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Sarkar A, Al-Said T, Naqvi SWA, Ahmed A, Fernandes L, Madhusoodhanan R, Thuslim F, Yamamoto T, Al-Yamani F. A preliminary study on benthic nutrient exchange across sediment-water interfaces in a shallow marine protected area of the Northwestern Arabian Gulf. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106420. [PMID: 38430642 DOI: 10.1016/j.marenvres.2024.106420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/28/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Sedimentary processes are expected to play a crucial role in macronutrient cycling of the shallow Arabian Gulf. To investigate this aspect, sediment cores were collected from the shallow intertidal and subtidal expanses of the first Marine Protected Area (MPA) of Kuwait in the Northwestern Arabian Gulf (NAG). Porewater nutrient profiling and whole core incubation experiments were conducted to measure the nutrient fluxes, both with and without the addition of the nitrification inhibitor allylthiourea (ATU). The porewater data confirmed the potential of sediments to host multiple aerobic and anaerobic pathways of nutrient regeneration. The average (±SD) of net nutrient fluxes from several incubation experiments indicated that ammonium (NH4+) predominantly fluxed out of the sediment (3.81 ± 2.53 mmol m-2 d-1), followed by SiO44- (3.07 ± 1.21 mmol m-2 d-1). In contrast, the average PO43- flux was minimal, at only 0.06 ± 0.05 mmol m-2 d-1. Fluxes of NO3- (ranged from 0.07 ± 0.005 to 1.16 ± 0.35 mmol m-2 d-1) and NO2- (0.03 ± 0.003 to 0.71 ± 0.21 mmol m-2 d-1) were moderate, which either reduced or reversed in the presence of ATU (-0.001 ± 0.0001 to 0.01 ± 0.0001 mmol m-2 d-1 and -0.001 ± 0.0003 to 0.006 ± 0.001 mmol m-2 d-1 for NO3- and NO2- respectively). Thus, this study provides preliminary experimental evidence that nitrification can act as a source of NO3- and NO2- as well as contribute towards the relatively high concentrations of NO2- (>1 in the gulf waters.
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Affiliation(s)
- Amit Sarkar
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait.
| | - Turki Al-Said
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
| | - Syed Wajih Ahmad Naqvi
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait; CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Ayaz Ahmed
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
| | - Loreta Fernandes
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
| | - Rakhesh Madhusoodhanan
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
| | - Fathima Thuslim
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
| | - Takahiro Yamamoto
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
| | - Faiza Al-Yamani
- Kuwait Institute for Scientific Research, Salmiya, P. O. Box 1638, Salmiya, 22017, Kuwait
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2
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Wan XS, Sheng HX, Liu L, Shen H, Tang W, Zou W, Xu MN, Zheng Z, Tan E, Chen M, Zhang Y, Ward BB, Kao SJ. Particle-associated denitrification is the primary source of N 2O in oxic coastal waters. Nat Commun 2023; 14:8280. [PMID: 38092778 PMCID: PMC10719265 DOI: 10.1038/s41467-023-43997-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (N2O) emission to the atmosphere. The processes underpinning the N2O flux, however, remain poorly understood, leading to large uncertainties in assessing global N2O budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to N2O production throughout the estuarine-coastal gradient, sustaining intensive N2O flux to the atmosphere. Unexpectedly, denitrification, rather than ammonia oxidation as previously assumed, constitutes the major source of N2O in well-oxygenated coastal waters. Size-fractionated manipulation experiments with gene analysis further reveal niche partitioning of ammonia oxidizers and denitrifiers across the particle size spectrum; denitrification dominated on large particles and ammonia oxidizers on small particles. Total N2O production rate increases with substrate and particle concentrations, suggesting a crucial interplay between nutrients and particles in controlling N2O production. The controlling factors identified here may help understand climate feedback mechanisms between human activity and coastal oceans.
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Affiliation(s)
- Xianhui S Wan
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
| | - Hua-Xia Sheng
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Li Liu
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Hui Shen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Weiyi Tang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Wenbin Zou
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Min N Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Zhenzhen Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Mingming Chen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Yao Zhang
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Shuh-Ji Kao
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China.
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3
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Zhang W, Zhan S, Xiao J, Petit T, Schlesiger C, Mellin M, Hofmann JP, Heil T, Müller R, Leopold K, Oschatz M. Coordinative Stabilization of Single Bismuth Sites in a Carbon-Nitrogen Matrix to Generate Atom-Efficient Catalysts for Electrochemical Nitrate Reduction to Ammonia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302623. [PMID: 37544912 PMCID: PMC10558634 DOI: 10.1002/advs.202302623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Electrochemical nitrate reduction to ammonia powered by renewable electricity is not only a promising alternative to the established energy-intense and non-ecofriendly Haber-Bosch reaction for ammonia generation but also a future contributor to the ever-more important denitrification schemes. Nevertheless, this reaction is still impeded by the lack of understanding for the underlying reaction mechanism on the molecular scale which is necessary for the rational design of active, selective, and stable electrocatalysts. Herein, a novel single-site bismuth catalyst (Bi-N-C) for nitrate electroreduction is reported to produce ammonia with maximum Faradaic efficiency of 88.7% and at a high rate of 1.38 mg h-1 mgcat -1 at -0.35 V versus reversible hydrogen electrode (RHE). The active center (described as BiN2 C2 ) is uncovered by detailed structural analysis. Coupled density functional theory calculations are applied to analyze the reaction mechanism and potential rate-limiting steps for nitrate reduction based on the BiN2 C2 model. The findings highlight the importance of model catalysts to utilize the potential of nitrate reduction as a new-generation nitrogen-management technology based on the construction of efficient active sites.
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Affiliation(s)
- Wuyong Zhang
- Key Laboratory of Advanced Fuel Cells and Electrolyzers Technology of Zhejiang ProvinceQianwan Institute of CNITECHNingbo Institute of Materials Technology and EngineeringChinese Academy of SciencesNingboZhejiang315201P. R. China
- Center for Energy and Environmental Chemistry Jena (CEEC Jena)Institute for Technical Chemistry and Environmental ChemistryFriedrich‐Schiller‐University JenaPhilosophenweg 7a07743JenaGermany
| | - Shaoqi Zhan
- Department of Chemistry‐BMCUppsala UniversityBMC Box 576UppsalaS‐751 23Sweden
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3QZUK
| | - Jie Xiao
- Helmholtz‐Zentrum Berlin für Materialien und Energie GmbHAlbert‐Einstein‐Straße 1512489BerlinGermany
| | - Tristan Petit
- Helmholtz‐Zentrum Berlin für Materialien und Energie GmbHAlbert‐Einstein‐Straße 1512489BerlinGermany
| | - Christopher Schlesiger
- Institute for Optics and Atomic PhysicsTechnische Universität BerlinHardenbergstr. 3610623BerlinGermany
| | - Maximilian Mellin
- Surface Science LaboratoryDepartment of Materials and Earth SciencesTechnical University of DarmstadtOtto‐Berndt‐Straße 364287DarmstadtGermany
| | - Jan P. Hofmann
- Surface Science LaboratoryDepartment of Materials and Earth SciencesTechnical University of DarmstadtOtto‐Berndt‐Straße 364287DarmstadtGermany
| | - Tobias Heil
- Max Planck Institute of Colloids and InterfacesDepartment of Colloid ChemistryAm Mühlenberg 114476PotsdamGermany
| | - Riccarda Müller
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | - Kerstin Leopold
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | - Martin Oschatz
- Center for Energy and Environmental Chemistry Jena (CEEC Jena)Institute for Technical Chemistry and Environmental ChemistryFriedrich‐Schiller‐University JenaPhilosophenweg 7a07743JenaGermany
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Berube PM, O'Keefe TJ, Rasmussen A, LeMaster T, Chisholm SW. Production and cross-feeding of nitrite within Prochlorococcus populations. mBio 2023; 14:e0123623. [PMID: 37404012 PMCID: PMC10470740 DOI: 10.1128/mbio.01236-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Prochlorococcus is an abundant photosynthetic bacterium in the open ocean, where nitrogen (N) often limits phytoplankton growth. In the low-light-adapted LLI clade of Prochlorococcus, nearly all cells can assimilate nitrite (NO2-), with a subset capable of assimilating nitrate (NO3-). LLI cells are maximally abundant near the primary NO2- maximum layer, an oceanographic feature that may, in part, be due to incomplete assimilatory NO3- reduction and subsequent NO2- release by phytoplankton. We hypothesized that some Prochlorococcus exhibit incomplete assimilatory NO3- reduction and examined NO2- accumulation in cultures of three Prochlorococcus strains (MIT0915, MIT0917, and SB) and two Synechococcus strains (WH8102 and WH7803). Only MIT0917 and SB accumulated external NO2- during growth on NO3-. Approximately 20-30% of the NO3- transported into the cell by MIT0917 was released as NO2-, with the rest assimilated into biomass. We further observed that co-cultures using NO3- as the sole N source could be established for MIT0917 and Prochlorococcus strain MIT1214 that can assimilate NO2- but not NO3-. In these co-cultures, the NO2- released by MIT0917 is efficiently consumed by its partner strain, MIT1214. Our findings highlight the potential for emergent metabolic partnerships that are mediated by the production and consumption of N cycle intermediates within Prochlorococcus populations. IMPORTANCE Earth's biogeochemical cycles are substantially driven by microorganisms and their interactions. Given that N often limits marine photosynthesis, we investigated the potential for N cross-feeding within populations of Prochlorococcus, the numerically dominant photosynthetic cell in the subtropical open ocean. In laboratory cultures, some Prochlorococcus cells release extracellular NO2- during growth on NO3-. In the wild, Prochlorococcus populations are composed of multiple functional types, including those that cannot use NO3- but can still assimilate NO2-. We show that metabolic dependencies arise when Prochlorococcus strains with complementary NO2- production and consumption phenotypes are grown together on NO3-. These findings demonstrate the potential for emergent metabolic partnerships, possibly modulating ocean nutrient gradients, that are mediated by cross-feeding of N cycle intermediates.
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Affiliation(s)
- Paul M. Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tyler J. O'Keefe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anna Rasmussen
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Trent LeMaster
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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5
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Liu L, Chen M, Wan XS, Du C, Liu Z, Hu Z, Jiang ZP, Zhou K, Lin H, Shen H, Zhao D, Yuan L, Hou L, Yang JYT, Li X, Kao SJ, Zakem EJ, Qin W, Dai M, Zhang Y. Reduced nitrite accumulation at the primary nitrite maximum in the cyclonic eddies in the western North Pacific subtropical gyre. SCIENCE ADVANCES 2023; 9:eade2078. [PMID: 37585519 PMCID: PMC10431711 DOI: 10.1126/sciadv.ade2078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Nitrite, an intermediate product of the oxidation of ammonia to nitrate (nitrification), accumulates in upper oceans, forming the primary nitrite maximum (PNM). Nitrite concentrations in the PNM are relatively low in the western North Pacific subtropical gyre (wNPSG), where eddies are frequent and intense. To explain these low nitrite concentrations, we investigated nitrification in cyclonic eddies in the wNPSG. We detected relatively low half-saturation constants (i.e., high substrate affinities) for ammonia and nitrite oxidation at 150 to 200 meter water depth. Eddy-induced displacement of high-affinity nitrifiers and increased substrate supply enhanced ammonia and nitrite oxidation, depleting ambient substrate concentrations in the euphotic zone. Nitrite oxidation is more strongly enhanced by the cyclonic eddies than ammonia oxidation, reducing concentrations and accelerating the turnover of nitrite in the PNM. These findings demonstrate a spatial decoupling of the two steps of nitrification in response to mesoscale processes and provide insights into physical-ecological controls on the PNM.
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Affiliation(s)
- Li Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xianhui S. Wan
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Chuanjun Du
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhiyu Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhendong Hu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | | | - Kuanbo Zhou
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hongyang Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hui Shen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Duo Zhao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanying Yuan
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lei Hou
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jin-Yu T. Yang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaolin Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Emily J. Zakem
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Wei Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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6
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Ciccarese D, Tantawi O, Zhang IH, Plata D, Babbin AR. Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:275. [PMID: 38665198 PMCID: PMC11041763 DOI: 10.1038/s43247-023-00935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/18/2023] [Indexed: 04/28/2024]
Abstract
Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms-important primary producers for global carbon export-support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle's boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification.
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Affiliation(s)
- Davide Ciccarese
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Omar Tantawi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Irene H. Zhang
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Desiree Plata
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
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7
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Zhang IH, Sun X, Jayakumar A, Fortin SG, Ward BB, Babbin AR. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones. ISME COMMUNICATIONS 2023; 3:76. [PMID: 37474642 PMCID: PMC10359470 DOI: 10.1038/s43705-023-00284-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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Affiliation(s)
- Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Vigneron A, Cruaud P, Lovejoy C, Vincent WF. Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes. MICROBIOME 2023; 11:104. [PMID: 37173775 PMCID: PMC10176705 DOI: 10.1186/s40168-023-01537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/29/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. RESULTS Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. CONCLUSIONS Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.
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Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada.
| | - Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada
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9
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Gálvez-Roldán C, Cerna-Vargas JP, Rodríguez-Herva JJ, Krell T, Santamaría-Hernando S, López-Solanilla E. A Nitrate-Sensing Domain-Containing Chemoreceptor Is Required for Successful Entry and Virulence of Dickeya dadantii 3937 in Potato Plants. PHYTOPATHOLOGY 2023; 113:390-399. [PMID: 36399025 DOI: 10.1094/phyto-10-22-0367-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nitrate metabolism plays an important role in bacterial physiology. During the interaction of plant-pathogenic bacteria with their hosts, bacteria face variable conditions with respect to nitrate availability. Perception mechanisms through the chemosensory pathway drive the entry and control the colonization of the plant host in phytopathogenic bacteria. In this work, the identification and characterization of the nitrate- and nitrite-sensing (NIT) domain-containing chemoreceptor of Dickeya dadantii 3937 (Dd3937) allowed us to unveil the key role of nitrate sensing not only for the entry into the plant apoplast through wounds but also for infection success. We determined the specificity of this chemoreceptor to bind nitrate and nitrite, with a slight ligand preference for nitrate. Gene expression analysis showed that nitrate perception controls not only the expression of nitrate reductase genes involved in respiratory and assimilatory metabolic processes but also the expression of gyrA, hrpN, and bgxA, three well-known virulence determinants in Dd3937.
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Affiliation(s)
- Clara Gálvez-Roldán
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
| | - Jean Paul Cerna-Vargas
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José Juan Rodríguez-Herva
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Tino Krell
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Saray Santamaría-Hernando
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
| | - Emilia López-Solanilla
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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10
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Su J, Teng H(H, Wan X, Zhang J, Liu CQ. Direct Air Capture of CO 2 through Carbonate Alkalinity Generated by Phytoplankton Nitrate Assimilation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:550. [PMID: 36612873 PMCID: PMC9820007 DOI: 10.3390/ijerph20010550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/10/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Despite the consensus that keeping global temperature rise within 1.5 °C above pre-industrial level by 2100 reduces the chance for climate change to reach the point of no return, the newest Intergovernmental Panel on Climate Change (IPCC) report warns that the existing commitment of greenhouse gas emission reduction is only enough to contain the warming to 3-4 °C by 2100. The harsh reality not only calls for speedier deployment of existing CO2 reduction technologies but demands development of more cost-efficient carbon removal strategies. Here we report an ocean alkalinity-based CO2 sequestration scheme, taking advantage of proton consumption during nitrate assimilation by marine photosynthetic microbes, and the ensuing enhancement of seawater CO2 absorption. Benchtop experiments using a native marine phytoplankton community confirmed pH elevation from ~8.2 to ~10.2 in seawater, within 3-5 days of microbial culture in nitrate-containing media. The alkaline condition was able to sustain at continued nutrient supply but reverted to normalcy (pH ~8.2-8.4) once the biomass was removed. Measurements of δ13C in the dissolved inorganic carbon revealed a significant atmospheric CO2 contribution to the carbonate alkalinity in the experimental seawater, confirming the occurrence of direct carbon dioxide capture from the air. Thermodynamic calculation shows a theoretical carbon removal rate of ~0.13 mol CO2/L seawater, if the seawater pH is allowed to decrease from 10.2 to 8.2. A cost analysis (using a standard bioreactor wastewater treatment plant as a template for CO2 trapping, and a modified moving-bed biofilm reactor for nitrate recycling) indicated that a 1 Mt CO2/year operation is able to perform at a cost of ~$40/tCO2, 2.5-5.5 times cheaper than that offered by any of the currently available direct air capture technologies, and more in line with the price of $25-30/tCO2 suggested for rapid deployment of large-scale CCS systems.
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Affiliation(s)
- Jing Su
- School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Hui (Henry) Teng
- School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xiang Wan
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Geological Survey, Wuhan 430034, China
| | - Jianchao Zhang
- School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Cong-Qiang Liu
- School of Earth System Science, Tianjin University, Tianjin 300072, China
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11
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Padua S, Kripa V, Prema D, Mohamed KS, Jeyabaskaran R, Kaladharan P, Ratheesh L, Jenny B, Shylaja G, Joseph RV, Shyamala MP, Vysakhan P, John S, Babu A. Assessment of ecosystem health of a micro-level Ramsar coastal zone in the Vembanad Lake, Kerala, India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:95. [PMID: 36355338 PMCID: PMC9648893 DOI: 10.1007/s10661-022-10692-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Health of an ecosystem is very much important as we depend on its goods and services for our existence. Because of this, we need to continuously monitor its health for human benefit and for identifying areas for improvement of our natural systems. The present study tries to assess the condition of a coastal ecosystem within the Vembanad Lake, Kerala, India, using key water quality parameters at micro-level. Principal component analysis identified the minimum required water quality dataset for further analysis and was scored using linear scoring functions. The weighted additive method was used to integrate the individual scores to arrive at a final score representing the ecosystem health. Spline interpolation was applied to develop the ecosystem health map of the study area. Using this method, 35.8% area of the aquatic ecosystem studied was characterized as good, 32.2% as moderate, 26.2% as fair and 5.8% as poor. The assessment results can help the policymakers/managers to make appropriate decisions for the better management of the coastal ecosystems studied. Moreover, this methodology can be replicated for the assessment of coastal regions with similar ecosystem characteristics.
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Affiliation(s)
- Shelton Padua
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India.
| | - V Kripa
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
- Coastal Aquaculture Authority, Integrated Office Complex for Animal Husbandry and Fisheries Department, Government of India, Tamil Nadu, Chennai, 600 035, India
| | - D Prema
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - K S Mohamed
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
- Sustainable Seafood Network of India (SSNI), Thiruvananthapuram, 695001, Kerala, India
| | - R Jeyabaskaran
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - P Kaladharan
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - Lavanya Ratheesh
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - B Jenny
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - G Shylaja
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - Reena V Joseph
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - M P Shyamala
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - P Vysakhan
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - Seban John
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
| | - Akhil Babu
- ICAR - Central Marine Fisheries Research Institute, PO Box 1603, Kochi, 682018, Kerala, India
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12
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Sahoo TP, Vasavdutta S, Chanchpara A, Sahu N, Thiyagarajan I, Ray S, Chatterjee S, Thorat RB, Haldar S, Madhava AK. Pre-to-post COVID-19 lockdown and their environmental impacts on Ghoghla beach and Somnath beach, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:82140-82155. [PMID: 35750909 PMCID: PMC9244305 DOI: 10.1007/s11356-022-21586-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/16/2022] [Indexed: 05/22/2023]
Abstract
Environmental impact of COVID-19 imposed lockdown (2020) and the new normal condition (2021) on two different beaches of India (Ghoghla beach, Diu and Somnath beach, Veraval) were compared with the pre-lockdown era, 2013. The lockdown phase favored the natural restoration of the beaches and showed infinitesimal values of the parameters tested when compared with the pre-lockdown regime. However, the new normal situation in 2021 opened up the accessibility of these beaches to the tourists and pilgrims resulting in significant changes of water quality. The release of diluted sewage mixed with freshwater from the Somnath town to the sea has led to the drastic change in beach water quality. The mean cadmium concentration increased drastically in beach waters (Ghoghla: 1.35, 0.28 and 7.09 μg/L; Somnath: 0.45, 0.28 and 0.58 μg/L) during pre-to-post lockdown, respectively. However, post-lockdown resulted in the rise of toxic heavy metals in the sediments of Somnath beach but Ghoghla beach remained to be pristine which may be due to the Blue Flagship status. The total number of marine bacteria was higher during 2013 and 2021 when compared during lockdown describing greater human interventions. For instance, Vibrio spp. count in Ghoghla beach water during pre-lockdown phase was 7733 CFU/mL and this value reduced to 70 and 5 CFU/mL in the lockdown and post-lockdown phases. Interestingly, the diversity of planktonic and benthic components showed a different trend from pre-to-post lockdown due to significant change in the inorganic nutrients and metal bioaccumulation. To our knowledge, this will be the first comprehensive assessment to report the environmental and ecological health of Ghoghla beach and Somnath beach during the pre-to-post lockdown.
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Affiliation(s)
- Tarini Prasad Sahoo
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Sonpal Vasavdutta
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Amit Chanchpara
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Nosad Sahu
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Indirapriyatharsini Thiyagarajan
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Sanak Ray
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Shruti Chatterjee
- Applied Phycology and Biotechnology, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Ravikumar Bhagawan Thorat
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Soumya Haldar
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Anil Kumar Madhava
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India.
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13
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Laglera LM, Uskaikar H, Klaas C, Naqvi SWA, Wolf-Gladrow DA, Tovar-Sánchez A. Dissolved and particulate iron redox speciation during the LOHAFEX fertilization experiment. MARINE POLLUTION BULLETIN 2022; 184:114161. [PMID: 36179387 DOI: 10.1016/j.marpolbul.2022.114161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
The redox speciation of iron was determined during the iron fertilization LOHAFEX and for the first time, the chemiluminescence assay of filtered and unfiltered samples was systematically compared. We hypothesize that higher chemiluminescence in unfiltered samples was caused by Fe(II) adsorbed onto biological particles. Dissolved and particulate Fe(II) increased in the mixed layer steadily 6-fold during the first two weeks and decreased back to initial levels by the end of LOHAFEX. Both Fe(II) forms did not show diel cycles downplaying the role of photoreduction. The chemiluminescence of unfiltered samples across the patch boundaries showed strong gradients, correlated significantly to biomass and the photosynthetic efficiency and were higher at night, indicative of a biological control. At 150 m deep, a secondary maximum of dissolved Fe(II) was associated with maxima of nitrite and ammonium despite high oxygen concentrations. We hypothesize that during LOHAFEX, iron redox speciation was mostly regulated by trophic interactions.
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Affiliation(s)
- Luis M Laglera
- FI-TRACE, Departamento de Química, Universidad de las Islas Baleares, Palma, Balearic Islands 07122, Spain; Laboratori Interdisciplinari sobre Canvi Climàtic, Universidad de las Islas Baleares, Palma, Balearic Islands 07122, Spain.
| | - Hema Uskaikar
- National Institute of Oceanography, Dona Paula, Goa, India
| | - Christine Klaas
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | | | - Dieter A Wolf-Gladrow
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Antonio Tovar-Sánchez
- Department of Ecology and Coastal Management, Andalusian Institute for Marine Science, ICMAN (CSIC), Campus Universitario Río San Pedro, Puerto Real, Cádiz, Spain
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14
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Chen Y, Chen M, Chen J, Fan L, Zheng M, Qiu Y. Dual isotopes of nitrite in the Amundsen Sea in summer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157055. [PMID: 35780884 DOI: 10.1016/j.scitotenv.2022.157055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Nitrite (NO2-) is a key intermediate in the nitrogen (N) cycle, and its transformation is accomplished by microbial communities. However, due to few studies on the nitrite cycle, a clear assessment of the contribution to the marine biogeochemical cycle is missing. Here, we present data on nitrogen and oxygen isotopic composition of NO2- in the Amundsen Sea in summer, and explore the biogeochemical processes that influence the NO2- cycle. Extremely low δ15NNO2 and abnormally high δ18ONO2 were found in the upper waters of the Amundsen Sea, with δ15NNO2 as low as -58.4 ‰ and δ18ONO2 as high as 44.4 ‰. Enzymatic isotopic exchange reactions between nitrate and nitrite have been proposed to be responsible for these isotopic anomalies. The mirror-symmetrical variation between δ15NNO2 and δ18ONO2 suggests that the isotopic fractionation effects of nitrogen and oxygen are opposite in isotope exchange reactions. Dual isotopes of nitrite indicate that ammonia oxidation is the main source of nitrite, thus nitrification plays an important role in the formation of primary nitrite maximum in the upper Amundsen Sea. The nitrogen and oxygen isotopic compositions of nitrite provide support for clarifying multiple processes of marine nitrogen cycle.
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Affiliation(s)
- Yangjun Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Min Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| | - Jinxu Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Lingfang Fan
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Mingfang Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yusheng Qiu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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15
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Liao T, Wang S, Stüeken EE, Luo H. Phylogenomic evidence for the Origin of Obligately Anaerobic Anammox Bacteria around the Great Oxidation Event. Mol Biol Evol 2022; 39:6653777. [PMID: 35920138 PMCID: PMC9387917 DOI: 10.1093/molbev/msac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32–2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.
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Affiliation(s)
- Tianhua Liao
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Eva E Stüeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, Bute Building, Queen's Terrace, KY16 9TS, UK
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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16
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Phytoplankton Communities and Their Relationship with Environmental Factors in the Waters around Macau. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137788. [PMID: 35805446 PMCID: PMC9265806 DOI: 10.3390/ijerph19137788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
An investigation of the waters around Macau collected 43 phytoplankton species belonging to 29 genera and 5 phyla, including 32 species from 22 genera of Bacillariophyta, 7 species from 3 genera of Pyrrophyta, 2 species from 2 genera of Cyanophyta, and 1 genus and 1 species from both Euglenophyta and Chromophyta. The dominant phytoplankton species in the study areas were Skeletonema costatum (Greville) Cleve, Aulacoseira granulata (Ehrenberg) Simonsen, Thalassiothrix frauenfeidii Grunow, and Thalassionema nitzschioides Grunow. The phytoplankton abundance in the waters around Macau was between 46,607.14 and 1,355,000 cells/m3, with the highest abundance noted in station S8. Diatoms were the main contributor to phytoplankton abundance in station S8, accounting for 96.2% of the total abundance. Station S4 exhibited the lowest phytoplankton abundance of 46,607.1 cells/m3, with diatoms and Chromophytaaccounting for 58.6% and 29.9% of the total phytoplankton abundance, respectively. Biodiversity analysis results showed that the phytoplankton richness index was 1.18−3.61, the uniformity index was 0.24−0.78, and the Shannon−Wiener index was 0.94−3.41. Correlation analysis revealed that ammonia nitrogen was significantly negatively correlated with the phytoplankton richness, uniformity, and Shannon−Wiener indices. Nitrite nitrogen, nitrate nitrogen, inorganic nitrogen, salinity, turbidity, and pH were positively correlated with the phytoplankton evenness index and Shannon−Wiener index. Cluster and non-metric multidimensional scaling analyses demonstrated that the phytoplankton community structure in the waters around Macau could be divided into three groups, with A. granulata, S. costatum, T. frauenfeidii, T. nitzschioides, Chaetoceros curvisetus Cleve, and Chaetoceros diadema (Ehrenberg) Gran being predominant in different grouping communities (contribution% > 10%). Biota-Environment Stepwise Analysis (BIOENV) showed a significant correlation between the phytoplankton community and nitrite nitrogen content in the waters around Macau (correlation: 0.5544, Mantel test: statistic 0.4196, p = 0.009), which was consistent with the results of the canonical correspondence analysis.
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17
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Oshiki M, Netsu H, Kuroda K, Narihiro T, Fujii N, Kindaichi T, Suzuki Y, Watari T, Hatamoto M, Yamaguchi T, Araki N, Okabe S. Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors. Environ Microbiol 2022; 24:3735-3750. [PMID: 35672869 DOI: 10.1111/1462-2920.16085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022]
Abstract
Aerobic ammonia and nitrite oxidation reactions are fundamental biogeochemical reactions contributing to the global nitrogen cycle. Although aerobic nitrite oxidation yields 4.8-folds less Gibbs free energy (∆Gr ) than aerobic ammonia oxidation in the NH4 + -feeding marine recirculating trickling biofilter reactors operated in the present study, nitrite-oxidizing and not ammonia-oxidizing Nitrospira (sublineage IV) outnumbered ammonia-oxidizing Nitrosomonas (relative abundance; 53.8% and 7.59% respectively). CO2 assimilation efficiencies during ammonia or nitrite oxidation were 0.077 μmol-14 CO2 /μmol-NH3 and 0.053-0.054 μmol-14 CO2 /μmol-NO2 - respectively, and the difference between ammonia and nitrite oxidation was much smaller than the difference of ∆Gr . Free-energy efficiency of nitrite oxidation was higher than ammonia oxidation (31%-32% and 13% respectively), and high CO2 assimilation and free-energy efficiencies were a determinant for the dominance of Nitrospira over Nitrosomonas. Washout of Nitrospira and Nitrosomonas from the trickling biofilter reactors was also examined by quantitative PCR assay. Normalized copy numbers of Nitrosomonas amoA were 1.5- to 1.7-folds greater than Nitrospira nxrB and 16S rRNA gene in the reactor effluents. Nitrosomonas was more susceptible for washout than Nitrospira in the trickling biofilter reactors, which was another determinant for the dominance of Nitrospira in the trickling biofilter reactors.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.,Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Hirotoshi Netsu
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Naoki Fujii
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Yoshiyuki Suzuki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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18
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Panja AK, Vasavdutta S, Sahoo TP, Shinde AH, Thorat RB, Chatterjee S, Ray S, Madhava AK, Haldar S. Impact of 2nd wave of COVID-19-related lockdown on coastal water quality at Diu, western coast of India and role of total alkalinity on bacterial loads. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45971-45980. [PMID: 35156166 PMCID: PMC8852930 DOI: 10.1007/s11356-022-19168-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/07/2022] [Indexed: 05/30/2023]
Abstract
A detailed coastal water monitoring near Diu coast, western part of India was performed from October, 2020 to May, 2021 covering the 2nd lockdown time. Average monthly fluctuation from 7 different sampling stations of total 9 physico-chemical parameters such as pH, salinity, turbidity, nitrite (NO2), nitrate (NO3), ammonia (NH3), phosphate (PO4), total alkalinity and silicate were recorded. Initially, Mann-Kendall trend test for all the 9 parameters showed non-zero trend, which may be either linear or non-linear. During 2nd lockdown period, there was a fluctuation of value for parameters like pH, salinity, nitrate, nitrite and phosphate. Average total bacterial count and differential bacterial count also gradually decreased from March, 2021 sampling. Principal component analysis (PCA) plot covering all the physico-chemical parameters as well as the differential bacterial count showed a distinct cluster of all bacterial count with total alkalinity value. Subsequently, mathematical equation was formulated between total alkalinity value and all differential bacterial count. Upto our knowledge, this is the first report where mathematical equation was formulated to obtain value of different bacterial load based on the derived total alkalinity value of the coastal water samples near Diu, India.
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Affiliation(s)
- Atanu Kumar Panja
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
| | - Sonpal Vasavdutta
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
| | - Tarini Prasad Sahoo
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
| | - Ambika H Shinde
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ravikumar Bhagawan Thorat
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shruti Chatterjee
- Applied Phycology and Biotechnology Division, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
| | - Sanak Ray
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anil Kumar Madhava
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Soumya Haldar
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364 002, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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19
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Hogle SL, Hackl T, Bundy RM, Park J, Satinsky B, Hiltunen T, Biller S, Berube PM, Chisholm SW. Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean. THE ISME JOURNAL 2022; 16:1636-1646. [PMID: 35241788 PMCID: PMC9122953 DOI: 10.1038/s41396-022-01215-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria.
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Affiliation(s)
- Shane L Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, University of Turku, Turku, Finland.
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Randelle M Bundy
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Jiwoon Park
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Brandon Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Teppo Hiltunen
- Department of Biology, University of Turku, Turku, Finland
| | - Steven Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Nguyen TTH, Zakem EJ, Ebrahimi A, Schwartzman J, Caglar T, Amarnath K, Alcolombri U, Peaudecerf FJ, Hwa T, Stocker R, Cordero OX, Levine NM. Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates. Nat Commun 2022; 13:1657. [PMID: 35351873 PMCID: PMC8964765 DOI: 10.1038/s41467-022-29297-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent microbial dynamics on ocean-scale particulate carbon fluxes is poorly understood. Here we scale-up essential features of particle-associated microbial dynamics to understand the large-scale vertical carbon flux in the ocean. Our model provides mechanistic insight into the microbial contribution to the particulate organic carbon flux profile. We show that the enhanced transfer of carbon to depth can result from populations struggling to establish colonies on sinking particles due to diffusive nutrient loss, cell detachment, and mortality. These dynamics are controlled by the interaction between multiple biotic and abiotic factors. Accurately capturing particle-microbe interactions is essential for predicting variability in large-scale carbon cycling. Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean.
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21
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The marine nitrogen cycle: new developments and global change. Nat Rev Microbiol 2022; 20:401-414. [PMID: 35132241 DOI: 10.1038/s41579-022-00687-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/25/2022]
Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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22
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Follett CL, Dutkiewicz S, Ribalet F, Zakem E, Caron D, Armbrust EV, Follows MJ. Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus. Proc Natl Acad Sci U S A 2022; 119:e2110993118. [PMID: 34983874 PMCID: PMC8764666 DOI: 10.1073/pnas.2110993118] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 11/26/2022] Open
Abstract
Prochlorococcus is both the smallest and numerically most abundant photosynthesizing organism on the planet. While thriving in the warm oligotrophic gyres, Prochlorococcus concentrations drop rapidly in higher-latitude regions. Transect data from the North Pacific show the collapse occurring at a wide range of temperatures and latitudes (temperature is often hypothesized to cause this shift), suggesting an ecological mechanism may be at play. An often used size-based theory of phytoplankton community structure that has been incorporated into computational models correctly predicts the dominance of Prochlorococcus in the gyres, and the relative dominance of larger cells at high latitudes. However, both theory and computational models fail to explain the poleward collapse. When heterotrophic bacteria and predators that prey nonspecifically on both Prochlorococcus and bacteria are included in the theoretical framework, the collapse of Prochlorococcus occurs with increasing nutrient supplies. The poleward collapse of Prochlorococcus populations then naturally emerges when this mechanism of "shared predation" is implemented in a complex global ecosystem model. Additionally, the theory correctly predicts trends in both the abundance and mean size of the heterotrophic bacteria. These results suggest that ecological controls need to be considered to understand the biogeography of Prochlorococcus and predict its changes under future ocean conditions. Indirect interactions within a microbial network can be essential in setting community structure.
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Affiliation(s)
- Christopher L Follett
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139;
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - François Ribalet
- School of Oceanography, University of Washington, Seattle, WA 98195
| | - Emily Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - David Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | | | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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23
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Li L, Pujari L, Wu C, Huang D, Wei Y, Guo C, Zhang G, Xu W, Liu H, Wang X, Wang M, Sun J. Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean. Front Microbiol 2021; 12:616956. [PMID: 34456881 PMCID: PMC8385211 DOI: 10.3389/fmicb.2021.616956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.
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Affiliation(s)
- Liuyang Li
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Laxman Pujari
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Chao Wu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Danyue Huang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqiu Wei
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Congcong Guo
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Wenzhe Xu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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24
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Cryptic Constituents: The Paradox of High Flux–Low Concentration Components of Aquatic Ecosystems. WATER 2021. [DOI: 10.3390/w13162301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The interface between terrestrial ecosystems and inland waters is an important link in the global carbon cycle. However, the extent to which allochthonous organic matter entering freshwater systems plays a major role in microbial and higher-trophic-level processes is under debate. Human perturbations can alter fluxes of terrestrial carbon to aquatic environments in complex ways. The biomass and production of aquatic microbes are traditionally thought to be resource limited via stoichiometric constraints such as nutrient ratios or the carbon standing stock at a given timepoint. Low concentrations of a particular constituent, however, can be strong evidence of its importance in food webs. High fluxes of a constituent are often associated with low concentrations due to high uptake rates, particularly in aquatic food webs. A focus on biomass rather than turnover can lead investigators to misconstrue dissolved organic carbon use by bacteria. By combining tracer methods with mass balance calculations, we reveal hidden patterns in aquatic ecosystems that emphasize fluxes, turnover rates, and molecular interactions. We suggest that this approach will improve forecasts of aquatic ecosystem responses to warming or altered nitrogen usage.
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25
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Dalziel BD, Novak M, Watson JR, Ellner SP. Collective behaviour can stabilize ecosystems. Nat Ecol Evol 2021; 5:1435-1440. [PMID: 34385617 DOI: 10.1038/s41559-021-01517-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/18/2021] [Indexed: 11/09/2022]
Abstract
Collective behaviour is common in bacteria, plants and animals, and therefore occurs across ecosystems, from biofilms to cities. With collective behaviour, social interactions among individuals propagate to affect the behaviour of groups, whereas group-level responses in turn affect individual behaviour. These cross-scale feedback loops between individuals, populations and their environments can provide fitness benefits, such as the efficient exploitation of uncertain resources, as well as costs, such as increased resource competition. Although the social mechanics of collective behaviour are increasingly well-studied, its role in ecosystems remains poorly understood. Here we introduce collective movement into a model of consumer-resource dynamics to demonstrate that collective behaviour can attenuate consumer-resource cycles and promote species coexistence. We focus on collective movement as a particularly well-understood example of collective behaviour. Adding collective movement to canonical unstable ecological scenarios causes emergent social-ecological feedback, which mitigates conditions that would otherwise result in extinction. Collective behaviour could play a key part in the maintenance of biodiversity.
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Affiliation(s)
- Benjamin D Dalziel
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA. .,Department of Mathematics, Oregon State University, Corvallis, OR, USA.
| | - Mark Novak
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - James R Watson
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Stephen P Ellner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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26
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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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27
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Gazitúa MC, Vik DR, Roux S, Gregory AC, Bolduc B, Widner B, Mulholland MR, Hallam SJ, Ulloa O, Sullivan MB. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. THE ISME JOURNAL 2021; 15:981-998. [PMID: 33199808 PMCID: PMC8115048 DOI: 10.1038/s41396-020-00825-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 01/29/2023]
Abstract
Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
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Affiliation(s)
- M. Consuelo Gazitúa
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA ,Viromica Consulting, Santiago, Chile
| | - Dean R. Vik
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Simon Roux
- grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Ann C. Gregory
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Benjamin Bolduc
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Brittany Widner
- grid.261368.80000 0001 2164 3177Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, VA USA ,grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Margaret R. Mulholland
- grid.261368.80000 0001 2164 3177Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, VA USA
| | - Steven J. Hallam
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - Osvaldo Ulloa
- grid.5380.e0000 0001 2298 9663Departamento de Oceanografía & Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Matthew B. Sullivan
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH USA
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28
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Nev OA, Lindsay RJ, Jepson A, Butt L, Beardmore RE, Gudelj I. Predicting microbial growth dynamics in response to nutrient availability. PLoS Comput Biol 2021; 17:e1008817. [PMID: 33735173 PMCID: PMC8009381 DOI: 10.1371/journal.pcbi.1008817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 03/30/2021] [Accepted: 02/17/2021] [Indexed: 01/04/2023] Open
Abstract
Developing mathematical models to accurately predict microbial growth dynamics remains a key challenge in ecology, evolution, biotechnology, and public health. To reproduce and grow, microbes need to take up essential nutrients from the environment, and mathematical models classically assume that the nutrient uptake rate is a saturating function of the nutrient concentration. In nature, microbes experience different levels of nutrient availability at all environmental scales, yet parameters shaping the nutrient uptake function are commonly estimated for a single initial nutrient concentration. This hampers the models from accurately capturing microbial dynamics when the environmental conditions change. To address this problem, we conduct growth experiments for a range of micro-organisms, including human fungal pathogens, baker's yeast, and common coliform bacteria, and uncover the following patterns. We observed that the maximal nutrient uptake rate and biomass yield were both decreasing functions of initial nutrient concentration. While a functional form for the relationship between biomass yield and initial nutrient concentration has been previously derived from first metabolic principles, here we also derive the form of the relationship between maximal nutrient uptake rate and initial nutrient concentration. Incorporating these two functions into a model of microbial growth allows for variable growth parameters and enables us to substantially improve predictions for microbial dynamics in a range of initial nutrient concentrations, compared to keeping growth parameters fixed.
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Affiliation(s)
- Olga A. Nev
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Richard J. Lindsay
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Alys Jepson
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Lisa Butt
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Robert E. Beardmore
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Ivana Gudelj
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
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29
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Semedo M, Lopes E, Baptista MS, Oller-Ruiz A, Gilabert J, Tomasino MP, Magalhães C. Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific. Front Microbiol 2021; 12:624071. [PMID: 33732221 PMCID: PMC7959781 DOI: 10.3389/fmicb.2021.624071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3– concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.
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Affiliation(s)
- Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Eva Lopes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ainhoa Oller-Ruiz
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Javier Gilabert
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
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30
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Ofaim S, Sulheim S, Almaas E, Sher D, Segrè D. Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus. Front Genet 2021; 12:586293. [PMID: 33633777 PMCID: PMC7900632 DOI: 10.3389/fgene.2021.586293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.
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Affiliation(s)
- Shany Ofaim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Snorre Sulheim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Department of Physics, Boston University, Boston, MA, United States.,Department of Biology, Boston University, Boston, MA, United States
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31
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Zakem EJ, Polz MF, Follows MJ. Redox-informed models of global biogeochemical cycles. Nat Commun 2020; 11:5680. [PMID: 33173062 PMCID: PMC7656242 DOI: 10.1038/s41467-020-19454-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments. “Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keefe Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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32
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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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33
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Wu P, Zakem EJ, Dutkiewicz S, Zhang Y. Biomagnification of Methylmercury in a Marine Plankton Ecosystem. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:5446-5455. [PMID: 32054263 DOI: 10.1021/acs.est.9b06075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Methylmercury is greatly bioconcentrated and biomagnified in marine plankton ecosystems, and these communities form the basis of marine food webs. Therefore, the evaluation of the potential exposure of methylmercury to higher trophic levels, including humans, requires a better understanding of its distribution in the ocean and the factors that control its biomagnification. In this study, a coupled physical/ecological model is used to simulate the trophic transfer of monomethylmercury (MMHg) in a marine plankton ecosystem. The model includes phytoplankton, a microbial community, herbivorous zooplankton (HZ), and carnivorous zooplankton (CZ). The model captures both shorter food chains in oligotrophic regions, with small HZ feeding on small phytoplankton, and longer chains in higher nutrient conditions, with larger HZ feeding on larger phytoplankton and larger CZ feeding on larger HZ. In the model, trophic dilution occurs in the food webs that involve small zooplankton, as the grazing fluxes of small zooplankton are insufficient to accumulate more MMHg in themselves than in their prey. The model suggests that biomagnification is more prominent in large zooplankton and that the microbial community plays an important role in the trophic transfer of MMHg. Sensitivity analyses show that with increasing body size, the sensitivity of the trophic magnification ratio to grazing, mortality rates, and food assimilation efficiency (AEC) increases, while the sensitivity to excretion rates decreases. More predation or a longer zooplankton lifespan may lead to more prominent biomagnification, especially for large species. Because lower AEC results in more predation, modeled ratios of MMHg concentrations between large plankton are doubled or even tripled when the AEC decreases from 50% to 10%. This suggests that the biomagnification of large zooplankton is particularly sensitive to food assimilation efficiency.
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Affiliation(s)
- Peipei Wu
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, School of Atmospheric Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Emily J Zakem
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 United States
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Yanxu Zhang
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, School of Atmospheric Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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Zhang Y, Qin W, Hou L, Zakem EJ, Wan X, Zhao Z, Liu L, Hunt KA, Jiao N, Kao SJ, Tang K, Xie X, Shen J, Li Y, Chen M, Dai X, Liu C, Deng W, Dai M, Ingalls AE, Stahl DA, Herndl GJ. Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. Proc Natl Acad Sci U S A 2020; 117:4823-4830. [PMID: 32071230 PMCID: PMC7060736 DOI: 10.1073/pnas.1912367117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.
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Affiliation(s)
- Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China;
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, WA 98195
| | - Lei Hou
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Xianhui Wan
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
| | - Zihao Zhao
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, A-1090 Vienna, Austria
| | - Li Liu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Xiabing Xie
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
| | - Jiaming Shen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Yufang Li
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Xiaofeng Dai
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Chang Liu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Wenchao Deng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, A-1090 Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, The Netherlands
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Manasrah R, Alsaad L, Trabeen K, Rasheed M, Al-Absi E, Dixon LK, Al-Sawalmih A. Physical and chemical properties of seawater during 2013-2015 in the 400 m water column in the northern Gulf of Aqaba, Red Sea. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:188. [PMID: 32076865 DOI: 10.1007/s10661-020-8134-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
This research investigated physical (temperature, salinity, and density) and chemical (dissolved oxygen, ammonium, nitrate, nitrite, phosphate, and silicate) properties of offshore seawater in the Red Sea northern Gulf of Aqaba; Jordanian Site were measured during 2013-2015 to assess the temporal and seasonal variation of the upper 400 m of the water column. The study also investigated seasonal variations, assessing the relationships of temperature with physical and chemical parameters. The average value of temperature for all data was 23.03 ± 1.58 °C. Temperature followed an expected seasonal cycle during 2013-2015, with well-mixed conditions in the upper 400 m of the water column during spring (Feb-Apr) and stratification during summer (Jul-Aug). There were no significant differences among years for temperature, but highly significant differences among months and depths. The average value of salinity (psu) for all data was 40.60 ± 0.10 with significant positive or negative differences among years, months, and depths. In general, dissolved oxygen, ammonium, nitrate, nitrite, and phosphate data showed positive or negative significant differences among months and depths with no significant annual variations. Silicate only showed significant differences among depths. Correlation tests between temperature and other parameters in the upper 25 m of the water column revealed significant inverse-relationships between temperature and all other parameters (other than salinity) that were attributed to the dominant thermal controls on seawater density, to the thermodynamic controls on oxygen solubility and to seasonal increases in light irradiance that allowed nutrient consumption by primary producers. In the intermediate water column (100-150 m), similar correlations were found as in the 0-25 m data, except for silicate. In the deeper waters (300-400 m), only salinity, density, and phosphate showed significant correlations with temperature, and indicated that the seasonal effects of primary production at depth were minimal. In general, the values of all parameters during the years 2013-2015 in the upper 400 m were comparable with previous studies (e.g., 1998-2003). In conclusion, this research manifested the strong correlation of temperature with some chemical parameters and presumed seasonal controls on primary production. Given the general lack of interannual variation, water quality in the northern Gulf of Aqaba appears relatively stable.
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Affiliation(s)
- Riyad Manasrah
- Faculty of Basic and Marine Sciences, The University of Jordan/Aqaba, PO Box 2595, Aqaba, 77110, Jordan
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Lojen Alsaad
- Faculty of Basic and Marine Sciences, The University of Jordan/Aqaba, PO Box 2595, Aqaba, 77110, Jordan
| | - Khalid Trabeen
- Marine Science Station, The University of Jordan and Yamouk University, PO Box 195, Aqaba, 77110, Jordan
| | - Mohammad Rasheed
- Chemistry Department, Faculty of Sciences, The University of Jordan, Amman, 11942, Jordan
| | - Eman Al-Absi
- Faculty of Basic and Marine Sciences, The University of Jordan/Aqaba, PO Box 2595, Aqaba, 77110, Jordan
| | - L Kellie Dixon
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Ali Al-Sawalmih
- Marine Science Station, The University of Jordan and Yamouk University, PO Box 195, Aqaba, 77110, Jordan.
- Dept. of Biomaterials, Max-Planck Institute for Colloids and Interfaces, Potsdam, 14476, Germany.
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36
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Ellwood MJ, Strzepek RF, Strutton PG, Trull TW, Fourquez M, Boyd PW. Distinct iron cycling in a Southern Ocean eddy. Nat Commun 2020; 11:825. [PMID: 32047154 PMCID: PMC7012851 DOI: 10.1038/s41467-020-14464-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/07/2020] [Indexed: 11/09/2022] Open
Abstract
Mesoscale eddies are ubiquitous in the iron-limited Southern Ocean, controlling ocean-atmosphere exchange processes, however their influence on phytoplankton productivity remains unknown. Here we probed the biogeochemical cycling of iron (Fe) in a cold-core eddy. In-eddy surface dissolved Fe (dFe) concentrations and phytoplankton productivity were exceedingly low relative to external waters. In-eddy phytoplankton Fe-to-carbon uptake ratios were elevated 2–6 fold, indicating upregulated intracellular Fe acquisition resulting in a dFe residence time of ~1 day. Heavy dFe isotope values were measured for in-eddy surface waters highlighting extensive trafficking of dFe by cells. Below the euphotic zone, dFe isotope values were lighter and coincident with peaks in recycled nutrients and cell abundance, indicating enhanced microbially-mediated Fe recycling. Our measurements show that the isolated nature of Southern Ocean eddies can produce distinctly different Fe biogeochemistry compared to surrounding waters with cells upregulating iron uptake and using recycling processes to sustain themselves. Eddies are common ocean features that isolate large swaths of seawater, but it is unclear how they influence productivity of phytoplankton trapped inside. Here Ellwood and colleagues use stable and radiogenic isotopes to characterize a Southern Ocean eddy, finding vanishingly low iron concentrations that drive low productivity across the region.
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Affiliation(s)
- Michael J Ellwood
- Research School of Earth Sciences, Australian National University, Canberra, Australia.
| | - Robert F Strzepek
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Peter G Strutton
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia.,Australian Research Council Centre of Excellence for Climate Extremes, University of Tasmania, Hobart, Australia
| | | | - Marion Fourquez
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
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37
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Zakem EJ, Mahadevan A, Lauderdale JM, Follows MJ. Stable aerobic and anaerobic coexistence in anoxic marine zones. THE ISME JOURNAL 2020; 14:288-301. [PMID: 31624350 PMCID: PMC6908664 DOI: 10.1038/s41396-019-0523-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/23/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | | | - Jonathan M Lauderdale
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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38
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Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, La Clair JJ, Chisholm SW, Stepanauskas R. Charting the Complexity of the Marine Microbiome through Single-Cell Genomics. Cell 2019; 179:1623-1635.e11. [PMID: 31835036 PMCID: PMC6919566 DOI: 10.1016/j.cell.2019.11.017] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/30/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022]
Abstract
Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.
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Affiliation(s)
- Maria G Pachiadaki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA; Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Joseph Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Oliver Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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Zhu B, Chen S, Zhao C, Zhong W, Zeng R, Yang S. Effects of Marichromatium gracile YL28 on the nitrogen management in the aquaculture pond water. BIORESOURCE TECHNOLOGY 2019; 292:121917. [PMID: 31408778 DOI: 10.1016/j.biortech.2019.121917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 07/22/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Nitrogen pollution in aquaculture needs the efficient and cost-effective in-situ technology. This study aims to apply Marichromatium gracile YL28 to in-situ bioremediation and test its ability to maintain the nitrogen balance in aquaculture. In laboratory aquaculture system, approximately 99.96% of nitrite (1 mg/L) was removed within 7 d through denitrification coupled with assimilatory nitrate reduction. Ammonium (3.5 mg/L) of 95.6% was directly assimilated by YL28 within 7 d. Moreover, in zero exchange water from shrimp (Penaeus vannamei) aquaculture field trials (20 days), YL28 significantly reduced the ammonium accumulation (0.6 mg/L) and 99.3% of nitrite (1.25 mg/L). Toxicological studies with the Institute of Cancer Research (ICR) mice and Oryzias melastigma indicated that M. gracile YL28 can be safely applied in aquatic ecosystems. All results demonstrate that strain YL28 has high promise for future applications of removing inorganic nitrogen and maintaining the nitrogen balance from in-situ aquaculture.
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Affiliation(s)
- Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48863, USA
| | - Chungui Zhao
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China
| | - Weihua Zhong
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China.
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In situ determination of Si, N, and P utilization by the demosponge Tethya citrina: A benthic-chamber approach. PLoS One 2019; 14:e0218787. [PMID: 31283799 PMCID: PMC6613687 DOI: 10.1371/journal.pone.0218787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/11/2019] [Indexed: 11/23/2022] Open
Abstract
Sponges consume dissolved silicon (DSi) to build their skeletons. Few studies have attempted to quantify DSi utilization by these organisms and all available determinations come from laboratory measurements. Here we measured DSi consumption rates of the sponge Tethya citrina in its natural habitat, conducting 24h incubations in benthic chambers. Sponges consumed DSi at an average rate of 0.046 ± 0.018 μmol h-1 mL-1 when DSi availability in its habitat was 8.3 ± 1.8 μM. Such DSi consumption rates significantly matched the values predicted by a kinetic model elsewhere developed previously for this species through laboratory incubations. These results support the use of laboratory incubations as a suitable approach to learn about DSi consumption. During the field incubations, utilization of other dissolved inorganic nutrients by this low-microbial-abundance (LMA) sponge was also measured. The sponges were net sources of ammonium (-0.043 ± 0.031 μmol h-1 mL-1), nitrate (-0.063 ± 0.031 μmol h-1 mL-1), nitrite (-0.007 ± 0.003 μmol h-1 mL-1), and phosphate (-0.004 ± 0.005 μmol h-1 mL-1), in agreement with the general pattern in other LMA species. The detected effluxes were among the lowest reported for sponges, which agreed with the low respiration rates characterizing this species (0.35 ± 0.11 μmol-O2 h-1 mL-1). Despite relatively low flux, the dense population of T. citrina modifies the availability of dissolved inorganic nutrients in the demersal water of its habitat, contributing up to 14% of nitrate and nitrite stocks. Through these effects, the bottom layer contacting the benthic communities where siliceous LMA sponges abound can be partially depleted in DSi, but can benefit from inputs of N and P dissolved inorganic nutrients that are critical to primary producers.
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Lau E, Frame CH, Nolan EJ, Stewart FJ, Dillard ZW, Lukich DP, Mihalik NE, Yauch KE, Kinker MA, Waychoff SL. Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone. PLoS One 2019; 14:e0217136. [PMID: 31112557 PMCID: PMC6529010 DOI: 10.1371/journal.pone.0217136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2-) and NO2- to nitrate (NO3-), plays a vital role in ocean nitrogen cycling. Characterizing the distribution of nitrifying organisms over environmental gradients can help predict how nitrogen availability may change with shifting ocean conditions, for example, due to loss of dissolved oxygen (O2). We characterized the distribution of nitrifiers at 5 depths spanning the oxic to hypoxic zone of the offshore Benguela upwelling system above the continental slope off Namibia. Based on 16S rRNA gene amplicon sequencing, the proportional abundance of nitrifiers (ammonia and nitrite oxidizers) increased with depth, driven by an increase in ammonia-oxidizing archaea (AOA; Thaumarchaeota) to up to 33% of the community at hypoxic depths where O2 concentrations fell to ~25 μM. The AOA community transitioned from being dominated by a few members at oxic depths to a more even representation of taxa in the hypoxic zone. In comparison, the community of NO2--oxidizing bacteria (NOB), composed primarily of Nitrospinae, was far less abundant and exhibited higher evenness at all depths. The AOA:NOB ratio declined with depth from 41:1 in the oxic zone to 27:1 under hypoxia, suggesting potential variation in the balance between NO2- production and consumption via nitrification. Indeed, in contrast to prior observations from more O2-depleted sites closer to shore, NO2- did not accumulate at hypoxic depths near this offshore site, potentially due in part to a tightened coupling between AOA and NOB.
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Affiliation(s)
- Evan Lau
- Department of Biology, Menlo College, Atherton, California, United States of America
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
- * E-mail:
| | - Caitlin H. Frame
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - E. Joseph Nolan
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zachary W. Dillard
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Daniel P. Lukich
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Nicole E. Mihalik
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Katelyn E. Yauch
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Marcus A. Kinker
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Samantha L. Waychoff
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
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Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold C, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H. Low yield and abiotic origin of N 2O formed by the complete nitrifier Nitrospira inopinata. Nat Commun 2019; 10:1836. [PMID: 31015413 PMCID: PMC6478695 DOI: 10.1038/s41467-019-09790-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 03/27/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.
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Affiliation(s)
- K Dimitri Kits
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Man-Young Jung
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Julia Vierheilig
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Division of Water Quality and Health, Krems, 3500, Austria
- Interuniversity Cooperation Centre for Water and Health, Krems, 3500, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christopher J Sedlacek
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Shurong Liu
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Craig Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - Andreas Richter
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Holger Wissel
- Institute of Bio- and Geosciences-Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences-Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Holger Daims
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
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Bueno E, Sit B, Waldor MK, Cava F. Anaerobic nitrate reduction divergently governs population expansion of the enteropathogen Vibrio cholerae. Nat Microbiol 2018; 3:1346-1353. [PMID: 30275512 PMCID: PMC6443258 DOI: 10.1038/s41564-018-0253-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/28/2018] [Indexed: 12/17/2022]
Abstract
To survive and proliferate in the absence of oxygen, many enteric pathogens can undergo anaerobic respiration within the host by using nitrate (NO3-) as electron acceptor 1,2. In these bacteria, NO3- is typically reduced by a nitrate reductase to nitrite (NO2-), a toxic intermediate that is further reduced by a nitrite reductase3. However, Vibrio cholerae, the intestinal pathogen that causes cholera, lacks a nitrite reductase, leading to NO2- accumulation during nitrate reduction4. Thus, V. cholerae is thought to be unable to undergo NO3--dependent anaerobic respiration4. Here, we show that during hypoxic growth, NO3- reduction in V. cholerae divergently impacts bacterial fitness in a manner dependent on environmental pH. Remarkably, in alkaline conditions, V. cholerae can reduce NO3- to support population growth. Conversely, in acidic conditions, accumulation of NO2- from NO3- reduction simultaneously limits population expansion and preserves cell viability by lowering fermentative acid production. Interestingly, other bacterial species such as Salmonella typhimurium, enterohemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium also reproduced this pH-dependent response suggesting that this mechanism might be conserved within enteric pathogens. Our findings explain how a bacterial pathogen can use a single redox reaction to divergently regulate population expansion depending on fluctuating environmental pH.
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Affiliation(s)
- Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Brandon Sit
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew K Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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