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Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island. Microorganisms 2022; 10:microorganisms10050952. [PMID: 35630397 PMCID: PMC9143208 DOI: 10.3390/microorganisms10050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023] Open
Abstract
Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.
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Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria. THE ISME JOURNAL 2022; 16:958-971. [PMID: 34743174 PMCID: PMC8941013 DOI: 10.1038/s41396-021-01144-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
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Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems 2022; 7:e0127021. [PMID: 35076275 PMCID: PMC8788347 DOI: 10.1128/msystems.01270-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)—the largest estuary on the west coast of North America—and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.
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Hampel JJ, McCarthy MJ, Aalto SL, Newell SE. Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida). Front Microbiol 2020; 11:1541. [PMID: 32754132 PMCID: PMC7366250 DOI: 10.3389/fmicb.2020.01541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH4+) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R2 = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH4+ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, United States.,Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Mark J McCarthy
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Sanni L Aalto
- Section for Aquaculture, The North Sea Research Centre, DTU Aqua, Technical University of Denmark, Hirtshals, Denmark
| | - Silvia E Newell
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
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Carstensen J, Conley DJ, Almroth-Rosell E, Asmala E, Bonsdorff E, Fleming-Lehtinen V, Gustafsson BG, Gustafsson C, Heiskanen AS, Janas U, Norkko A, Slomp C, Villnäs A, Voss M, Zilius M. Factors regulating the coastal nutrient filter in the Baltic Sea. AMBIO 2020; 49:1194-1210. [PMID: 31707582 PMCID: PMC7128010 DOI: 10.1007/s13280-019-01282-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 05/30/2023]
Abstract
The coastal zone of the Baltic Sea is diverse with strong regional differences in the physico-chemical setting. This diversity is also reflected in the importance of different biogeochemical processes altering nutrient and organic matter fluxes on the passage from land to sea. This review investigates the most important processes for removal of nutrients and organic matter, and the factors that regulate the efficiency of the coastal filter. Nitrogen removal through denitrification is high in lagoons receiving large inputs of nitrate and organic matter. Phosphorus burial is high in archipelagos with substantial sedimentation, but the stability of different burial forms varies across the Baltic Sea. Organic matter processes are tightly linked to the nitrogen and phosphorus cycles. Moreover, these processes are strongly modulated depending on composition of vegetation and fauna. Managing coastal ecosystems to improve the effectiveness of the coastal filter can reduce eutrophication in the open Baltic Sea.
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Affiliation(s)
- Jacob Carstensen
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Daniel J. Conley
- Department of Geology, Lund University, Sölvegatan 12, 223 62 Lund, Sweden
| | | | - Eero Asmala
- Tvärminne Zoological Station, University of Helsinki, J.A. Palmenin tie 260, 10900 Hanko, Finland
| | - Erik Bonsdorff
- Environmental and Marine Biology, Åbo Akademi University, BioCity, 20500 Turku, Finland
| | | | - Bo G. Gustafsson
- Tvärminne Zoological Station, University of Helsinki, J.A. Palmenin tie 260, 10900 Hanko, Finland
- Stockholm University Baltic Sea Centre, 106 91 Stockholm, Sweden
| | - Camilla Gustafsson
- Tvärminne Zoological Station, University of Helsinki, J.A. Palmenin tie 260, 10900 Hanko, Finland
| | | | - Urzsula Janas
- Department of Experimental Ecology of Marine Organisms, Institute of Oceanography, University of Gdańsk, al. Marsz. J. Pilsudskiego 46, 81-378 Gdynia, Poland
| | - Alf Norkko
- Tvärminne Zoological Station, University of Helsinki, J.A. Palmenin tie 260, 10900 Hanko, Finland
| | - Caroline Slomp
- Department of Earth Sciences, Utrecht University, Princetonlaan 8A, 3584 CB Utrecht, The Netherlands
| | - Anna Villnäs
- Tvärminne Zoological Station, University of Helsinki, J.A. Palmenin tie 260, 10900 Hanko, Finland
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, Seestr. 15, 18119 Rostock, Germany
| | - Mindaugas Zilius
- Marine Research Institute, Universiteto al. 17, 92294 Klaipeda, Lithuania
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Happel EM, Markussen T, Teikari JE, Huchaiah V, Alneberg J, Andersson AF, Sivonen K, Middelboe M, Kisand V, Riemann L. Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites. FEMS Microbiol Ecol 2019; 95:5545591. [PMID: 31397876 DOI: 10.1093/femsec/fiz123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.
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Affiliation(s)
- Elisabeth M Happel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Trine Markussen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jonna E Teikari
- University of Helsinki, Department of Microbiology, Helsinki, Finland
| | - Vimala Huchaiah
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Johannes Alneberg
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Kaarina Sivonen
- University of Helsinki, Department of Microbiology, Helsinki, Finland
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Veljo Kisand
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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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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Untangling hidden nutrient dynamics: rapid ammonium cycling and single-cell ammonium assimilation in marine plankton communities. ISME JOURNAL 2019; 13:1960-1974. [PMID: 30911131 PMCID: PMC6776039 DOI: 10.1038/s41396-019-0386-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 11/30/2022]
Abstract
Ammonium is a central nutrient in aquatic systems. Yet, cell-specific ammonium assimilation among diverse functional plankton is poorly documented in field communities. Combining stable-isotope incubations (15N-ammonium, 15N2 and 13C-bicarbonate) with secondary-ion mass spectrometry, we quantified bulk ammonium dynamics, N2-fixation and carbon (C) fixation, as well as single-cell ammonium assimilation and C-fixation within plankton communities in nitrogen (N)-depleted surface waters during summer in the Baltic Sea. Ammonium production resulted from regenerated (≥91%) and new production (N2-fixation, ≤9%), supporting primary production by 78–97 and 2–16%, respectively. Ammonium was produced and consumed at balanced rates, and rapidly recycled within 1 h, as shown previously, facilitating an efficient ammonium transfer within plankton communities. N2-fixing cyanobacteria poorly assimilated ammonium, whereas heterotrophic bacteria and picocyanobacteria accounted for its highest consumption (~20 and ~20–40%, respectively). Surprisingly, ammonium assimilation and C-fixation were similarly fast for picocyanobacteria (non-N2-fixing Synechococcus) and large diatoms (Chaetoceros). Yet, the population biomass was high for Synechococcus but low for Chaetoceros. Hence, autotrophic picocyanobacteria and heterotrophic bacteria, with their high single-cell assimilation rates and dominating population biomass, competed for the same nutrient source and drove rapid ammonium dynamics in N-depleted marine waters.
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