604 marine biology & hydrobiology ,Biogeochemistry ,NITRITE ,DENITRIFICATION ,16. Peace & justice ,OXYGENE ,Nitrogen ,ANAEROBIC AMMONIUM OXIDATION ,Oceanography ,chemistry ,13. Climate action ,Anammox ,General Earth and Planetary Sciences ,Environmental science ,Nitrification ,DEFICIENT CONDITIONS ,MARINE - Abstract
Oxygen minimum zones are expanding globally, and at present account for around 20-40% of oceanic nitrogen loss. Heterotrophic denitrification and anammox-anaerobic ammonium oxidation with nitrite-are responsible for most nitrogen loss in these low-oxygen waters. Anammox is particularly significant in the eastern tropical South Pacific, one of the largest oxygen minimum zones globally. However, the factors that regulate anammox-driven nitrogen loss have remained unclear. Here, we present a comprehensive nitrogen budget for the eastern tropical South Pacific oxygen minimum zone, using measurements of nutrient concentrations, experimentally determined rates of nitrogen transformation and a numerical model of export production. Anammox was the dominant mode of nitrogen loss at the time of sampling. Rates of anammox, and related nitrogen transformations, were greatest in the productive shelf waters, and tailed off with distance from the coast. Within the shelf region, anammox activity peaked in both upper and bottom waters. Overall, rates of nitrogen transformation, including anammox, were strongly correlated with the export of organic matter. We suggest that the sinking of organic matter, and thus the release of ammonium into the water column, together with benthic ammonium release, fuel nitrogen loss from oxygen minimum zones.
- Published
- 2013
27. Nitrite oxidation in the Namibian oxygen minimum zone
- Author
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Marcel M. M. Kuypers, Moritz Holtappels, Phyllis Lam, Marlene Mark Jensen, Marcel Günter, Gaute Lavik, and Jessika Füssel
- Subjects
Denitrification ,Nitrogen ,Oceans and Seas ,Microbial metabolism ,chemistry.chemical_element ,Biology ,Microbiology ,chemistry.chemical_compound ,Nitrate ,Ammonia ,Seawater ,Nitrite ,Nitrogen cycle ,In Situ Hybridization, Fluorescence ,Nitrites ,Ecology, Evolution, Behavior and Systematics ,Nitrates ,Bacteria ,Nitrogen Isotopes ,Ecology ,Namibia ,Nitrification ,Oxygen ,chemistry ,Anammox ,Environmental chemistry ,Original Article ,Water Microbiology ,Oxidation-Reduction - Abstract
Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in (15)N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (≤372 nM NO(2)(-) d(-1)) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ~9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO(3)(-) was re-oxidized back to NO(3)(-) via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.
- Published
- 2012
28. Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones
- Author
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Marlene Mark Jensen, Niels Peter Revsbech, Marcel Günter, Phyllis Lam, Gaute Lavik, Sergio Contreras, Julie LaRoche, Marcel M. M. Kuypers, and Tim Kalvelage
- Subjects
0106 biological sciences ,010504 meteorology & atmospheric sciences ,lcsh:Medicine ,Marine and Aquatic Sciences ,Oceanography ,01 natural sciences ,Oxygen ,Marine Conservation ,chemistry.chemical_compound ,Marine bacteriophage ,Nutrient ,Global Change Ecology ,Microbial Physiology ,lcsh:Science ,Conservation Science ,Multidisciplinary ,Ecology ,Chemical Oceanography ,Marine Ecology ,Nitrogen ,Anammox ,Environmental chemistry ,Anaerobic exercise ,Oxidation-Reduction ,Research Article ,inorganic chemicals ,chemistry.chemical_element ,Marine Biology ,Biology ,Microbiology ,Ammonia ,Marine Monitoring ,14. Life underwater ,SDG 14 - Life Below Water ,0105 earth and related environmental sciences ,Chemical Ecology ,010604 marine biology & hydrobiology ,lcsh:R ,Biological Oceanography ,Marine Environments ,Quaternary Ammonium Compounds ,chemistry ,13. Climate action ,Earth Sciences ,lcsh:Q ,Surface water ,Ecological Environments - Abstract
Nutrient measurements indicate that 30-50% of the total nitrogen (N) loss in the ocean occurs in oxygen minimum zones (OMZs). This pelagic N-removal takes place within only ~0.1% of the ocean volume, hence moderate variations in the extent of OMZs due to global warming may have a large impact on the global N-cycle. We examined the effect of oxygen (O(2)) on anammox, NH(3) oxidation and NO(3)(-) reduction in (15)N-labeling experiments with varying O(2) concentrations (0-25 µmol L(-1)) in the Namibian and Peruvian OMZs. Our results show that O(2) is a major controlling factor for anammox activity in OMZ waters. Based on our O(2) assays we estimate the upper limit for anammox to be ~20 µmol L(-1). In contrast, NH(3) oxidation to NO(2)(-) and NO(3)(-) reduction to NO(2)(-) as the main NH(4)(+) and NO(2)(-) sources for anammox were only moderately affected by changing O(2) concentrations. Intriguingly, aerobic NH(3) oxidation was active at non-detectable concentrations of O(2), while anaerobic NO(3)(-) reduction was fully active up to at least 25 µmol L(-1) O(2). Hence, aerobic and anaerobic N-cycle pathways in OMZs can co-occur over a larger range of O(2) concentrations than previously assumed. The zone where N-loss can occur is primarily controlled by the O(2)-sensitivity of anammox itself, and not by any effects of O(2) on the tightly coupled pathways of aerobic NH(3) oxidation and NO(3)(-) reduction. With anammox bacteria in the marine environment being active at O(2) levels ~20 times higher than those known to inhibit their cultured counterparts, the oceanic volume potentially acting as a N-sink increases tenfold. The predicted expansion of OMZs may enlarge this volume even further. Our study provides the first robust estimates of O(2) sensitivities for processes directly and indirectly connected with N-loss. These are essential to assess the effects of ocean de-oxygenation on oceanic N-cycling.
- Published
- 2011
29. Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre
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Marcel M. M. Kuypers, Hannah Halm, Timothy G. Ferdelman, Thorsten Dittmar, Steven D'Hondt, Julie LaRoche, Phyllis Lam, and Gaute Lavik
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Nitrogen ,Biology ,Cyanobacteria ,Microbiology ,Polymerase Chain Reaction ,Ocean gyre ,Nitrogen Fixation ,Dissolved organic carbon ,Seawater ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,Phylogeny ,South Pacific Gyre ,geography ,Carbon Isotopes ,geography.geographical_feature_category ,Pacific Ocean ,Nitrogen Isotopes ,Ecology ,Heterotrophic Processes ,biology.organism_classification ,Isotopes of nitrogen ,Trichodesmium ,Nitrogen fixation ,Original Article ,Diazotroph ,Seasons ,Water Microbiology ,Gammaproteobacteria - Abstract
Oceanic subtropical gyres are considered biological deserts because of the extremely low availability of nutrients and thus minimum productivities. The major source of nutrient nitrogen in these ecosystems is N(2)-fixation. The South Pacific Gyre (SPG) is the largest ocean gyre in the world, but measurements of N(2)-fixation therein, or identification of microorganisms involved, are scarce. In the 2006/2007 austral summer, we investigated nitrogen and carbon assimilation at 11 stations throughout the SPG. In the ultra-oligotrophic waters of the SPG, the chlorophyll maxima reached as deep as 200 m. Surface primary production seemed limited by nitrogen, as dissolved inorganic carbon uptake was stimulated upon additions of (15)N-labeled ammonium and leucine in our incubation experiments. N(2)-fixation was detectable throughout the upper 200 m at most stations, with rates ranging from 0.001 to 0.19 nM N h(-1). N(2)-fixation in the SPG may account for the production of 8-20% of global oceanic new nitrogen. Interestingly, comparable (15)N(2)-fixation rates were measured under light and dark conditions. Meanwhile, phylogenetic analyses for the functional gene biomarker nifH and its transcripts could not detect any common photoautotrophic diazotrophs, such as, Trichodesmium, but a prevalence of γ-proteobacteria and the unicellular photoheterotrophic Group A cyanobacteria. The dominance of these likely heterotrophic diazotrophs was further verified by quantitative PCR. Hence, our combined results show that the ultra-oligotrophic SPG harbors a hitherto unknown heterotrophic diazotrophic community, clearly distinct from other oceanic gyres previously visited.
- Published
- 2011
30. Intensive nitrogen loss over the omani shelf due to anammox coupled with dissimilatory nitrite reduction to ammonium
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Phyllis Lam, Mike M. M. Jetten, Birgit Gaye, Marlene Mark Jensen, Birgit Nagel, Niels Peter Revsbech, and Marcel M. M. Kuypers
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Denitrification ,Oman ,Nitrogen ,Oceans and Seas ,Biology ,Oxygen minimum zone ,Microbiology ,chemistry.chemical_compound ,Seawater ,Ammonium ,Organic matter ,Nitrite ,Nitrites ,Ecology, Evolution, Behavior and Systematics ,chemistry.chemical_classification ,Bacteria ,Nitrogen Isotopes ,Ecology ,Anoxic waters ,Carbon ,Oxygen ,Quaternary Ammonium Compounds ,Oceanography ,chemistry ,Anammox ,Ecological Microbiology ,Upwelling ,Original Article ,Oxidation-Reduction - Abstract
A combination of stable isotopes ((15)N) and molecular ecological approaches was used to investigate the vertical distribution and mechanisms of biological N(2) production along a transect from the Omani coast to the central-northeastern (NE) Arabian Sea. The Arabian Sea harbors the thickest oxygen minimum zone (OMZ) in the world's oceans, and is considered to be a major site of oceanic nitrogen (N) loss. Short (48 h) anoxic incubations with (15)N-labeled substrates and functional gene expression analyses showed that the anammox process was highly active, whereas denitrification was hardly detectable in the OMZ over the Omani shelf at least at the time of our sampling. Anammox was coupled with dissimilatory nitrite reduction to ammonium (DNRA), resulting in the production of double-(15)N-labeled N(2) from (15)NO(2)(-), a signal often taken as the lone evidence for denitrification in the past. Although the central-NE Arabian Sea has conventionally been regarded as the primary N-loss region, low potential N-loss rates at sporadic depths were detected at best. N-loss activities in this region likely experience high spatiotemporal variabilities as linked to the availability of organic matter. Our finding of greater N-loss associated with the more productive Omani upwelling region is consistent with results from other major OMZs. The close reliance of anammox on DNRA also highlights the need to take into account the effects of coupling N-transformations on oceanic N-loss and subsequent N-balance estimates.
- Published
- 2011
31. Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones
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Phyllis Lam and Marcel M. M. Kuypers
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chemistry.chemical_classification ,Biogeochemical cycle ,Denitrification ,Nitrates ,Bacteria ,Ecology ,Oceans and Seas ,Nitrogen Cycle ,Oceanography ,Anoxic waters ,Oxygen ,chemistry.chemical_compound ,chemistry ,Nitrate ,Anammox ,Nitrification ,Organic matter ,Nitrogen cycle - Abstract
Oxygen minimum zones (OMZs) harbor unique microbial communities that rely on alternative electron acceptors for respiration. Conditions therein enable an almost complete nitrogen (N) cycle and substantial N-loss. N-loss in OMZs is attributable to anammox and heterotrophic denitrification, whereas nitrate reduction to nitrite along with dissimilatory nitrate reduction to ammonium are major remineralization pathways. Despite virtually anoxic conditions, nitrification also occurs in OMZs, converting remineralized ammonium to N-oxides. The concurrence of all these processes provides a direct channel from organic N to the ultimate N-loss, whereas most individual processes are likely controlled by organic matter. Many microorganisms inhabiting the OMZs are capable of multiple functions in the N- and other elemental cycles. Their versatile metabolic potentials versus actual activities present a challenge to ecophysiological and biogeochemical measurements. These challenges need to be tackled before we can realistically predict how N-cycling in OMZs, and thus oceanic N-balance, will respond to future global perturbations.
- Published
- 2011
32. GeneFISH--an in situ technique for linking gene presence and cell identity in environmental microorganisms
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Cristina, Moraru, Phyllis, Lam, Bernhard M, Fuchs, Marcel M M, Kuypers, and Rudolf, Amann
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Aquatic Organisms ,Base Sequence ,Molecular Sequence Data ,Polynucleotides ,Crenarchaeota ,Sequence Analysis, DNA ,Models, Theoretical ,Nucleic Acid Denaturation ,Polymerase Chain Reaction ,Sensitivity and Specificity ,Africa, Southern ,Genes, Archaeal ,RNA, Ribosomal, 16S ,Escherichia coli ,Seawater ,Oligonucleotide Probes ,Oxidoreductases ,Atlantic Ocean ,Oxidation-Reduction ,In Situ Hybridization, Fluorescence ,Phylogeny ,Gene Library - Abstract
Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH - a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA-targeted catalysed reporter deposition - fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the T(m) of probes, targets and hybrids was estimated based on theoretical calculations and in vitro measurements. It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia.
- Published
- 2010
33. A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones
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Boran Kartal, Phyllis Lam, Bernhard M. Fuchs, Marc Strous, S. Wajih A. Naqvi, Rudolf Amann, Marcel M. M. Kuypers, Dagmar Woebken, and Mike S. M. Jetten
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DNA, Bacterial ,Genotype ,Molecular Sequence Data ,Population ,Zoology ,DNA, Ribosomal ,Microbiology ,Bacteria, Anaerobic ,RNA, Ribosomal, 16S ,Sequence Homology, Nucleic Acid ,DNA, Ribosomal Spacer ,Cluster Analysis ,Seawater ,Internal transcribed spacer ,education ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Phylotype ,education.field_of_study ,biology ,Ecology ,Genes, rRNA ,Biodiversity ,Sequence Analysis, DNA ,Ribosomal RNA ,biology.organism_classification ,16S ribosomal RNA ,RNA, Bacterial ,Anammox ,Ecological Microbiology ,Candidatus ,Scalindua - Abstract
The anaerobic oxidation of ammonium (anammox) contributes significantly to the global loss of fixed nitrogen and is carried out by a deep branching monophyletic group of bacteria within the phylum Planctomycetes. Various studies have implicated anammox to be the most important process responsible for the nitrogen loss in the marine oxygen minimum zones (OMZs) with a low diversity of marine anammox bacteria. This comprehensive study investigated the anammox bacteria in the suboxic zone of the Black Sea and in three major OMZs (off Namibia, Peru and in the Arabian Sea). The diversity and population composition of anammox bacteria were investigated by both, the 16S rRNA gene sequences and the 16S-23S rRNA internal transcribed spacer (ITS). Our results showed that the anammox bacterial sequences of the investigated samples were all closely related to the Candidatus Scalindua genus. However, a greater microdiversity of marine anammox bacteria than previously assumed was observed. Both phylogenetic markers supported the classification of all sequences in two distinct anammox bacterial phylotypes: Candidatus Scalindua clades 1 and 2. Scalindua 1 could be further divided into four distinct clusters, all comprised of sequences from either the Namibian or the Peruvian OMZ. Scalindua 2 consisted of sequences from the Arabian Sea and the Peruvian OMZ and included one previously published 16S rRNA gene sequence from Lake Tanganyika and one from South China Sea sediment (97.9-99.4% sequence identity). This cluster showed only
- Published
- 2008
34. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs
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Rudolf Amann, Marc Mußmann, Phyllis Lam, Bernhard M. Fuchs, Ulrich Lass, Anja van der Plas, Torben Stührmann, Volker Brüchert, Marcel M. M. Kuypers, Volker Mohrholz, and Gaute Lavik
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Oceans and Seas ,Molecular Sequence Data ,chemistry.chemical_element ,Biology ,chemistry.chemical_compound ,Nitrate ,RNA, Ribosomal, 16S ,Proteobacteria ,Ecosystem ,Seawater ,Hydrogen Sulfide ,Phylogeny ,geography ,Multidisciplinary ,geography.geographical_feature_category ,Continental shelf ,Sulfates ,Nekton ,fungi ,Bacterioplankton ,Eutrophication ,Sulfur ,Namibia ,Oceanography ,Biodegradation, Environmental ,chemistry ,Benthic zone ,Oxidation-Reduction - Abstract
Coastal waters support approximately 90 per cent of global fisheries and are therefore an important food reserve for our planet. Eutrophication of these waters, due to human activity, leads to severe oxygen depletion and the episodic occurrence of hydrogen sulphide-toxic to multi-cellular life-with disastrous consequences for coastal ecosytems. Here we show that an area of approximately 7,000 km(2) of African shelf, covered by sulphidic water, was detoxified by blooming bacteria that oxidized the biologically harmful sulphide to environmentally harmless colloidal sulphur and sulphate. Combined chemical analyses, stoichiometric modelling, isotopic incubations, comparative 16S ribosomal RNA, functional gene sequence analyses and fluorescence in situ hybridization indicate that the detoxification proceeded by chemolithotrophic oxidation of sulphide with nitrate and was mainly catalysed by two discrete populations of gamma- and epsilon-proteobacteria. Chemolithotrophic bacteria, accounting for approximately 20 per cent of the bacterioplankton in sulphidic waters, created a buffer zone between the toxic sulphidic subsurface waters and the oxic surface waters, where fish and other nekton live. This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been observed in an open-ocean system. The data suggest that sulphide can be completely consumed by bacteria in the subsurface waters and, thus, can be overlooked by remote sensing or monitoring of shallow coastal waters. Consequently, sulphidic bottom waters on continental shelves may be more common than previously believed, and could therefore have an important but as yet neglected effect on benthic communities.
- Published
- 2007
35. Fluids from aging ocean crust that support microbial life
- Author
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Phyllis Lam, Michael S. Rappé, Stephen J. Giovannoni, James P. Cowen, H. Paul Johnson, M. Hutnak, Fabien Kenig, and David A. Butterfield
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Geologic Sediments ,Geochemistry ,Carboxylic Acids ,Electrons ,Biology ,Bacterial Physiological Phenomena ,chemistry.chemical_compound ,Paleontology ,Oceanic crust ,Ammonia ,Nitrogen Fixation ,Seawater ,Hydrogen Sulfide ,Sulfate ,Phylogeny ,geography ,Multidisciplinary ,geography.geographical_feature_category ,Nitrates ,Pacific Ocean ,Bacteria ,Sulfates ,Thermophile ,Temperature ,Biogeochemistry ,Mid-ocean ridge ,Crust ,Genes, rRNA ,biology.organism_classification ,Archaea ,Hydrocarbons ,chemistry ,Fermentation ,Oceanic basin ,Oxidation-Reduction ,Hydrogen - Abstract
Little is known about the potential for life in the vast, low-temperature (
- Published
- 2003
36. Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone
- Author
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Dimitri Gutiérrez, Ellen C. Hopmans, Dagmar Woebken, Michelle Graco, Jayne E. Rattray, Phyllis Lam, Siegfried Krüger, Gaute Lavik, Jaap S. Sinninghe Damsté, M. Robert Hamersley, and Marcel M. M. Kuypers
- Subjects
Denitrification ,biology ,Microorganism ,Aquatic Science ,Oceanography ,Oxygen minimum zone ,biology.organism_classification ,Anammoxosome ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Anammox ,Environmental chemistry ,Scalindua ,Ammonium ,Ladderane - Abstract
We investigated the microbial pathways of nitrogen (N) loss in an April 2005 transect through the Peruvian oxygen minimum zone (OMZ) at 12°S latitude using short anaerobic incubations with 15N-labeled substrates and molecular–ecological and lipid–biomarker studies. In incubations with 15NH4+, immediate production of 14N15N, but not 15N15N, indicated that N2 was produced by the pairing of labeled 15NH4+ with in situ 14NO2- via anaerobic ammonium oxidation (anammox). Supporting this finding, we also found anammox-related 16S ribosomal ribonucleic acid gene sequences similar to those previously known from other marine water columns in which anammox activity was measured. We identified and enumerated anammox bacteria via fluorescence in situ hybridization and quantitative polymerase chain reaction and found ladderane membrane lipids specific to anammox bacteria wherever anammox activity was measured by our isotope tracer method. However, in incubations with 15NO3- or 15NO2-, in which denitrification would have been expected to produce 15N15N by pairing of oxidized 15N ions, 15N15N production was not detected before 24 h, showing that denitrification of fixed N to N2 was not taking place in our samples. At the time and locality of our study, anammox, rather than denitrification, was responsible for N2 production in the Peruvian OMZ waters.
37. Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea
- Author
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Carsten J. Schubert, Marlene Mark Jensen, Phyllis Lam, Beat Müller, Rudolf Amann, Marcell M.M. Kuypers, Bo Thamdrup, Gaute Lavik, and Daniel Frank Mcginnis
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Multidisciplinary ,biology ,Nitrosopumilus ,Ammonia monooxygenase ,biology.organism_classification ,chemistry.chemical_compound ,Nitrate ,chemistry ,Crenarchaeota ,Anammox ,Botany ,Nitrification ,Nitrite ,Nitrogen cycle - Abstract
Active expression of putative ammonia monooxygenase gene subunit A ( amoA ) of marine group I Crenarchaeota has been detected in the Black Sea water column. It reached its maximum, as quantified by reverse-transcription quantitative PCR, exactly at the nitrate maximum or the nitrification zone modeled in the lower oxic zone. Crenarchaeal amoA expression could explain 74.5% of the nitrite variations in the lower oxic zone. In comparison, amoA expression by γ-proteobacterial ammonia-oxidizing bacteria (AOB) showed two distinct maxima, one in the modeled nitrification zone and one in the suboxic zone. Neither the amoA expression by crenarchaea nor that by β-proteobacterial AOB was significantly elevated in this latter zone. Nitrification in the suboxic zone, most likely microaerobic in nature, was verified by 15 NO 2 − and 15 N 15 N production in 15 NH 4 + incubations with no measurable oxygen. It provided a direct local source of nitrite for anammox in the suboxic zone. Both ammonia-oxidizing crenarchaea and γ-proteobacterial AOB were important nitrifiers in the Black Sea and were likely coupled to anammox in indirect and direct manners respectively. Each process supplied about half of the nitrite required by anammox, based on 15 N-incubation experiments and modeled calculations. Because anammox is a major nitrogen loss in marine suboxic waters, such nitrification–anammox coupling potentially occurring also in oceanic oxygen minimum zones would act as a short circuit connecting regenerated ammonium to direct nitrogen loss, thus reducing the presumed direct contribution from deep-sea nitrate.
38. High rates of denitrification and nitrous oxide emission in biological soil crusts from the Sultanate of Oman
- Author
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Abed, Raeid M. M., Phyllis Lam, Dirk de Beer, and Peter Stief
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