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Physical mixing in coastal waters controls and decouples nitrification via biomass dilution. Proc Natl Acad Sci U S A 2021; 118:2004877118. [PMID: 33903227 PMCID: PMC8106330 DOI: 10.1073/pnas.2004877118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Changes in both quantity and speciation of nitrogen in coastal waters impact phytoplankton communities, contributing to eutrophication and harmful algal blooms. Multidisciplinary oceanographic time series of high resolution are rare but crucial for identifying complex mechanisms that underlie such anthropogenic impacts. Analysis and modeling of such a time series from a seasonally stratified fjord showed that dilution of nitrifier biomass by variable winter mixing altered the timing and rates of nitrification, which converts ammonia to nitrite and nitrate. This reveals a link among climate-sensitive physical dynamics, nitrifier abundance, and diversity, with controls on phytoplankton ecology. The findings imply that explicit measurement and modeling of microbial communities will be required to project impacts of climate change on coastal ecosystems. Nitrification is a central process of the aquatic nitrogen cycle that controls the supply of nitrate used in other key processes, such as phytoplankton growth and denitrification. Through time series observation and modeling of a seasonally stratified, eutrophic coastal basin, we demonstrate that physical dilution of nitrifying microorganisms by water column mixing can delay and decouple nitrification. The findings are based on a 4-y, weekly time series in the subsurface water of Bedford Basin, Nova Scotia, Canada, that included measurement of functional (amoA) and phylogenetic (16S rRNA) marker genes. In years with colder winters, more intense winter mixing resulted in strong dilution of resident nitrifiers in subsurface water, delaying nitrification for weeks to months despite availability of ammonium and oxygen. Delayed regrowth of nitrifiers also led to transient accumulation of nitrite (3 to 8 μmol · kgsw−1) due to decoupling of ammonia and nitrite oxidation. Nitrite accumulation was enhanced by ammonia-oxidizing bacteria (Nitrosomonadaceae) with fast enzyme kinetics, which temporarily outcompeted the ammonia-oxidizing archaea (Nitrosopumilus) that dominated under more stable conditions. The study reveals how physical mixing can drive seasonal and interannual variations in nitrification through control of microbial biomass and diversity. Variable, mixing-induced effects on functionally specialized microbial communities are likely relevant to biogeochemical transformation rates in other seasonally stratified water columns. The detailed study reveals a complex mechanism through which weather and climate variability impacts nitrogen speciation, with implications for coastal ecosystem productivity. It also emphasizes the value of high-frequency, multiparameter time series for identifying complex controls of biogeochemical processes in aquatic systems.
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52
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Back DY, Ha SY, Else B, Hanson M, Jones SF, Shin KH, Tatarek A, Wiktor JM, Cicek N, Alam S, Mundy CJ. On the impact of wastewater effluent on phytoplankton in the Arctic coastal zone: A case study in the Kitikmeot Sea of the Canadian Arctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:143861. [PMID: 33383224 DOI: 10.1016/j.scitotenv.2020.143861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
We present a case study on the impact of effluent from a wastewater lagoon-wetland system on phytoplankton and local primary production near a coastal Arctic community (Cambridge Bay) over spring to fall 2018. Results are also placed within an interannual and regional context for the surrounding Kitikmeot Sea. We find the shallow, relatively fresh Kitikmeot Sea is one of the most nutrient-deplete regions of the Arctic Ocean with NO3- + NO2- concentrations below the surface mixed layer rarely exceeding 2 μmol L-1 and a N:Si:P ratio of 1:6:1. The fjordal-type bathymetry of the main study site and a persistent pycnocline below the bay's exit sill led to slightly elevated N:Si:P of 3:11:1 through trapping of wastewater-sourced N at depth via sinking and remineralization of primary production. Total production in Cambridge Bay over the 3-month open water period was 12.1 g C m-2 with 70% of this production occurring during the 1-month discharge of wastewater into the system. Local primary production responded rapidly to high NO3- + NO2-, NH4+ and PON concentrations provided by wastewater effluent, comprising up to 20% of the production during the discharge period. Remaining production was mostly explained by the deep nutrient pool in the bay, which was only accessed towards the end of the discharge period as the diatom-dominated deep chlorophyll maximum settled below the pycnocline. Although not yet eutrophic, caution is raised at the rapid response of the marine system to wastewater release with a strong recommendation to develop a research and monitoring plan for the bay.
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Affiliation(s)
- Dong-Young Back
- Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
| | - Sun-Yong Ha
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Brent Else
- Department of Geography, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mark Hanson
- Department of Environment and Geography, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Samantha F Jones
- Department of Geography, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Kyung-Hoon Shin
- Department of Marine Sciences and Convergent Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Agnieszka Tatarek
- Department of Ecology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Józef M Wiktor
- Department of Ecology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Nazim Cicek
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Shah Alam
- Department of Community and Government Services, Government of Nunavut, Cambridge Bay, NU X0B 0C0, Canada
| | - C J Mundy
- Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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53
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Temino-Boes R, García-Bartual R, Romero I, Romero-Lopez R. Future trends of dissolved inorganic nitrogen concentrations in Northwestern Mediterranean coastal waters under climate change. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 282:111739. [PMID: 33461817 DOI: 10.1016/j.jenvman.2020.111739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/04/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Coastal ecosystems are amongst the most vulnerable to climate change, due to their location at the land-sea interface. In coastal waters, the nitrogen cycle can be significantly altered by rising temperatures and other factors derived from climate change, affecting phytoplankton and higher trophic levels. This research analyzes the effect of meteorological variables on dissolved inorganic nitrogen (DIN) species in coastal inshore waters of a Northwestern Mediterranean region under climate change. We built simple mathematical schemes based on artificial neural networks (ANN), trained with field data. Then, we used regional climatic projections for the Spanish Mediterranean coast to provide inputs to the trained ANNs, and thus, allowing the estimation of future DIN trends throughout the 21st century. The results obtained indicate that nitrite and nitrate concentrations are expected to decrease mainly due to rising temperatures and decreasing continental inputs. Major changes are projected for the winter season, driven by a rise in minimum temperatures which decrease the nitrite and nitrate peaks observed at low temperatures. Ammonium concentrations are not expected to undergo a significant annual trend but may either increase or decrease during some months. These results entail a preliminary simplified approach to estimate the impact of meteorological changes on DIN concentrations in coastal waters under climate change.
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Affiliation(s)
- Regina Temino-Boes
- Instituto de Ingeniería del Agua y del Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, Valencia, 46022, Spain.
| | - Rafael García-Bartual
- Instituto de Ingeniería del Agua y del Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, Valencia, 46022, Spain
| | - Inmaculada Romero
- Instituto de Ingeniería del Agua y del Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, Valencia, 46022, Spain
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54
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Parsons C, Stüeken EE, Rosen CJ, Mateos K, Anderson RE. Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. GEOBIOLOGY 2021; 19:18-34. [PMID: 33108025 PMCID: PMC7894544 DOI: 10.1111/gbi.12419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N2 . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.
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Affiliation(s)
- Chris Parsons
- Carleton CollegeNorthfieldMNUSA
- Massachusetts Institute of TechnologyCambridgeMAUSA
| | | | | | | | - Rika E. Anderson
- Carleton CollegeNorthfieldMNUSA
- NASA NExSS Virtual Planetary LaboratoryUniversity of WashingtonSeattleWAUSA
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55
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Liu Y, Ding H, Sun Y, Li Y, Lu A. Genome Analysis of a Marine Bacterium Halomonas sp. and Its Role in Nitrate Reduction under the Influence of Photoelectrons. Microorganisms 2020; 8:E1529. [PMID: 33027938 PMCID: PMC7650824 DOI: 10.3390/microorganisms8101529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 11/17/2022] Open
Abstract
The solar light response and photoelectrons produced by widespread semiconducting mineral play important roles in biogeochemical cycles on Earth's surface. To explore the potential influence of photoelectrons generated by semiconducting mineral particles on nitrate-reducing microorganisms in the photic zone, a marine heterotrophic denitrifier Halomonas sp. strain 3727 was isolated from seawater in the photic zone of the Yellow Sea, China. This strain was classified as a Halomonadaceae. Whole-genome analysis indicated that this strain possessed genes encoding the nitrogen metabolism, i.e., narG, nasA, nirBD, norZ, nosB, and nxr, which sustained dissimilatory nitrate reduction, assimilatory nitrate reduction, and nitrite oxidation. This strain also possessed genes related to carbon, sulfur, and other metabolisms, hinting at its substantial metabolic flexibility. A series of microcosm experiments in a simulative photoelectron system was conducted, and the results suggested that this bacterial strain could use simulated photoelectrons with different energy for nitrate reduction. Nitrite, as an intermediate product, was accumulated during the nitrate reduction with limited ammonia residue. The nitrite and ammonia productions differed with or without different energy electron supplies. Nitrite was the main product accounting for 30.03% to 68.40% of the total nitrogen in photoelectron supplement systems, and ammonia accounted for 3.77% to 8.52%. However, in open-circuit systems, nitrite and ammonia proportions were 26.77% and 11.17%, respectively, and nitrogen loss in the liquid was not observed. This study reveals that photoelectrons can serve as electron donors for nitrogen transformation mediated by Halomonas sp. strain 3727, which reveals an underlying impact on the nitrogen biogeochemical cycle in the marine photic zone.
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Affiliation(s)
| | - Hongrui Ding
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, 100871 Beijing, China; (Y.L.); (Y.S.); (Y.L.)
| | | | | | - Anhuai Lu
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, 100871 Beijing, China; (Y.L.); (Y.S.); (Y.L.)
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56
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Carreira C, Nunes RF, Mestre O, Moura I, Pauleta SR. The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase. J Biol Inorg Chem 2020; 25:927-940. [PMID: 32851479 DOI: 10.1007/s00775-020-01812-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 11/27/2022]
Abstract
Increasing atmospheric concentration of N2O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N2O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N2O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N2O. In addition, the biochemical properties of N2O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N2O reductase accessory genes. N2O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N2O reductase in an active state.
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Affiliation(s)
- Cíntia Carreira
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Rute F Nunes
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Olga Mestre
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Isabel Moura
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal.
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57
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Decline in Phytoplankton Biomass along Indian Coastal Waters due to COVID-19 Lockdown. REMOTE SENSING 2020. [DOI: 10.3390/rs12162584] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The SARS-CoV-2 (or COVID-19) lockdown in India, which started at an early stage of its infection curve, has been one of the strictest in the world. Air quality has improved in all urban centers in India, a major emitter of greenhouse gases (GHG). This study is based on the hypothesis that an abrupt halt in all urban activities resulted in a massive decline in NO2 emissions and has also altered coastal nitrogen (N) inputs; in-turn, this affected the trophic status of coastal waters across the country. We present the first evidence of an overall decline in pre-monsoon chlorophyll-a, a proxy for phytoplankton biomass, in coastal waters off urban centers during the peak of the lockdown in April. The preliminary field data and indirect evidence suggests the reduction in coastal chlorophyll-a could be linked to a net decline in nutrient loading, particularly of bioavailable N through watershed fluxes and atmospheric deposition. The preliminary results stress the importance of a further understanding of the relationship between fluctuations in anthropogenic N, due to lockdown measures and coastal ecosystem responses, as countries open-up to a business-as-usual scenario.
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58
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Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
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59
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Wang L, Lim CK, Klotz MG. High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. Microorganisms 2020; 8:E693. [PMID: 32397339 PMCID: PMC7285500 DOI: 10.3390/microorganisms8050693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022] Open
Abstract
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world's oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C-107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.
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Affiliation(s)
- Lin Wang
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Martin G. Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
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60
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Yau YY, Baker DM, Thibodeau B. Quantifying the Impact of Anthropogenic Atmospheric Nitrogen Deposition on the Generation of Hypoxia under Future Emission Scenarios in Chinese Coastal Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3920-3928. [PMID: 32126755 DOI: 10.1021/acs.est.0c00706] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atmospheric deposition is an important source of nitrogen to coastal waters. In nitrogen-limited waters, the atmosphere can contribute significantly to eutrophication and hypoxia. This is especially true in China, where nitrogen emissions have increased dramatically and are projected to further increase in the future. Here, we modeled the potential future impact of change in atmospheric nitrogen deposition on hypoxia in Chinese coastal seas. We used changes in nitrogen deposition under two IPCC scenarios that included emission regulation and climate change (representative concentration pathway (RCP) 4.5 and 8.5) to evaluate the impacts of such deposition on hypoxia in the 2030s and 2100s. We found that by 2030 the extent of hypoxic areas would increase up to 5% in China seas under RCP 8.5 due to the projected increase in nitrogen deposition. However, the hypoxia extent was projected to decrease by up to 9% by 2100 once emission regulations included in RCP 4.5 and 8.5 are implemented. The South China Sea was found to be the most sensitive region to changes in nitrogen loads, which indicates that more effort in emissions control is needed to avoid expansion of the hypoxic zones in that specific region.
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Affiliation(s)
- Yu Yan Yau
- Department of Earth Sciences and Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - David M Baker
- School of Biological Sciences and Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - Benoit Thibodeau
- Department of Earth Sciences and Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong
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61
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Naafs BDA, Monteiro FM, Pearson A, Higgins MB, Pancost RD, Ridgwell A. Fundamentally different global marine nitrogen cycling in response to severe ocean deoxygenation. Proc Natl Acad Sci U S A 2019; 116:24979-24984. [PMID: 31767742 PMCID: PMC6911173 DOI: 10.1073/pnas.1905553116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The present-day marine nitrogen (N) cycle is strongly regulated by biology. Deficiencies in the availability of fixed and readily bioavailable nitrogen relative to phosphate (P) in the surface ocean are largely corrected by the activity of diazotrophs. This feedback system, termed the "nitrostat," is thought to have provided close regulation of fixed-N speciation and inventory relative to P since the Proterozoic. In contrast, during intervals of intense deoxygenation such as Cretaceous ocean anoxic event (OAE) 2, a few regional sedimentary δ15N records hint at the existence of a different mode of marine N cycling in which ammonium plays a major role in regulating export production. However, the global-scale dynamics during this time remain unknown. Here, using an Earth System model and taking the example of OAE 2, we provide insights into the global marine nitrogen cycle under severe ocean deoxygenation. Specifically, we find that the ocean can exhibit fundamental transitions in the species of nitrogen dominating the fixed-N inventory--from nitrate (NO3-) to ammonium (NH4+)--and that as this transition occurs, the inventory can partially collapse relative to P due to progressive spatial decoupling between the loci of NH4+ oxidation, NO3- reduction, and nitrogen fixation. This finding is relatively independent of the specific state of ocean circulation and is consistent with nitrogen isotope and redox proxy data. The substantive reduction in the ocean fixed-N inventory at an intermediate state of deoxygenation may represent a biogeochemical vulnerability with potential implications for past and future (warmer) oceans.
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Affiliation(s)
- B David A Naafs
- Organic Geochemistry Unit, School of Chemistry, School of Earth Sciences, Cabot Institute for the Environment, University of Bristol, Bristol BS8 1TA, United Kingdom;
| | - Fanny M Monteiro
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, United Kingdom
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
| | | | - Richard D Pancost
- Organic Geochemistry Unit, School of Chemistry, School of Earth Sciences, Cabot Institute for the Environment, University of Bristol, Bristol BS8 1TA, United Kingdom
| | - Andy Ridgwell
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, United Kingdom
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521
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62
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Preiner M, Xavier JC, Vieira ADN, Kleinermanns K, Allen JF, Martin WF. Catalysts, autocatalysis and the origin of metabolism. Interface Focus 2019; 9:20190072. [PMID: 31641438 PMCID: PMC6802133 DOI: 10.1098/rsfs.2019.0072] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2 and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H2–CO2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, then understanding reactions and catalysts that operate under such conditions is crucial for understanding origins.
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Affiliation(s)
- Martina Preiner
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
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63
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Lammer H, Sproß L, Grenfell JL, Scherf M, Fossati L, Lendl M, Cubillos PE. The Role of N 2 as a Geo-Biosignature for the Detection and Characterization of Earth-like Habitats. ASTROBIOLOGY 2019; 19:927-950. [PMID: 31314591 DOI: 10.1089/ast.2018.1914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since the Archean, N2 has been a major atmospheric constituent in Earth's atmosphere. Nitrogen is an essential element in the building blocks of life; therefore, the geobiological nitrogen cycle is a fundamental factor in the long-term evolution of both Earth and Earth-like exoplanets. We discuss the development of Earth's N2 atmosphere since the planet's formation and its relation with the geobiological cycle. Then we suggest atmospheric evolution scenarios and their possible interaction with life-forms: first for a stagnant-lid anoxic world, second for a tectonically active anoxic world, and third for an oxidized tectonically active world. Furthermore, we discuss a possible demise of present Earth's biosphere and its effects on the atmosphere. Since life-forms are the most efficient means for recycling deposited nitrogen back into the atmosphere at present, they sustain its surface partial pressure at high levels. Also, the simultaneous presence of significant N2 and O2 is chemically incompatible in an atmosphere over geological timescales. Thus, we argue that an N2-dominated atmosphere in combination with O2 on Earth-like planets within circumstellar habitable zones can be considered as a geo-biosignature. Terrestrial planets with such atmospheres will have an operating tectonic regime connected with an aerobic biosphere, whereas other scenarios in most cases end up with a CO2-dominated atmosphere. We conclude with implications for the search for life on Earth-like exoplanets inside the habitable zones of M to K stars.
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Affiliation(s)
- Helmut Lammer
- 1Austrian Academy of Sciences, Space Research Institute, Graz, Austria
| | - Laurenz Sproß
- 1Austrian Academy of Sciences, Space Research Institute, Graz, Austria
- 2Institute of Physics, University of Graz, Graz, Austria
| | - John Lee Grenfell
- 3Department of Extrasolar Planets and Atmospheres, German Aerospace Center, Institute of Planetary Research, Berlin, Germany
| | - Manuel Scherf
- 1Austrian Academy of Sciences, Space Research Institute, Graz, Austria
| | - Luca Fossati
- 1Austrian Academy of Sciences, Space Research Institute, Graz, Austria
| | - Monika Lendl
- 1Austrian Academy of Sciences, Space Research Institute, Graz, Austria
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64
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Brown M, Penta WB, Jones B, Behrenfeld M. The ratio of single-turnover to multiple-turnover fluorescence varies predictably with growth rate and cellular chlorophyll in the green alga Dunaliella tertiolecta. PHOTOSYNTHESIS RESEARCH 2019; 140:65-76. [PMID: 30635858 DOI: 10.1007/s11120-018-00612-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
Marine phytoplankton experience a wide range of nutrient and light conditions in nature and respond to these conditions through changes in growth rate, chlorophyll concentration, and other physiological properties. Chlorophyll fluorescence is a non-invasive and efficient tool for characterizing changes in these physiological properties. In particular, the introduction of fast repetition rate fluorometry (FRRf) into studies of phytoplankton physiology has enabled detailed studies of photosynthetic components and kinetics. One property retrieved with an FRRf is the 'single-turnover' maximum fluorescence (FmST) when the primary electron acceptor, Qa, is reduced but the plastoquinone (PQ) pool is oxidized. A second retrieved property is the 'multiple-turnover' fluorescence (FMT) when both Qa and PQ are reduced. Here, variations in FmST and FMT were measured in the green alga Dunaliella tertiolecta grown under nitrate-limited, light-limited, and replete conditions. The ratio of FmST to FMT (ST/MT) showed a consistent relationship with cellular chlorophyll in D. tertiolecta across all growth conditions. However, the ST/MT ratio decreased with growth rate under nitrate-limited conditions but increased with growth rate under light-limited conditions. In addition, cells from light-limited conditions showed a high accumulation of Qb-nonreducing centers, while cells from nitrate-limited conditions showed little to none. We propose that these findings reflect differences in the reduction and oxidation rates of plastoquinone due to the unique impacts of light and nitrate limitation on the stoichiometry of light-harvesting components and downstream electron acceptors.
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Affiliation(s)
- Matthew Brown
- Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA.
| | - William Bryce Penta
- Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, OR, 97331, USA
| | - Bethan Jones
- Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA
| | - Mike Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA
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65
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Piché-Choquette S, Constant P. Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes. Appl Environ Microbiol 2019; 85:e02418-18. [PMID: 30658976 PMCID: PMC6414374 DOI: 10.1128/aem.02418-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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66
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Dang H, Klotz MG, Lovell CR, Sievert SM. Editorial: The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients. Front Microbiol 2019; 10:115. [PMID: 30800101 PMCID: PMC6375845 DOI: 10.3389/fmicb.2019.00115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Martin G Klotz
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,School of Molecular Biosciences, Washington State University, Richland, WA, United States
| | - Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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67
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Li Y, Tang K, Zhang L, Zhao Z, Xie X, Chen CTA, Wang D, Jiao N, Zhang Y. Coupled Carbon, Sulfur, and Nitrogen Cycles Mediated by Microorganisms in the Water Column of a Shallow-Water Hydrothermal Ecosystem. Front Microbiol 2018; 9:2718. [PMID: 30555427 PMCID: PMC6282030 DOI: 10.3389/fmicb.2018.02718] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/24/2018] [Indexed: 12/22/2022] Open
Abstract
Shallow-water hydrothermal vent ecosystems are distinctly different from deep-sea vents, as other than geothermal, sunlight is one of their primary sources of energy, so their resulting microbial communities differ to some extent. Yet compared with deep-sea systems, less is known about the active microbial community in shallow-water ecosystems. Thus, we studied the community compositions, their metabolic pathways, and possible coupling of microbially driven biogeochemical cycles in a shallow-water hydrothermal vent system off Kueishantao Islet, Taiwan, using high-throughput 16S rRNA sequences and metatranscriptome analyses. Gammaproteobacteria and Epsilonbacteraeota were the major active bacterial groups in the 16S rRNA libraries and the metatranscriptomes, and involved in the carbon, sulfur, and nitrogen metabolic pathways. As core players, Thiomicrospira, Thiomicrorhabdus, Thiothrix, Sulfurovum, and Arcobacter derived energy from the oxidation of reduced sulfur compounds and fixed dissolved inorganic carbon (DIC) by the Calvin-Benson-Bassham (CBB) or reverse tricarboxylic acid cycles. Sox-dependent and reverse sulfate reduction were the main pathways of energy generation, and probably coupled to denitrification by providing electrons to nitrate and nitrite. Sulfur-reducing Nautiliaceae members, accounting for a small proportion in the community, obtained energy by the oxidation of hydrogen, which also supplies metabolic energy for some sulfur-oxidizing bacteria. In addition, ammonia and nitrite oxidation is another type of energy generation in this hydrothermal system, with marker gene sequences belonging to Thaumarchaeota/Crenarchaeota and Nitrospina, respectively, and ammonia and nitrite oxidation was likely coupled to denitrification by providing substrate for nitrate and nitrite reduction to nitric oxide. Moreover, unlike the deep-sea systems, cyanobacteria may also actively participate in major metabolic pathways. This study helps us to better understand biogeochemical processes mediated by microorganisms and possible coupling of the carbon, sulfur, and nitrogen cycles in these unique ecosystems.
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Affiliation(s)
- Yufang Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lianbao Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zihao Zhao
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria
| | - Xiabing Xie
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | | | - Deli Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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68
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Matantseva O, Pozdnyakov I, Voss M, Liskow I, Skarlato S. The Uncoupled Assimilation of Carbon and Nitrogen from Urea and Glycine by the Bloom-forming Dinoflagellate Prorocentrum minimum. Protist 2018; 169:603-614. [DOI: 10.1016/j.protis.2018.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 11/24/2022]
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69
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Natural forcing of the North Atlantic nitrogen cycle in the Anthropocene. Proc Natl Acad Sci U S A 2018; 115:10606-10611. [PMID: 30275314 DOI: 10.1073/pnas.1801049115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human alteration of the global nitrogen cycle intensified over the 1900s. Model simulations suggest that large swaths of the open ocean, including the North Atlantic and the western Pacific, have already been affected by anthropogenic nitrogen through atmospheric transport and deposition. Here we report an ∼130-year-long record of the 15N/14N of skeleton-bound organic matter in a coral from the outer reef of Bermuda, which provides a test of the hypothesis that anthropogenic atmospheric nitrogen has significantly augmented the nitrogen supply to the open North Atlantic surface ocean. The Bermuda 15N/14N record does not show a long-term decline in the Anthropocene of the amplitude predicted by model simulations or observed in a western Pacific coral 15N/14N record. Rather, the decadal variations in the Bermuda 15N/14N record appear to be driven by the North Atlantic Oscillation, most likely through changes in the formation rate of Subtropical Mode Water. Given that anthropogenic nitrogen emissions have been decreasing in North America since the 1990s, this study suggests that in the coming decades, the open North Atlantic will remain minimally affected by anthropogenic nitrogen deposition.
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70
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Cerqueira T, Barroso C, Froufe H, Egas C, Bettencourt R. Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields. MICROBIAL ECOLOGY 2018; 76:387-403. [PMID: 29354879 DOI: 10.1007/s00248-018-1144-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/02/2018] [Indexed: 05/25/2023]
Abstract
The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.
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Affiliation(s)
- Teresa Cerqueira
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 9901-862, Horta, Portugal.
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal.
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal.
| | - Cristina Barroso
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Hugo Froufe
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Raul Bettencourt
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal
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71
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Li YY, Chen XH, Xie ZX, Li DX, Wu PF, Kong LF, Lin L, Kao SJ, Wang DZ. Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean. Front Microbiol 2018; 9:797. [PMID: 29922238 PMCID: PMC5996900 DOI: 10.3389/fmicb.2018.00797] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Abstract
Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta-, and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NOX-N was significantly correlated with structure and distribution of N2-fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A (urtA) and ferredoxin-nitrate reductase, while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of vital ecological importance in N-deficient regimes.
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Affiliation(s)
- Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
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72
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Dos Santos CB, Silva MAM, de Souza MFL, da Silva DML. Nitrogen distribution in a tropical urbanized estuarine system in northeastern Brazil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2018; 190:68. [PMID: 29313110 DOI: 10.1007/s10661-017-6420-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen enters estuaries mostly through fluvial discharge and tide, although anthropogenic sources are known to influence the amount of this element in these aquatic ecosystems. Thus, the objective of this work was to verify which river (Cachoeira, Fundão, and/or Santana) exerts greater influence on the distribution of dissolved N forms (Dissolved Organic Nitrogen and Dissolved Inorganic Nitrogen = NH3/NH4+, NO2-, and NO3-) along a tropical urbanized estuarine system in northeastern Brazil. The studies estuarine system lies with in urban municipality, and the upper portion of the Cachoeira river estuary receives the treated effluent from this municipality through a sewage treatment station and untreated effluents from nearby villages. The selected sampling stations were located near the outfall of the rivers in the estuaries to the treatment plant and the villages. Of all the nitrogen forms, dissolved organic nitrogen (DON) prevailed in the estuarine system, followed by nitrate (NO3-) as the main inorganic form. The highest concentrations were recorded in the fluvial portion and upper estuary of Cachoeira river in the dry season. Based on the N concentrations found in the estuarine system, Cachoeira river has the greatest anthropogenic influence due to the amount of untreated effluents from the villages and treated effluents from the sewage treatment plant (STP) in the upper portion of the estuary.
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Affiliation(s)
| | - Maria Aparecida Macêdo Silva
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, 45662-900, Brazil
| | - Marcelo F Landim de Souza
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, 45662-900, Brazil
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73
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Coates CJ, Wyman M. A denitrifying community associated with a major, marine nitrogen fixer. Environ Microbiol 2017; 19:4978-4992. [PMID: 29194965 DOI: 10.1111/1462-2920.14007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The diazotrophic cyanobacterium, Trichodesmium, is an integral component of the marine nitrogen cycle and contributes significant amounts of new nitrogen to oligotrophic, tropical/subtropical ocean surface waters. Trichodesmium forms macroscopic, fusiform (tufts), spherical (puffs) and raft-like colonies that provide a pseudobenthic habitat for a host of other organisms including marine invertebrates, microeukaryotes and numerous other microbes. The diversity and activity of denitrifying bacteria found in association with the colonies was interrogated using a series of molecular-based methodologies targeting the gene encoding the terminal step in the denitrification pathway, nitrous oxide reductase (nosZ). Trichodesmium spp. sampled from geographically isolated ocean provinces (the Atlantic Ocean, the Red Sea and the Indian Ocean) were shown to harbor highly similar, taxonomically related communities of denitrifiers whose members are affiliated with the Roseobacter clade within the Rhodobacteraceae (Alphaproteobacteria). These organisms were actively expressing nosZ in samples taken from the mid-Atlantic Ocean and Red Sea implying that Trichodesmium colonies are potential sites of nitrous oxide consumption and perhaps earlier steps in the denitrification pathway also. It is proposed that coupled nitrification of newly fixed N is the most likely source of nitrogen oxides supporting nitrous oxide cycling within Trichodesmium colonies.
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Affiliation(s)
- Christopher J Coates
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.,Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Michael Wyman
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
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74
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Bertagnolli AD, Ulloa O. Hydrography shapes community composition and diversity of amoA-containing Thaumarchaeota in the coastal waters off central Chile. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:717-728. [PMID: 28836743 DOI: 10.1111/1758-2229.12579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Thaumarchaea are often abundant in low oxygen marine environments, and recent kinetic studies indicate a capacity for aerobic ammonia oxidation at vanishingly low oxygen levels (nM). However, molecular diversity surveys targeting this group to high sequencing coverage are limited, and how these populations are coupled to changes in dissolved oxygen remains unknown. In this study, the ammonia monooxygenase subunit A (amoA) gene was sequenced from samples collected in the Chilean coast (36.5 °S), a system prone to recurrent seasonal hypoxia and anoxia, at several depths over one year, to read depths that saturated coverage statistics. Temperature, salinity and depth displayed a stronger impact on community composition than chemical and biological variables, such as dissolved oxygen. The Nitrosopumilus water-column A clade (WCA) displayed high proportional representation in all samples (42%-100% of all amoA OTUs). The two dominant WCA OTUs displayed differences in their distributions that were inversely correlated with one another, providing the first evidence for intra-subgroup specific differences in the distributions among closely related WCA Thaumarcheota. Nitrosopumilus water-column B (WCB) representatives displayed increased proportional abundances (42%) at deeper depths during the spring and summer, were highly coupled to decreased dissolved oxygen conditions and were non-detectable during the austral winter. The depth of sequencing also enabled observation of lower abundance taxa that are typically not observed in marine environments, such as members of the genus Nitrosotalea amid austral winter surface waters. This study highlights a strong coupling between Thaumarchaeal community diversity and hydrographic variables, is the first to highlight intra-subclade depth specific shifts in community diversity amongst members of the WCA clade, and links the WCB clade to upwelling conditions associated with seasonal oxygen depletion.
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Affiliation(s)
- Anthony D Bertagnolli
- Department of Oceanography and Millennium Institute of Oceanography, Universidad de Concepción, Concepción, P.O. Box 160 C, Chile
| | - Osvaldo Ulloa
- Department of Oceanography and Millennium Institute of Oceanography, Universidad de Concepción, Concepción, P.O. Box 160 C, Chile
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75
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Sciberras M, Tait K, Brochain G, Hiddink JG, Hale R, Godbold JA, Solan M. Mediation of nitrogen by post-disturbance shelf communities experiencing organic matter enrichment. BIOGEOCHEMISTRY 2017; 135:135-153. [PMID: 32009695 PMCID: PMC6961516 DOI: 10.1007/s10533-017-0370-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 08/15/2017] [Indexed: 05/26/2023]
Abstract
Microbes and benthic macro-invertebrates interact in sediments to play a major role in the biogeochemical cycling of organic matter, but the extent to which their contributions are modified following natural and anthropogenic changes has received little attention. Here, we investigate how nitrogen transformations, ascertained from changes in archaeal and bacterial N-cycling microbes and water macronutrient concentrations ([NH4-N], [NO2-N], [NO3-N]), in sand and sandy mud sediments differ when macrofaunal communities that have previously experienced contrasting levels of chronic fishing disturbance are exposed to organic matter enrichment. We find that differences in macrofaunal community structure related to differences in fishing activity affect the capacity of the macrofauna to mediate microbial nitrogen cycling in sand, but not in sandy mud environments. Whilst we found no evidence for a change in ammonia oxidiser community structure, we did find an increase in archaeal and bacterial denitrifier (AnirKa, nirS) and anammox (hzo) transcripts in macrofaunal communities characterized by higher ratios of suspension to deposit feeders, and a lower density but higher biomass of sediment-reworking fauna. Our findings suggest that nitrogen transformation in shelf sandy sediments is dependent on the stimulation of specific nitrogen cycling pathways that are associated with differences in the composition and context-dependent expression of the functional traits that belong to the resident bioturbating macrofauna community.
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Affiliation(s)
- Marija Sciberras
- School of Ocean Sciences, Bangor University, Askew St, Menai Bridge, Anglesey LL59 5AB UK
| | - Karen Tait
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH UK
| | - Guillaume Brochain
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH UK
| | - Jan G. Hiddink
- School of Ocean Sciences, Bangor University, Askew St, Menai Bridge, Anglesey LL59 5AB UK
| | - Rachel Hale
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH UK
| | - Jasmin A. Godbold
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH UK
| | - Martin Solan
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH UK
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76
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Goldberg SJ, Nelson CE, Viviani DA, Shulse CN, Church MJ. Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean. Environ Microbiol 2017; 19:3450-3464. [PMID: 28618153 DOI: 10.1111/1462-2920.13825] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022]
Abstract
Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean.
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Affiliation(s)
- S J Goldberg
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - C E Nelson
- Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - D A Viviani
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - C N Shulse
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - M J Church
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
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77
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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78
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Godbold JA, Hale R, Wood CL, Solan M. Vulnerability of macronutrients to the concurrent effects of enhanced temperature and atmospheric pCO 2 in representative shelf sea sediment habitats. BIOGEOCHEMISTRY 2017; 135:89-102. [PMID: 32009693 PMCID: PMC6961501 DOI: 10.1007/s10533-017-0340-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/26/2017] [Indexed: 05/26/2023]
Abstract
Fundamental changes in seawater carbonate chemistry and sea surface temperatures associated with the ocean uptake of anthropogenic CO2 are accelerating, but investigations of the susceptibility of biogeochemical processes to the simultaneous occurrence of multiple components of climate change are uncommon. Here, we quantify how concurrent changes in enhanced temperature and atmospheric pCO2, coupled with an associated shift in macrofaunal community structure and behavior (sediment particle reworking and bioirrigation), modify net carbon and nutrient concentrations (NH4-N, NOx-N, PO4-P) in representative shelf sea sediment habitats (mud, sandy-mud, muddy-sand and sand) of the Celtic Sea. We show that net concentrations of organic carbon, nitrogen and phosphate are, irrespective of sediment type, largely unaffected by a simultaneous increase in temperature and atmospheric pCO2. However, our analyses also reveal that a reduction in macrofaunal species richness and total abundance occurs under future environmental conditions, varies across a gradient of cohesive to non-cohesive sediments, and negatively moderates biogeochemical processes, in particular nitrification. Our findings indicate that future environmental conditions are unlikely to have strong direct effects on biogeochemical processes but, particularly in muddy sands, the abundance, activity, composition and functional role of invertebrate communities are likely to be altered in ways that will be sufficient to regulate the function of the microbial community and the availability of nutrients in shelf sea waters.
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Affiliation(s)
- Jasmin A. Godbold
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, European Way, Southampton, SO14 3ZH UK
- Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ UK
| | - Rachel Hale
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, European Way, Southampton, SO14 3ZH UK
| | - Christina L. Wood
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, European Way, Southampton, SO14 3ZH UK
| | - Martin Solan
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, European Way, Southampton, SO14 3ZH UK
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79
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80
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Gao M, Liu J, Qiao Y, Zhao M, Zhang XH. Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors. MICROBIAL ECOLOGY 2017; 73:602-615. [PMID: 27924403 DOI: 10.1007/s00248-016-0906-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.
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Affiliation(s)
- Minghong Gao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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81
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Rush D, Sinninghe Damsté JS. Lipids as paleomarkers to constrain the marine nitrogen cycle. Environ Microbiol 2017; 19:2119-2132. [PMID: 28142226 PMCID: PMC5516240 DOI: 10.1111/1462-2920.13682] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 11/30/2022]
Abstract
Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past.
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Affiliation(s)
- Darci Rush
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, P.O. Box 59 1790 AB, The Netherlands.,School of Civil Engineering and Geosciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, P.O. Box 59 1790 AB, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, TA Utrecht, P.O. Box 80.121, 3508, The Netherlands
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82
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Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science 2016; 353:1272-7. [DOI: 10.1126/science.aaf4507] [Citation(s) in RCA: 1097] [Impact Index Per Article: 137.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/23/2016] [Indexed: 12/30/2022]
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83
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Zielinski BL, Allen AE, Carpenter EJ, Coles VJ, Crump BC, Doherty M, Foster RA, Goes JI, Gomes HR, Hood RR, McCrow JP, Montoya JP, Moustafa A, Satinsky BM, Sharma S, Smith CB, Yager PL, Paul JH. Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume. PLoS One 2016; 11:e0160929. [PMID: 27598790 PMCID: PMC5012681 DOI: 10.1371/journal.pone.0160929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 07/27/2016] [Indexed: 11/24/2022] Open
Abstract
The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function.
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Affiliation(s)
- Brian L. Zielinski
- University of South Florida College of Marine Science, St. Petersburg, FL, United States of America
| | - Andrew E. Allen
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States of America
| | - Edward J. Carpenter
- Romberg Tiburon Center, San Francisco State University, Tiburon, California, United States of America
| | - Victoria J. Coles
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Byron C. Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Mary Doherty
- Rhodes College, Memphis, TN, United States of America
| | - Rachel A. Foster
- Ocean Sciences, University of California, Santa Cruz, CA, United States of America
- Department of Ecology, Environment, and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Joaquim I. Goes
- Lamont Doherty Earth Observatory, Columbia University, Palisades, NY, United States of America
| | - Helga R. Gomes
- Lamont Doherty Earth Observatory, Columbia University, Palisades, NY, United States of America
| | - Raleigh R. Hood
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - John P. McCrow
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States of America
| | - Joseph P. Montoya
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
| | - Brandon M. Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Shalabh Sharma
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - Christa B. Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - Patricia L. Yager
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - John H. Paul
- University of South Florida College of Marine Science, St. Petersburg, FL, United States of America
- * E-mail:
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84
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Abstract
The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors.
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85
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Zhou H, Dang H, Klotz MG. Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas. Front Microbiol 2016; 7:1111. [PMID: 27489551 PMCID: PMC4951488 DOI: 10.3389/fmicb.2016.01111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater SiO32−-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation between the shallow-water and deep-water sediment diazotrophic communities and suggests that the in situ physical and geochemical conditions play a more important role than geographical contiguity in determining the community similarity of the diazotrophic microbiota in marginal sea sediments.
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Affiliation(s)
- Haixia Zhou
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China; Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China)Qingdao, China; Department of Food Quality and Safety, College of Life Science, Dezhou UniversityDezhou, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University Xiamen, China
| | - Martin G Klotz
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China; Department of Biology and School of Earth and Environmental Sciences, Queens College, City University of New YorkQueens, NY, USA
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86
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Raes EJ, Bodrossy L, Van de Kamp J, Holmes B, Hardman-Mountford N, Thompson PA, McInnes AS, Waite AM. Reduction of the Powerful Greenhouse Gas N2O in the South-Eastern Indian Ocean. PLoS One 2016; 11:e0145996. [PMID: 26800249 PMCID: PMC4723335 DOI: 10.1371/journal.pone.0145996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 11/29/2015] [Indexed: 11/22/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and a key catalyst of stratospheric ozone depletion. Yet, little data exist about the sink and source terms of the production and reduction of N2O outside the well-known oxygen minimum zones (OMZ). Here we show the presence of functional marker genes for the reduction of N2O in the last step of the denitrification process (nitrous oxide reductase genes; nosZ) in oxygenated surface waters (180–250 O2 μmol.kg-1) in the south-eastern Indian Ocean. Overall copy numbers indicated that nosZ genes represented a significant proportion of the microbial community, which is unexpected in these oxygenated waters. Our data show strong temperature sensitivity for nosZ genes and reaction rates along a vast latitudinal gradient (32°S-12°S). These data suggest a large N2O sink in the warmer Tropical waters of the south-eastern Indian Ocean. Clone sequencing from PCR products revealed that most denitrification genes belonged to Rhodobacteraceae. Our work highlights the need to investigate the feedback and tight linkages between nitrification and denitrification (both sources of N2O, but the latter also a source of bioavailable N losses) in the understudied yet strategic Indian Ocean and other oligotrophic systems.
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Affiliation(s)
- Eric J. Raes
- The Oceans Institute, University of Western Australia, M047 35 Stirling Hwy Crawley, 6009 WA, Australia
- CSIRO Oceans and Atmosphere Flagship, Private Bag 5, Wembley, 6913 WA, Australia
- * E-mail:
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Jodie Van de Kamp
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Bronwyn Holmes
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Nick Hardman-Mountford
- The Oceans Institute, University of Western Australia, M047 35 Stirling Hwy Crawley, 6009 WA, Australia
- CSIRO Oceans and Atmosphere Flagship, Private Bag 5, Wembley, 6913 WA, Australia
| | - Peter A. Thompson
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Allison S. McInnes
- University of Technology, Sydney, Plant Functional Biology & Climate Change, City campus 15 Broadway Ultimo NSW 2007, Australia
| | - Anya M. Waite
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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87
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 488] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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88
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Oulas A, Polymenakou PN, Seshadri R, Tripp HJ, Mandalakis M, Paez-Espino AD, Pati A, Chain P, Nomikou P, Carey S, Kilias S, Christakis C, Kotoulas G, Magoulas A, Ivanova NN, Kyrpides NC. Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environ Microbiol 2015; 18:1122-36. [PMID: 26487573 DOI: 10.1111/1462-2920.13095] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/16/2015] [Indexed: 11/27/2022]
Abstract
Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.
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Affiliation(s)
- Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Paraskevi N Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Rekha Seshadri
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - H James Tripp
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - A David Paez-Espino
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - Amrita Pati
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Paraskevi Nomikou
- National and Kapodistrian University of Athens, Faculty of Geology and Geoenvironment, Athens, Greece
| | - Steven Carey
- Graduate School of Oceanography, University of Rhode Island, Kingston, RI, USA
| | - Stephanos Kilias
- National and Kapodistrian University of Athens, Faculty of Geology and Geoenvironment, Athens, Greece
| | - Christos Christakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Natalia N Ivanova
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos C Kyrpides
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Biological Sciences, King Abdulaziz, Jeddah, Saudia Arabia
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89
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Middelburg JJ, Mueller CE, Veuger B, Larsson AI, Form A, van Oevelen D. Discovery of symbiotic nitrogen fixation and chemoautotrophy in cold-water corals. Sci Rep 2015; 5:17962. [PMID: 26644069 PMCID: PMC4672307 DOI: 10.1038/srep17962] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/09/2015] [Indexed: 11/17/2022] Open
Abstract
Cold-water corals (CWC) are widely distributed around the world forming extensive reefs at par with tropical coral reefs. They are hotspots of biodiversity and organic matter processing in the world’s deep oceans. Living in the dark they lack photosynthetic symbionts and are therefore considered to depend entirely on the limited flux of organic resources from the surface ocean. While symbiotic relations in tropical corals are known to be key to their survival in oligotrophic conditions, the full metabolic capacity of CWC has yet to be revealed. Here we report isotope tracer evidence for efficient nitrogen recycling, including nitrogen assimilation, regeneration, nitrification and denitrification. Moreover, we also discovered chemoautotrophy and nitrogen fixation in CWC and transfer of fixed nitrogen and inorganic carbon into bulk coral tissue and tissue compounds (fatty acids and amino acids). This unrecognized yet versatile metabolic machinery of CWC conserves precious limiting resources and provides access to new nitrogen and organic carbon resources that may be essential for CWC to survive in the resource-depleted dark ocean.
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Affiliation(s)
- Jack J Middelburg
- Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Christina E Mueller
- Department of Ecosystem Studies, Royal Netherlands Institute for Sea Research (NIOZ-Yerseke), P.O. Box 140, 4400 AC Yerseke, The Netherlands
| | - Bart Veuger
- Department of Ecosystem Studies, Royal Netherlands Institute for Sea Research (NIOZ-Yerseke), P.O. Box 140, 4400 AC Yerseke, The Netherlands
| | - Ann I Larsson
- Dept. of Marine Sciences, Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Armin Form
- GEOMAR, Helmholtz Centre for Ocean Research, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Dick van Oevelen
- Department of Ecosystem Studies, Royal Netherlands Institute for Sea Research (NIOZ-Yerseke), P.O. Box 140, 4400 AC Yerseke, The Netherlands
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90
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Affiliation(s)
- Edward H. Allison
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA 98195, USA
| | - Hannah R. Bassett
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA 98195, USA
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91
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Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions. Appl Environ Microbiol 2015; 81:7114-24. [PMID: 26231655 DOI: 10.1128/aem.01986-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 07/29/2015] [Indexed: 01/28/2023] Open
Abstract
Permeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole.
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92
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von Schneidemesser E, Monks PS, Allan JD, Bruhwiler L, Forster P, Fowler D, Lauer A, Morgan WT, Paasonen P, Righi M, Sindelarova K, Sutton MA. Chemistry and the Linkages between Air Quality and Climate Change. Chem Rev 2015; 115:3856-97. [PMID: 25926133 DOI: 10.1021/acs.chemrev.5b00089] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Paul S Monks
- ‡Department of Chemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
| | | | | | | | - David Fowler
- ∇Centre for Ecology and Hydrology, Natural Environment Research Council, Edinburgh EH26 0QB, United Kingdom
| | - Axel Lauer
- †Institute for Advanced Sustainability Studies, 14467 Potsdam, Germany
| | | | - Pauli Paasonen
- ○Department of Physics, University of Helsinki, 00100 Helsinki, Finland
| | - Mattia Righi
- ◆Deutsches Zentrum für Luft- und Raumfahrt, Institut für Physik der Atmosphäre, 82234 Oberpfaffenhofen, Germany
| | - Katerina Sindelarova
- ¶UPMC Univ. Paris 06, Université Versailles St-Quentin; CNRS/INSU; LATMOS-IPSL, UMR 8190 Paris, France.,□Department of Atmospheric Physics, Faculty of Mathematics and Physics, Charles University, 116 36 Prague, Czech Republic
| | - Mark A Sutton
- ∇Centre for Ecology and Hydrology, Natural Environment Research Council, Edinburgh EH26 0QB, United Kingdom
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93
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Braeckman U, Van Colen C, Guilini K, Van Gansbeke D, Soetaert K, Vincx M, Vanaverbeke J. Empirical evidence reveals seasonally dependent reduction in nitrification in coastal sediments subjected to near future ocean acidification. PLoS One 2014; 9:e108153. [PMID: 25329898 PMCID: PMC4199590 DOI: 10.1371/journal.pone.0108153] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/31/2014] [Indexed: 11/19/2022] Open
Abstract
Research so far has provided little evidence that benthic biogeochemical cycling is affected by ocean acidification under realistic climate change scenarios. We measured nutrient exchange and sediment community oxygen consumption (SCOC) rates to estimate nitrification in natural coastal permeable and fine sandy sediments under pre-phytoplankton bloom and bloom conditions. Ocean acidification, as mimicked in the laboratory by a realistic pH decrease of 0.3, significantly reduced SCOC on average by 60% and benthic nitrification rates on average by 94% in both sediment types in February (pre-bloom period), but not in April (bloom period). No changes in macrofauna functional community (density, structural and functional diversity) were observed between ambient and acidified conditions, suggesting that changes in benthic biogeochemical cycling were predominantly mediated by changes in the activity of the microbial community during the short-term incubations (14 days), rather than by changes in engineering effects of bioturbating and bio-irrigating macrofauna. As benthic nitrification makes up the gross of ocean nitrification, a slowdown of this nitrogen cycling pathway in both permeable and fine sediments in winter, could therefore have global impacts on coupled nitrification-denitrification and hence eventually on pelagic nutrient availability.
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Affiliation(s)
- Ulrike Braeckman
- Ghent University, Department of Biology, Marine Biology Research Group, Ghent, Belgium
- * E-mail:
| | - Carl Van Colen
- Ghent University, Department of Biology, Marine Biology Research Group, Ghent, Belgium
| | - Katja Guilini
- Ghent University, Department of Biology, Marine Biology Research Group, Ghent, Belgium
| | - Dirk Van Gansbeke
- Ghent University, Department of Biology, Marine Biology Research Group, Ghent, Belgium
| | - Karline Soetaert
- Netherlands Institute for Sea Research, Department of Ecosystem Studies, Yerseke, The Netherlands
| | - Magda Vincx
- Ghent University, Department of Biology, Marine Biology Research Group, Ghent, Belgium
| | - Jan Vanaverbeke
- Ghent University, Department of Biology, Marine Biology Research Group, Ghent, Belgium
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94
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Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria. ISME JOURNAL 2014; 8:2530-42. [PMID: 25226029 DOI: 10.1038/ismej.2014.167] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 11/08/2022]
Abstract
Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed 'diazotrophs') are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.
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95
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Abstract
The global biogeochemical nitrogen cycle is essential for life on Earth. Many of the underlying biotic reactions are catalyzed by a multitude of prokaryotic and eukaryotic life forms whereas others are exclusively carried out by microorganisms. The last century has seen the rise of a dramatic imbalance in the global nitrogen cycle due to human behavior that was mainly caused by the invention of the Haber-Bosch process. Its main product, ammonia, is a chemically reactive and biotically favorable form of bound nitrogen. The anthropogenic supply of reduced nitrogen to the biosphere in the form of ammonia, for example during environmental fertilization, livestock farming, and industrial processes, is mandatory in feeding an increasing world population. In this chapter, environmental ammonia pollution is linked to the activity of microbial metalloenzymes involved in respiratory energy metabolism and bioenergetics. Ammonia-producing multiheme cytochromes c are discussed as paradigm enzymes.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287, Darmstadt, Germany,
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96
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Fowler D, Coyle M, Skiba U, Sutton MA, Cape JN, Reis S, Sheppard LJ, Jenkins A, Grizzetti B, Galloway JN, Vitousek P, Leach A, Bouwman AF, Butterbach-Bahl K, Dentener F, Stevenson D, Amann M, Voss M. The global nitrogen cycle in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130164. [PMID: 23713126 DOI: 10.1098/rstb.2013.0164] [Citation(s) in RCA: 502] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Global nitrogen fixation contributes 413 Tg of reactive nitrogen (Nr) to terrestrial and marine ecosystems annually of which anthropogenic activities are responsible for half, 210 Tg N. The majority of the transformations of anthropogenic Nr are on land (240 Tg N yr(-1)) within soils and vegetation where reduced Nr contributes most of the input through the use of fertilizer nitrogen in agriculture. Leakages from the use of fertilizer Nr contribute to nitrate (NO3(-)) in drainage waters from agricultural land and emissions of trace Nr compounds to the atmosphere. Emissions, mainly of ammonia (NH3) from land together with combustion related emissions of nitrogen oxides (NOx), contribute 100 Tg N yr(-1) to the atmosphere, which are transported between countries and processed within the atmosphere, generating secondary pollutants, including ozone and other photochemical oxidants and aerosols, especially ammonium nitrate (NH4NO3) and ammonium sulfate (NH4)2SO4. Leaching and riverine transport of NO3 contribute 40-70 Tg N yr(-1) to coastal waters and the open ocean, which together with the 30 Tg input to oceans from atmospheric deposition combine with marine biological nitrogen fixation (140 Tg N yr(-1)) to double the ocean processing of Nr. Some of the marine Nr is buried in sediments, the remainder being denitrified back to the atmosphere as N2 or N2O. The marine processing is of a similar magnitude to that in terrestrial soils and vegetation, but has a larger fraction of natural origin. The lifetime of Nr in the atmosphere, with the exception of N2O, is only a few weeks, while in terrestrial ecosystems, with the exception of peatlands (where it can be 10(2)-10(3) years), the lifetime is a few decades. In the ocean, the lifetime of Nr is less well known but seems to be longer than in terrestrial ecosystems and may represent an important long-term source of N2O that will respond very slowly to control measures on the sources of Nr from which it is produced.
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Affiliation(s)
- David Fowler
- NERC Centre for Ecology and Hydrology, Penicuik, UK.
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97
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Fowler D, Pyle JA, Raven JA, Sutton MA. The global nitrogen cycle in the twenty-first century: introduction. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130165. [PMID: 23713127 DOI: 10.1098/rstb.2013.0165] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- David Fowler
- NERC, Centre for Ecology and Hydrology, Penicuik EH26 0QB, UK.
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