1
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Lin G, Gao D, Yang P, Liu S, Sun D, Lin X. Editorial: Linking microbial-driven key processes with carbon and nitrogen cycling in estuarine, coastal, and the nearshore areas. Front Microbiol 2024; 15:1382148. [PMID: 38562475 PMCID: PMC10982486 DOI: 10.3389/fmicb.2024.1382148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Dengzhou Gao
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Ping Yang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Shuting Liu
- Department of Environmental and Sustainability Sciences, Kean University, Union, NJ, United States
| | - Dongyao Sun
- School of Geography Science and Geomatics Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Xianbiao Lin
- Key Laboratory of Marine Chemistry Theory and Technology, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao, China
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2
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Guider JT, Yoshimura KM, Block KR, Biddle JF, Shah Walter SR. Archaeal blooms and busts in an estuarine time series. Environ Microbiol 2024; 26:e16584. [PMID: 38372423 DOI: 10.1111/1462-2920.16584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22-0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.
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Affiliation(s)
- Justin T Guider
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Kristin M Yoshimura
- Department of Biology, James Madison University, Harrisonburg, Virginia, USA
| | - Kaleigh R Block
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
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3
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Huang BC, Li GF, Ren ZQ, Ji XM, Wang Y, Gu YN, Li JP, Chang RR, Fan NS, Jin RC. Light-Driven Electron Uptake from Nonfermentative Organic Matter to Expedite Nitrogen Dissimilation by Chemolithotrophic Anammox Consortia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12732-12740. [PMID: 37590181 DOI: 10.1021/acs.est.3c04160] [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: 08/19/2023]
Abstract
Nonphotosynthetic microorganisms are typically unable to directly utilize light energy, but light might change the metabolic pathway of these bacteria indirectly by forming intermediates such as reactive oxygen species (ROS). This work investigated the role of light on nitrogen conversion by anaerobic ammonium oxidation (anammox) consortia. The results showed that high intensity light (>20000 lx) caused ca. 50% inhibition of anammox activity, and total ROS reached 167% at 60,000 lx. Surprisingly, 200 lx light was found to induce unexpected promotion of the nitrogen conversion rate, and ultraviolet light (<420 nm) was identified as the main contributor. Metagenomic and metatranscriptomic analyses revealed that the gene encoding cytochrome c peroxidase was highly expressed only under 200 lx light. 15N isotope tracing, gene abundance quantification, and external H2O2 addition experiments showed that photoinduced trace H2O2 triggered cytochrome c peroxidase expression to take up electrons from extracellular nonfermentative organics to synthesize NADH and ATP, thereby expediting nitrogen dissimulation of anammox consortia. External supplying reduced humic acid into a low-intensity light exposure system would result in a maximal 1.7-fold increase in the nitrogen conversion rate. These interesting findings may provide insight into the niche differentiation and widespread nature of anammox bacteria in natural ecotopes.
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Affiliation(s)
- Bao-Cheng Huang
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Gui-Feng Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhi-Qi Ren
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiao-Ming Ji
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ye Wang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ye-Nan Gu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jing-Peng Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Rong-Rong Chang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Nian-Si Fan
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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4
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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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5
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Lu Y, Lv Y, Zhang Y, Liu Q, Xu X, Xiao X, Xu J. Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea. Environ Microbiol 2023; 25:410-427. [PMID: 36448268 DOI: 10.1111/1462-2920.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.
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Affiliation(s)
- Ye Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yongxin Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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6
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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7
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Stukel MR, Gerard T, Kelly TB, Knapp AN, Laiz-Carrión R, Lamkin JT, Landry MR, Malca E, Selph KE, Shiroza A, Shropshire TA, Swalethorp R. Plankton food webs in the oligotrophic Gulf of Mexico spawning grounds of Atlantic bluefin tuna. JOURNAL OF PLANKTON RESEARCH 2022; 44:763-781. [PMID: 36045950 PMCID: PMC9424712 DOI: 10.1093/plankt/fbab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 06/15/2023]
Abstract
We used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic bluefin tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show extensive nutrient regeneration fueling primary productivity (mostly by cyanobacteria and other picophytoplankton) in the upper euphotic zone. The food web is dominated by the microbial loop (>70% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). By contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <10% of the net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on podonid cladocerans and other suspension-feeding zooplankton, which in turn derive much of their nutrition from nano- and micro-phytoplankton (mixotrophic flagellates, and to a lesser extent, diatoms). This allows ABT larvae to maintain a comparatively low trophic level (~4.2 for preflexion and postflexion larvae), which increases trophic transfer from phytoplankton to larval fish.
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Affiliation(s)
| | - Trika Gerard
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, FL 33149, USA
| | - Thomas B Kelly
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Angela N Knapp
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Raúl Laiz-Carrión
- Centro Oceanográfico De Malaga, Instituto Español Del Oceanografía, Fuengirola, Spain
| | - John T Lamkin
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, FL 33149, USA
| | - Michael R Landry
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0227, USA
| | - Estrella Malca
- Cooperative Institute For Marine and Atmospheric Studies, University Of Miami, Miami, FL 33149, USA
| | - Karen E Selph
- Department of Oceanography, University of Hawaii At Manoa, Honolulu, HI 96822, USA
| | - Akihiro Shiroza
- Cooperative Institute For Marine and Atmospheric Studies, University Of Miami, Miami, FL 33149, USA
| | - Taylor A Shropshire
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
- Center for Ocean-Atmospheric Prediction Studies, Florida State University, Tallahassee, FL 32306, USA
| | - Rasmus Swalethorp
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0227, USA
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8
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Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations. mSystems 2022; 7:e0147721. [PMID: 35695431 PMCID: PMC9239043 DOI: 10.1128/msystems.01477-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Some marine microbes are seemingly “ubiquitous,” thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (“Candidatus Nitrosopelagicus brevis”) populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in “Ca. N. brevis” at HOT, driven by a higher rate of homologous recombination. In contrast, “Ca. N. brevis” at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of “Ca. N. brevis.” IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA “Candidatus Nitrosopelagicus brevis” in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to “Ca. N. brevis” have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.
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9
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Alcamán-Arias ME, Cifuentes-Anticevic J, Díez B, Testa G, Troncoso M, Bello E, Farías L. Surface Ammonia-Oxidizer Abundance During the Late Summer in the West Antarctic Coastal System. Front Microbiol 2022; 13:821902. [PMID: 35401462 PMCID: PMC8992545 DOI: 10.3389/fmicb.2022.821902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 01/04/2023] Open
Abstract
Marine ammonia oxidizers that oxidize ammonium to nitrite are abundant in polar waters, especially during the winter in the deeper mixed-layer of West Antarctic Peninsula (WAP) waters. However, the activity and abundance of ammonia-oxidizers during the summer in surface coastal Antarctic waters remain unclear. In this study, the ammonia-oxidation rates, abundance and identity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were evaluated in the marine surface layer (to 30 m depth) in Chile Bay (Greenwich Island, WAP) over three consecutive late-summer periods (2017, 2018, and 2019). Ammonia-oxidation rates of 68.31 nmol N L−1 day−1 (2018) and 37.28 nmol N L−1 day−1 (2019) were detected from illuminated 2 m seawater incubations. However, high ammonia-oxidation rates between 267.75 and 109.38 nmol N L−1 day−1 were obtained under the dark condition at 30 m in 2018 and 2019, respectively. During the late-summer sampling periods both stratifying and mixing events occurring in the water column over short timescales (February–March). Metagenomic analysis of seven nitrogen cycle modules revealed the presence of ammonia-oxidizers, such as the Archaea Nitrosopumilus and the Bacteria Nitrosomonas and Nitrosospira, with AOA often being more abundant than AOB. However, quantification of specific amoA gene transcripts showed number of AOB being two orders of magnitude higher than AOA, with Nitrosomonas representing the most transcriptionally active AOB in the surface waters. Additionally, Candidatus Nitrosopelagicus and Nitrosopumilus, phylogenetically related to surface members of the NP-ε and NP-γ clades respectively, were the predominant AOA. Our findings expand the known distribution of ammonium-oxidizers to the marine surface layer, exposing their potential ecological role in supporting the marine Antarctic system during the productive summer periods.
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Affiliation(s)
- María E Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Center for Climate and Resilience Research (CR)2, Santiago, Chile.,Escuela de Medicina, Universidad Espíritu Santo, Guayaquil, Ecuador
| | | | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Giovanni Testa
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Programa de Postgrado en Oceanografía, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Research Center Dynamics of High Latitude Marine Ecosystems (IDEAL), Punta Arenas, Chile
| | | | - Estrella Bello
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Center for Climate and Resilience Research (CR)2, Santiago, Chile
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10
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DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 2022; 12:4257. [PMID: 35277525 PMCID: PMC8917147 DOI: 10.1038/s41598-022-07980-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022] Open
Abstract
The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
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11
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Sow SLS, Brown MV, Clarke LJ, Bissett A, van de Kamp J, Trull TW, Raes EJ, Seymour JR, Bramucci AR, Ostrowski M, Boyd PW, Deagle BE, Pardo PC, Sloyan BM, Bodrossy L. Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors. Environ Microbiol 2022; 24:2449-2466. [PMID: 35049099 PMCID: PMC9303206 DOI: 10.1111/1462-2920.15906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/13/2022] [Indexed: 11/27/2022]
Abstract
We investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.
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Affiliation(s)
- Swan L S Sow
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, New South Wales, 2308, Australia
| | - Laurence J Clarke
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia.,Australian Antarctic Division, Channel Highway, Kingston, Tasmania, 7050, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Thomas W Trull
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Eric J Raes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Anna R Bramucci
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania, 7050, Australia.,National Collections & Marine Infrastructure, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Paula C Pardo
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Bernadette M Sloyan
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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12
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Abstract
A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.
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Affiliation(s)
- David A Hutchins
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA;
| | - Sergio A Sañudo-Wilhelmy
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA;
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089, USA;
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13
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. FRONTIERS IN PLANT SCIENCE 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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14
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Lamichhane P, Veerana M, Lim JS, Mumtaz S, Shrestha B, Kaushik NK, Park G, Choi EH. Low-Temperature Plasma-Assisted Nitrogen Fixation for Corn Plant Growth and Development. Int J Mol Sci 2021; 22:5360. [PMID: 34069725 PMCID: PMC8161386 DOI: 10.3390/ijms22105360] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022] Open
Abstract
Nitrogen fixation is crucial for plants as it is utilized for the biosynthesis of almost all biomolecules. Most of our atmosphere consists of nitrogen, but plants cannot straightforwardly assimilate this from the air, and natural nitrogen fixation is inadequate to meet the extreme necessities of global nutrition. In this study, nitrogen fixation in water was achieved by an AC-driven non-thermal atmospheric pressure nitrogen plasma jet. In addition, Mg, Al, or Zn was immersed in the water, which neutralized the plasma-treated water and increased the rate of nitrogen reduction to ammonia due to the additional hydrogen generated by the reaction between the plasma-generated acid and metal. The effect of the plasma-activated water, with and without metal ions, on germination and growth in corn plants (Zea Mays) was investigated. The germination rate was found to be higher with plasma-treated water and more efficient in the presence of metal ions. Stem lengths and germination rates were significantly increased with respect to those produced by DI water irrigation. The plants responded to the abundance of nitrogen by producing intensely green leaves because of their increased chlorophyll and protein contents. Based on this report, non-thermal plasma reactors could be used to substantially enhance seed germination and seedling growth.
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Affiliation(s)
- Pradeep Lamichhane
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Mayura Veerana
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Jun Sup Lim
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Sohail Mumtaz
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Bhanu Shrestha
- Department of Electronic Engineering, Kwangwoon University, Seoul 01897, Korea;
| | - Nagendra Kumar Kaushik
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Gyungsoon Park
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Eun Ha Choi
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
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15
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Shafiee RT, Snow JT, Hester S, Zhang Q, Rickaby REM. Proteomic response of the marine ammonia-oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity. Environ Microbiol 2021; 24:835-849. [PMID: 33876540 DOI: 10.1111/1462-2920.15491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/25/2021] [Indexed: 11/26/2022]
Abstract
Dissolved iron (Fe) is vanishingly low in the oceans, with ecological success conferred to microorganisms that can restructure their biochemistry to maintain high growth rates during Fe scarcity. Chemolithoautotrophic ammonia-oxidising archaea (AOA) are highly abundant in the oceans, constituting ~30% of cells below the photic zone. Here we examine the proteomic response of the AOA isolate Nitrosopumilus maritimus to growth-limiting Fe concentrations. Under Fe limitation, we observed a significant reduction in the intensity of Fe-dense ferredoxins associated with respiratory complex I whilst complex III and IV proteins with more central roles in the electron transport chain remain unchanged. We concomitantly observed an increase in the intensity of Fe-free functional alternatives such as flavodoxin and plastocyanin, thioredoxin and alkyl hydroperoxide which are known to mediate electron transport and reactive oxygen species detoxification, respectively. Under Fe limitation, we found a marked increase in the intensity of the ABC phosphonate transport system (Phn), highlighting an intriguing link between Fe and P cycling in N. maritimus. We hypothesise that an elevated uptake of exogenous phosphonates under Fe limitation may either supplement N. maritimus' endogenous methylphosphonate biosynthesis pathway - which requires Fe - or enhance the production of phosphonate-containing exopolysaccharides known to efficiently bind environmental Fe.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Joseph T Snow
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Svenja Hester
- Department of Biochemistry, South Parks Road, University of Oxford, Oxfordshire, OX1 3QU, UK
| | - Qiong Zhang
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
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16
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Shafiee RT, Diver PJ, Snow JT, Zhang Q, Rickaby REM. Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches. ISME COMMUNICATIONS 2021; 1:1. [PMID: 37938628 PMCID: PMC9723733 DOI: 10.1038/s43705-021-00001-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022]
Abstract
Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK.
| | - Poppy J Diver
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Joseph T Snow
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Qiong Zhang
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
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17
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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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18
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Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. Appl Environ Microbiol 2020; 86:AEM.00736-20. [PMID: 32631866 DOI: 10.1128/aem.00736-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
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19
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Xu Y, Lu J, Wang Y, Liu G, Wan X, Hua Y, Zhu D, Zhao J. Diversity and abundance of comammox bacteria in the sediments of an urban lake. J Appl Microbiol 2020; 128:1647-1657. [PMID: 31989773 DOI: 10.1111/jam.14593] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 02/01/2023]
Abstract
AIMS Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia-oxidizing microbe exists in urban lakes and to determine the factors influencing its existence. METHODS AND RESULTS This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia-oxidizing micro-organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co-existed with ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 108 , 1·07 × 108 , 3·24 × 107 and 3·21 × 1011 copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria. CONCLUSIONS Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments. SIGNIFICANCE AND IMPACT OF THE STUDY Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.
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Affiliation(s)
- Y Xu
- Laboratory of Eco-Environmental Engineering Research of Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, China
| | - J Lu
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
| | - Y Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - G Liu
- Laboratory of Eco-Environmental Engineering Research of Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, China
| | - X Wan
- Laboratory of Eco-Environmental Engineering Research of Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, China
| | - Y Hua
- Laboratory of Eco-Environmental Engineering Research of Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, China
| | - D Zhu
- Laboratory of Eco-Environmental Engineering Research of Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, China
| | - J Zhao
- Laboratory of Eco-Environmental Engineering Research of Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, China
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20
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Shafiee RT, Snow JT, Zhang Q, Rickaby REM. Iron requirements and uptake strategies of the globally abundant marine ammonia-oxidising archaeon, Nitrosopumilus maritimus SCM1. THE ISME JOURNAL 2019; 13:2295-2305. [PMID: 31076641 PMCID: PMC6776035 DOI: 10.1038/s41396-019-0434-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/04/2019] [Accepted: 04/15/2019] [Indexed: 01/08/2023]
Abstract
Ammonia-oxidising archaea (AOA) mediate the rate-limiting step of nitrification, the central component of the marine nitrogen cycle that converts ammonia to nitrite then nitrate. Competition with phytoplankton for ammonium and light inhibition are considered to restrict AOA activity to below the photic zone, but observations of surface nitrification now demand a further understanding of the factors driving AOA distribution and activity. Pico- to nanomolar concentrations of iron (Fe) limit the growth of microorganisms in a significant portion of the world's surface oceans, yet there is no examination of the role of Fe in AOA growth despite the process of ammonia oxidation being considered to rely on the micronutrient. Here we investigate the Fe requirements and Fe uptake strategies of the Nitrosopumilus maritimus strain SCM1, a strain representative of globally abundant marine AOA. Using trace metal clean culturing techniques, we found that N. maritimus growth is determined by Fe availability, displaying a free inorganic Fe (Fe') half saturation constant 1-2 orders of magnitude greater for cell growth than numerous marine phytoplankton and heterotrophic bacterial species driven by a reduced affinity for Fe'. In addition, we discovered that whilst unable to produce siderophores to enhance access to Fe, N. maritimus is able to use the exogenous siderophore desferrioxamine B (DFB), likely through a reductive uptake pathway analogous to that demonstrated in phytoplankton. Our work suggests AOA growth in surface waters may be Fe limited and advances our understanding of AOA physiology on the cellular and mechanistic levels with implications for ecosystem dynamics and the biogeochemical N-cycle.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxfordshire, OX1 3AN, UK.
| | - Joseph T Snow
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxfordshire, OX1 3AN, UK
| | - Qiong Zhang
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxfordshire, OX1 3AN, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxfordshire, OX1 3AN, UK
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21
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Martiny AC, Lomas MW, Fu W, Boyd PW, Chen YLL, Cutter GA, Ellwood MJ, Furuya K, Hashihama F, Kanda J, Karl DM, Kodama T, Li QP, Ma J, Moutin T, Woodward EMS, Moore JK. Biogeochemical controls of surface ocean phosphate. SCIENCE ADVANCES 2019; 5:eaax0341. [PMID: 31489372 PMCID: PMC6713502 DOI: 10.1126/sciadv.aax0341] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/18/2019] [Indexed: 05/26/2023]
Abstract
Surface ocean phosphate is commonly below the standard analytical detection limits, leading to an incomplete picture of the global variation and biogeochemical role of phosphate. A global compilation of phosphate measured using high-sensitivity methods revealed several previously unrecognized low-phosphate areas and clear regional differences. Both observational climatologies and Earth system models (ESMs) systematically overestimated surface phosphate. Furthermore, ESMs misrepresented the relationships between phosphate, phytoplankton biomass, and primary productivity. Atmospheric iron input and nitrogen fixation are known important controls on surface phosphate, but model simulations showed that differences in the iron-to-macronutrient ratio in the vertical nutrient supply and surface lateral transport are additional drivers of phosphate concentrations. Our study demonstrates the importance of accurately quantifying nutrients for understanding the regulation of ocean ecosystems and biogeochemistry now and under future climate conditions.
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Affiliation(s)
- Adam C. Martiny
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Weiwei Fu
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Philip W. Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yuh-ling L. Chen
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Gregory A. Cutter
- Department of Ocean, Earth, and Atmospheric Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Michael J. Ellwood
- Research School of Earth Sciences, Australian National University, Canberra, ACT 2601, Australia
| | - Ken Furuya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Fuminori Hashihama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Jota Kanda
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - David M. Karl
- Daniel K. Inouye Center for Microbial Oceanography, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Taketoshi Kodama
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 1-5939-22, Suido-cho, Chuo, Niigata, Japan
| | - Qian P. Li
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People’s Republic of China
| | - Jian Ma
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102, People’s Republic of China
| | - Thierry Moutin
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | | | - J. Keith Moore
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
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22
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Ijichi M, Itoh H, Hamasaki K. Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan. Arch Microbiol 2019; 201:1141-1146. [DOI: 10.1007/s00203-019-01680-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/14/2019] [Accepted: 05/21/2019] [Indexed: 11/30/2022]
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23
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Liu L, Li S, Han J, Lin W, Luo J. A Two-Step Strategy for the Rapid Enrichment of Nitrosocosmicus-Like Ammonia-Oxidizing Thaumarchaea. Front Microbiol 2019; 10:875. [PMID: 31105671 PMCID: PMC6491936 DOI: 10.3389/fmicb.2019.00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/04/2019] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are widely distributed on the earth and play a significant role in the global nitrogen cycle. Although dozens of AOA strains were obtained in the last 13 years, it is still necessary to obtain more AOA strains for the entire exploration of their ecology, physiology, and underlying biochemistry in different environments. In this study, we designed a two-step strategy for the rapid enrichment of Nitrosocosmicus–like AOA from soils. Firstly, combination of kanamycin and ampicillin was chosen as the selective stress for bacteria and quartz sands were used as the attachment of AOA cells during the first step cultivation; only after 40–75 days cultivation, AOA enrichments with abundance >20% were obtained. Secondly, combination of ciprofloxacin and azithromycin was chosen as the selective stress for the following cultivation; it is able to penetrate the biofilms and kill the bacterial cells inside the aggregate, contributing to the AOA enrichments reached high abundances (90%) only after one-time cultivation. Basing on this strategy, three AOA strains were obtained from agricultural soils only after 90–150 days cultivation. Phylogenetic analysis suggested these AOA belong to the soil group I.1b Thaumarchaeota and are closely related to the genus Nitrosocosmicus. In general, AOA enrichment or isolation is very difficult and time-consuming (an average of 2–3 years). Here, we provide a new strategy for the rapid enrichment of high abundance of Nitrosocosmicus-like AOA from soil, which gives a new solution to the AOA enrichment and cultivation in a short period.
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Affiliation(s)
- Liangting Liu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Surong Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiamin Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Weitie Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianfei Luo
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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24
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Zou D, Li Y, Kao S, Liu H, Li M. Genomic adaptation to eutrophication of ammonia‐oxidizing archaea in the Pearl River estuary. Environ Microbiol 2019; 21:2320-2332. [DOI: 10.1111/1462-2920.14613] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Dayu Zou
- SZU‐HKUST Joint PhD Program in Marine Environmental ScienceShenzhen University Shenzhen China
- Department of Ocean ScienceThe Hong Kong University of Science and Technology Hong Kong, SAR China
- Institute for Advanced Study, Shenzhen University Shenzhen China
| | - Yingdong Li
- Department of Ocean ScienceThe Hong Kong University of Science and Technology Hong Kong, SAR China
| | - Shuh‐Ji Kao
- State Key Laboratory of Marine Environmental ScienceXiamen University Xiamen China
| | - Hongbin Liu
- Department of Ocean ScienceThe Hong Kong University of Science and Technology Hong Kong, SAR China
| | - Meng Li
- SZU‐HKUST Joint PhD Program in Marine Environmental ScienceShenzhen University Shenzhen China
- Institute for Advanced Study, Shenzhen University Shenzhen China
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25
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Xia X, Cheung S, Endo H, Suzuki K, Liu H. Latitudinal and Vertical Variation of Synechococcus Assemblage Composition Along 170° W Transect From the South Pacific to the Arctic Ocean. MICROBIAL ECOLOGY 2019; 77:333-342. [PMID: 30610255 DOI: 10.1007/s00248-018-1308-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Synechococcus is one of the most widely distributed and abundant picocyanobacteria in the global oceans. Although latitudinal variation of Synechococcus assemblage in marine surface waters has been observed, few studies compared Synechococcus assemblage composition in surface and subsurface waters at the basin scale. Here, we report marine Synechococcus diversity in the surface and deep chlorophyll maximum (DCM) layers along 170° W from the South Pacific to the Arctic Ocean in summer. Along the transect, spatial niche partitioning of Synechococcus lineages in the surface waters was clearly observed. Species richness of surface Synechococcus assemblage was positively correlated with water temperature. Clade CRD1 was dominant in the areas (15° S-10° N and 35-40° N) associated with upwelling, and there were 3 different subclades with distinct distribution. CRD1-A was restricted in the North Equatorial Current (5-10° N), CRD1-B dominated in the equatorial upwelling region (15° S-0.17° N), and CRD1-C was only distributed in the North Pacific Current (35-40° N). Similarities between the Synechococcus assemblages in the surface and DCM layers were high at the upwelling regions and areas where the mixed layer was deep, while low in the Subtropical Gyres with strong stratification. Clade I, CRD1-B, and CRD1-C were major Synechococcus lineages in the DCM layer. In particular, clade I, which is composed of 7 subclades with distinct thermal niches, was widely distributed in the DCM layer. Overall, our results provide new insights into not only the latitudinal distribution of Synechococcus assemblages, but also their vertical variation in the central Pacific.
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Affiliation(s)
- Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Shunyuan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Hisashi Endo
- Faculty of Environmental Earth Science, Hokkaido University/JST-CREST, North 10 West 5, Kita-ku, Sapporo, 060-0810, Hokkaido, Japan
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University/JST-CREST, North 10 West 5, Kita-ku, Sapporo, 060-0810, Hokkaido, Japan.
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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26
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Abstract
Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.
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Affiliation(s)
- Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA;
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27
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Happel E, Bartl I, Voss M, Riemann L. Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea. Environ Microbiol 2018; 20:2913-2926. [PMID: 29921003 DOI: 10.1111/1462-2920.14293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/27/2022]
Abstract
Nitrification is important in nitrogen (N) cycling of aquatic environments, but knowledge about its regulation and importance is sparse. Here we examined nitrification and ammonia oxidizers in the Baltic Sea. We investigated two sites with different catchment characteristics (agricultural and forest), the Bay of Gdánsk (south) and the Öre Estuary (north), and measured pelagic nitrification rates and abundance, composition and expression of ammonia monooxygenase (amoA) genes. Highest nitrification rates were found in the nutrient rich Bay of Gdańsk. Interestingly, abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were orders of magnitude lower than reported from other sites. Although AOA were most abundant at both sites, the highest expression levels were from AOB. Interestingly, few AOA and AOB taxa dominated amoA gene expression, with a Nitrosomarinus related phylotype showing widespread expression. AOA and AOB communities differed between sites and depths, respectively, with the composition in rivers being distinct. A storm event, causing an even depth distribution of nitrification and particles in the Bay of Gdańsk, indicated that the presence of particles stimulate nitrification. The study highlights coastal regions as dynamic sites of extensive pelagic nitrification, which may affect local food web dynamics and loss of N mediated by denitrification.
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Affiliation(s)
- Elisabeth Happel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ines Bartl
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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28
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Endo H, Ogata H, Suzuki K. Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean. Sci Rep 2018; 8:10916. [PMID: 30026492 PMCID: PMC6053411 DOI: 10.1038/s41598-018-29039-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher nutrient uptake affinity. However, precise linkages between their ecological traits and geographical distributions remain poorly understood. Herein, we examined the basin-scale variability of the abundance and taxonomic composition of these two phytoplankton groups across 35 sites in the Pacific Ocean using DNA metabarcoding. The diatom community was generally dominated by a few genera at each sample site, whereas the haptophyte community consisted of a large number of genera in most of the sites. The coexistence of various haptophyte genera might be achieved by diversification of their ecophysiological traits such as mixotrophy. On the other hand, the diatom community might experience greater inter-genus competition due to the rapid uptake of nutrients. Our data further supports the notion that their distinct ecological strategies underlie the emergence of contrasting diversity patterns of these phytoplankton groups in the central Pacific at a basin scale.
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Affiliation(s)
- Hisashi Endo
- Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. .,CREST, Japan Science and Technology, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. .,Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. .,CREST, Japan Science and Technology, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.
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29
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Zakem EJ, Al-Haj A, Church MJ, van Dijken GL, Dutkiewicz S, Foster SQ, Fulweiler RW, Mills MM, Follows MJ. Ecological control of nitrite in the upper ocean. Nat Commun 2018; 9:1206. [PMID: 29572474 PMCID: PMC5865239 DOI: 10.1038/s41467-018-03553-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/22/2018] [Indexed: 11/15/2022] Open
Abstract
Microorganisms oxidize organic nitrogen to nitrate in a series of steps. Nitrite, an intermediate product, accumulates at the base of the sunlit layer in the subtropical ocean, forming a primary nitrite maximum, but can accumulate throughout the sunlit layer at higher latitudes. We model nitrifying chemoautotrophs in a marine ecosystem and demonstrate that microbial community interactions can explain the nitrite distributions. Our theoretical framework proposes that nitrite can accumulate to a higher concentration than ammonium because of differences in underlying redox chemistry and cell size between ammonia- and nitrite-oxidizing chemoautotrophs. Using ocean circulation models, we demonstrate that nitrifying microorganisms are excluded in the sunlit layer when phytoplankton are nitrogen-limited, but thrive at depth when phytoplankton become light-limited, resulting in nitrite accumulation there. However, nitrifying microorganisms may coexist in the sunlit layer when phytoplankton are iron- or light-limited (often in higher latitudes). These results improve understanding of the controls on nitrification, and provide a framework for representing chemoautotrophs and their biogeochemical effects in ocean models. Nitrite tends to peak at the base of the sunlit zone in the ocean, but the ecological drivers of the local and global distributions of nitrite are not known. Here, Zakem et al. use a marine ecosystem model to show how the interactions of nitrifying microbes mediate nitrite accumulation.
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Affiliation(s)
- Emily J Zakem
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Alia Al-Haj
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Gert L van Dijken
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sarah Q Foster
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Robinson W Fulweiler
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA.,Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Matthew M Mills
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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30
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Wan XS, Sheng HX, Dai M, Zhang Y, Shi D, Trull TW, Zhu Y, Lomas MW, Kao SJ. Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean. Nat Commun 2018; 9:915. [PMID: 29500422 PMCID: PMC5834513 DOI: 10.1038/s41467-018-03363-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/08/2018] [Indexed: 12/03/2022] Open
Abstract
Phytoplankton assimilation and microbial oxidation of ammonium are two critical conversion pathways in the marine nitrogen cycle. The underlying regulatory mechanisms of these two competing processes remain unclear. Here we show that ambient nitrate acts as a key variable to bifurcate ammonium flow through assimilation or oxidation, and the depth of the nitracline represents a robust spatial boundary between ammonium assimilators and oxidizers in the stratified ocean. Profiles of ammonium utilization show that phytoplankton assemblages in nitrate-depleted regimes have higher ammonium affinity than nitrifiers. In nitrate replete conditions, by contrast, phytoplankton reduce their ammonium reliance and thus enhance the success of nitrifiers. This finding helps to explain existing discrepancies in the understanding of light inhibition of surface nitrification in the global ocean, and provides further insights into the spatial linkages between oceanic nitrification and new production. The underlying regulatory mechanisms of phytoplankton assimilation and microbial oxidation of ammonium in the surface ocean are unclear. Here, using isotope labeling experiments, the authors show that ambient nitrate is a key variable bifurcating ammonium flow through assimilation or oxidation.
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Affiliation(s)
- Xianhui Sean Wan
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Hua-Xia Sheng
- 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
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Thomas W Trull
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, and CSIRO Oceans and Atmosphere, Hobart, 7001, Australia
| | - Yifan Zhu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China.
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31
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Wang L, Li Y, Niu L, Zhang W, Zhang H, Wang L, Wang P. Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments. CHEMOSPHERE 2018; 191:858-867. [PMID: 29107227 DOI: 10.1016/j.chemosphere.2017.10.067] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg-1) and copper (Cu, 50-500 mg kg-1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg-1 BDE 209 with a 100 mg kg-1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.
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Affiliation(s)
- Linqiong Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
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32
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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Tolar BB, Wallsgrove NJ, Popp BN, Hollibaugh JT. Oxidation of urea-derived nitrogen by thaumarchaeota-dominated marine nitrifying communities. Environ Microbiol 2016; 19:4838-4850. [PMID: 27422798 DOI: 10.1111/1462-2920.13457] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Urea nitrogen has been proposed to contribute significantly to nitrification by marine thaumarchaeotes. These inferences are based on distributions of thaumarchaeote urease genes rather than activity measurements. We found that ammonia oxidation rates were always higher than oxidation rates of urea-derived N in samples from coastal Georgia, USA (means ± SEM: 382 ± 35 versus 73 ± 24 nmol L-1 d-1 , Mann-Whitney U-test p < 0.0001), and the South Atlantic Bight (20 ± 8.8 versus 2.2 ± 1.7 nmol L-1 d-1 , p = 0.026) but not the Gulf of Alaska (8.8 ± 4.0 versus 1.5 ± 0.6, p > 0.05). Urea-derived N was relatively more important in samples from Antarctic continental shelf waters, though the difference was not statistically significant (19.4 ± 4.8 versus 12.0 ± 2.7 nmol L-1 d-1 , p > 0.05). We found only weak correlations between oxidation rates of urea-derived N and the abundance or transcription of putative Thaumarchaeota ureC genes. Dependence on urea-derived N does not appear to be directly related to pH or ammonium concentrations. Competition experiments and release of 15 NH3 suggest that urea is hydrolyzed to ammonia intracellularly, then a portion is lost to the dissolved pool. The contribution of urea-derived N to nitrification appears to be minor in temperate coastal waters, but may represent a significant portion of the nitrification flux in Antarctic coastal waters.
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Affiliation(s)
- Bradley B Tolar
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Natalie J Wallsgrove
- Department of Geology and Geophysics, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Brian N Popp
- Department of Geology and Geophysics, University of Hawai'i, Honolulu, HI, 96822, USA
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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