1
|
Chen J, Liu K, Liu Y. Synergistic molecular mechanism of degradation in dye wastewater by Rhodopseudomonas palustris intimately coupled carbon nanotube - Silver modified titanium dioxide photocatalytic composite with sodium alginate. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119913. [PMID: 38154222 DOI: 10.1016/j.jenvman.2023.119913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/07/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
The intimately coupled photocatalysis and biodegradation (ICPB), which combined the advantages of high oxidation capacity of photocatalysis and high mineralization rate of biodegradation, has demonstrated excellent removal performance in the degradation of azo dyes with highly toxic, refractory, mutagenic and carcinogenic. In order to explore the metagenomics mechanism of the ICPB system, a novel ICPB was prepared by coupling Rhodopseudomonas palustris (R. Palustris), carbon nanotube - silver modified titanium dioxide photocatalytic composite (CNT-Ag -TiO2, CAT) and sodium alginate (SA) (R. palustris/CAT@SA, R-CAT). Metagenomics sequencing was used to investigate the molecular mechanism of adaptation and degradation of dyes by photosynthetic microorganisms and the adaptive and synergistic interaction between photosynthetic microorganisms and photocatalyst. Experiments on the adaptability and degradability of photosynthetic microorganisms have proved that low concentration azo dyes could be utilized as carbon sources for growth of photosynthetic microorganisms. Metagenomics sequencing revealed that R. palustris was the main degrading bacterium in photosynthetic microorganisms and the functional genes related to carbohydrate metabolism, biological regulation and catalytic activity were abundant. It was found that the addition of photocatalyst significantly up-regulated the functional genes related to the catabolic process, electron transport, oxidoreductase activity and superoxide metabolism of organic matter in the photosynthetic microorganisms. Moreover, many key gene such as alpha-amylase, 1-acyl-sn-glycerol-3-phosphate acyltransferase, aldehyde dehydrogenase enrichment in microbial basal metabolism, such as enoyl-CoA hydratase, malate dehydrogenase, glutathione S-transferase enrichment in degrading azo dyes and electron transport, and many key gene such as undecaprenyl-diphosphatase, carbon storage regulator, DNA ligase enrichment in response to dyes and photocatalysts were discovered. These findings would contribute to a comprehensive understanding of the mechanism of degradation of dye wastewater by ICPB system, a series of genes was produced to adapt to environmental changes, and played synergistic role in terms of intermediate product degradation and electron transfer for degrading azo dyes. The photosynthetic microorganisms might be a promising microorganism for constructing ICPB system.
Collapse
Affiliation(s)
- Junfeng Chen
- School of Life Sciences, Qufu Normal University, Qufu, 273165, PR China.
| | - Kai Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, PR China
| | - Yanyan Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, PR China
| |
Collapse
|
2
|
Rasmussen AN, Francis CA. Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. THE ISME JOURNAL 2024; 18:wrae148. [PMID: 39077992 PMCID: PMC11334935 DOI: 10.1093/ismejo/wrae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/24/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024]
Abstract
Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.
Collapse
Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
- Oceans Department, Stanford University, Stanford, CA 94305, United States
| |
Collapse
|
3
|
Gwak JH, Awala SI, Kim SJ, Lee SH, Yang EJ, Park J, Jung J, Rhee SK. Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica. J Microbiol 2023; 61:967-980. [PMID: 38062325 DOI: 10.1007/s12275-023-00090-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.
Collapse
Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Sang-Hoon Lee
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eun-Jin Yang
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| |
Collapse
|
4
|
Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, Schleper C. Unexpected complexity of the ammonia monooxygenase in archaea. THE ISME JOURNAL 2023; 17:588-599. [PMID: 36721060 PMCID: PMC10030591 DOI: 10.1038/s41396-023-01367-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.
Collapse
Affiliation(s)
- Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Melcher
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Weiqiang Chen
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
| | - Rafael I Ponce-Toledo
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Stefanie Wienkoop
- Molecular Systems Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
| |
Collapse
|
5
|
Melcher M, Hodgskiss LH, Mardini MA, Schleper C, Rittmann SKMR. Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture. Front Microbiol 2023; 14:1076342. [PMID: 36876066 PMCID: PMC9978112 DOI: 10.3389/fmicb.2023.1076342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO2) concentrations aiming to understand the interplay between ammonia oxidation and CO2 fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO2 gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μmax) the biomass to ammonium yield (Y(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D crit. Due to changes in Y(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μmax. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.
Collapse
Affiliation(s)
- Michael Melcher
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Logan H Hodgskiss
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Mohammad Anas Mardini
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Arkeon GmbH, Tulln a.d. Donau, Austria.,Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| |
Collapse
|
6
|
Spataru P. Influence of organic ammonium derivatives on the equilibria between NH 4+, NO 2- and NO 3- ions in the Nistru River water. Sci Rep 2022; 12:13505. [PMID: 35931731 PMCID: PMC9355948 DOI: 10.1038/s41598-022-17568-3] [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: 05/17/2021] [Accepted: 07/27/2022] [Indexed: 11/27/2022] Open
Abstract
The toxic effects of ammonium derivatives in the river water depend dramatically on their natural or synthetic origins and on their chemical structures. It has been proved that 1-naphtylamine (1-NA) and diphenylamine (DPA) breaking impact on the ammonium oxidation and especially on nitrite ions oxidation processes in natural waters is associated with its toxicity. The NH4+ oxidation process slows down for about five days and ten days in river water samples with 0.5 mg/L DPA and corresponding 0.5 mg/L 1-NA. The NO2− oxidation delay in model samples of river water with 0.025 and 0.05 mg/L 1-NA, is four days and 35 days in the one with 0.5 mg/L 1-NA. For the sample with 0.05 mg/L DPA the delay of the NO2− oxidation is approximately of six days and 25 days for sample with 0.5 mg/L, DPA. The laboratory simulations have revealed: (1) absorption–desorption, the micro biotic reaction to the instantaneous increase of the concentration of ammonium ion in the river water (so-called shock/stress effect) and (2) the NH4+ increase stimulated by a certain (0.05 mg/L) concentration of 1-NA.The diethylamine (DEA) decomposition leads to increasing with approximately 3.8 mg/L NH4+ in river water samples of 20.0 mg/L DEA.
Collapse
Affiliation(s)
- Petru Spataru
- Institute of Chemistry of the Republic of Moldova, 3 Academiei str, Chisinau, MD-2028, Republic of Moldova.
| |
Collapse
|
7
|
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.
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Baker KD, Kellogg CTE, McClelland JW, Dunton KH, Crump BC. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons. Front Microbiol 2021; 12:601901. [PMID: 33643234 PMCID: PMC7906997 DOI: 10.3389/fmicb.2021.601901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
Collapse
Affiliation(s)
- Kristina D Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - James W McClelland
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Kenneth H Dunton
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
10
|
Yang Y, Herbold CW, Jung MY, Qin W, Cai M, Du H, Lin JG, Li X, Li M, Gu JD. Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration. WATER RESEARCH 2021; 191:116798. [PMID: 33444853 DOI: 10.1016/j.watres.2020.116798] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 05/04/2023]
Abstract
Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.
Collapse
Affiliation(s)
- Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Craig W Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Man-Young Jung
- Division of Biology Education, Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, South Korea; Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Faculty of Science Education, Jeju National University, Jeju 6324, South Korea
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, Washington, United States; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Huan Du
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Xiaoyan Li
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China; Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, China.
| |
Collapse
|
11
|
Zeng Y, Luo W, Li H, Yu Y. High diversity of planktonic prokaryotes in Arctic Kongsfjorden seawaters in summer 2015. Polar Biol 2021. [DOI: 10.1007/s00300-020-02791-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
12
|
Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, Nielsen JL, Mori K, Takahashi R, Virginia Armbrust E, Winkler MKH, DeLong EF, Li M, Lee PH, Zhou J, Zhang C, Zhang T, Stahl DA, Ingalls AE. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME JOURNAL 2020; 14:2595-2609. [PMID: 32636492 PMCID: PMC7490402 DOI: 10.1038/s41396-020-0710-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
Collapse
Affiliation(s)
- Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA.
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL, USA
| | - Haodong Liu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Xiaowu Huang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | | | - Baozhan Wang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shady A Amin
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | | | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China.,Department of Civil and Environmental Engineering, Imperial College London, London, UK
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Environment, Tsinghua University, Beijing, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA.
| |
Collapse
|
13
|
Ma C, Coffinet S, Lipp JS, Hinrichs KU, Zhang C. Marine Group II Euryarchaeota Contribute to the Archaeal Lipid Pool in Northwestern Pacific Ocean Surface Waters. Front Microbiol 2020; 11:1034. [PMID: 32582055 PMCID: PMC7291766 DOI: 10.3389/fmicb.2020.01034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Planktonic archaea include predominantly Marine Group I Thaumarchaeota (MG I) and Marine Group II Euryarchaeota (MG II), which play important roles in the oceanic carbon cycle. MG I produce specific lipids called isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs), which are being used in the sea surface temperature proxy named TEX86. Although MG II may be the most abundant planktonic archaeal group in surface water, their lipid composition remains poorly characterized because of the lack of cultured representatives. Circumstantial evidence from previous studies of marine suspended particulate matter suggests that MG II may produce both GDGTs and archaeol-based lipids. In this study, integration of the 16S rRNA gene quantification and sequencing and lipid analysis demonstrated that MG II contributed significantly to the pool of archaeal tetraether lipids in samples collected from MG II-dominated surface waters of the Northwestern Pacific Ocean (NWPO). The archaeal lipid composition in MG II-dominated NWPO waters differed significantly from that of known MG I cultures, containing relatively more 2G-OH-, 2G- and 1G- GDGTs, especially in their acyclic form. Lipid composition in NWPO waters was also markedly different from MG I-dominated surface water samples collected in the East China Sea. GDGTs from MG II-dominated samples seemed to respond to temperature similarly to GDGTs from the MG I-dominated samples, which calls for further study using pure cultures to determine the exact impact of MG II on GDGT-based proxies.
Collapse
Affiliation(s)
- Cenling Ma
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Sarah Coffinet
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
14
|
Wang Y, Lu L, Hong Y, Wu J, Zhu G, Ye F, Li Z. Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment. ENVIRONMENTAL RESEARCH 2020; 182:109083. [PMID: 31901627 DOI: 10.1016/j.envres.2019.109083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.
Collapse
Affiliation(s)
- Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Lunhui Lu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zhe Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
| |
Collapse
|
15
|
Orellana LH, Hatt JK, Iyer R, Chourey K, Hettich RL, Spain JC, Yang WH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. Sci Rep 2019; 9:17630. [PMID: 31772206 PMCID: PMC6879594 DOI: 10.1038/s41598-019-53679-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/14/2019] [Indexed: 01/29/2023] Open
Abstract
To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.
Collapse
Affiliation(s)
- Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Laboratorio de Enteropatogenos, Programa de Microbiología y Micología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jim C Spain
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida, USA
| | - Wendy H Yang
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joanne C Chee-Sanford
- U.S. Department of Agriculture, Agricultural Research Service, Urbana, Illinois, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, and Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | |
Collapse
|
16
|
Coastal Ocean Metagenomes and Curated Metagenome-Assembled Genomes from Marsh Landing, Sapelo Island (Georgia, USA). Microbiol Resour Announc 2019; 8:8/40/e00934-19. [PMID: 31582460 PMCID: PMC6776777 DOI: 10.1128/mra.00934-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Microbes play a dominant role in the biogeochemistry of coastal waters, which receive organic matter from diverse sources. We present metagenomes and 45 metagenome-assembled genomes (MAGs) from Sapelo Island, Georgia, to further understand coastal microbial populations. Notably, four MAGs are archaea, with two Thaumarchaeota and two marine group II Euryarchaeota.
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019; 21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.
Collapse
Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, Moss Landing, CA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA
| | | | | |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA;
| | | | | |
Collapse
|
20
|
Complete genome sequence of Bordetella sp. HZ20 sheds light on the ecological role of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment. Mar Genomics 2018. [DOI: 10.1016/j.margen.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
21
|
Kobayashi S, Hira D, Yoshida K, Toyofuku M, Shida Y, Ogasawara W, Yamaguchi T, Araki N, Oshiki M. Nitric Oxide Production from Nitrite Reduction and Hydroxylamine Oxidation by Copper-containing Dissimilatory Nitrite Reductase (NirK) from the Aerobic Ammonia-oxidizing Archaeon, Nitrososphaera viennensis. Microbes Environ 2018; 33:428-434. [PMID: 30318500 PMCID: PMC6308003 DOI: 10.1264/jsme2.me18058] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic ammonia-oxidizing archaea (AOA) play a crucial role in the global nitrogen cycle by oxidizing ammonia to nitrite, and nitric oxide (NO) is a key intermediate in AOA for sustaining aerobic ammonia oxidation activity. We herein heterologously expressed the NO-forming, copper-containing, dissimilatory nitrite reductase (NirK) from Nitrososphaera viennensis and investigated its enzymatic properties. The recombinant protein catalyzed the reduction of 15NO2− to 15NO, the oxidation of hydroxylamine (15NH2OH) to 15NO, and the production of 14–15N2O from 15NH2OH and 14NO2−. To the best of our knowledge, the present study is the first to document the enzymatic properties of AOA NirK.
Collapse
Affiliation(s)
- Shun Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Daisuke Hira
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University
| | - Keitaro Yoshida
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Masanori Toyofuku
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology
| | | | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| |
Collapse
|
22
|
Liu X, Pan J, Liu Y, Li M, Gu JD. Diversity and distribution of Archaea in global estuarine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:349-358. [PMID: 29753224 DOI: 10.1016/j.scitotenv.2018.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 05/12/2023]
Abstract
Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.
Collapse
Affiliation(s)
- Xiaobo Liu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, People's Republic of China.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Gómez-Consarnau L, Sachdeva R, Gifford SM, Cutter LS, Fuhrman JA, Sañudo-Wilhelmy SA, Moran MA. Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community. Environ Microbiol 2018; 20:2809-2823. [PMID: 29659156 DOI: 10.1111/1462-2920.14133] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 04/05/2018] [Indexed: 12/28/2022]
Abstract
Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B12 synthesis, but not of vitamin-B7 , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B1 synthesis transcripts. Furthermore, ambient vitamin-B1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature.
Collapse
Affiliation(s)
- Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, 22860, Mexico
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Scott M Gifford
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lynda S Cutter
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergio A Sañudo-Wilhelmy
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
25
|
Carini P, Dupont CL, Santoro AE. Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environ Microbiol 2018; 20:2112-2124. [PMID: 29626379 DOI: 10.1111/1462-2920.14107] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139-fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery.
Collapse
Affiliation(s)
- Paul Carini
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | | | - Alyson E Santoro
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| |
Collapse
|
26
|
Oremland RS, Saltikov CW, Stolz JF, Hollibaugh JT. Autotrophic microbial arsenotrophy in arsenic-rich soda lakes. FEMS Microbiol Lett 2018; 364:3940223. [PMID: 28859313 DOI: 10.1093/femsle/fnx146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/07/2017] [Indexed: 01/15/2023] Open
Abstract
A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth ('arsenotrophy'). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO3-) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase (arrA) and the discovery of its arsenite-oxidizing counterpart (arxA). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.
Collapse
Affiliation(s)
| | - Chad W Saltikov
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, CA 95064, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
27
|
Techtman SM, Mahmoudi N, Whitt KT, Campa MF, Fortney JL, Joyner DC, Hazen TC. Comparison of Thaumarchaeotal populations from four deep sea basins. FEMS Microbiol Ecol 2018; 93:4331633. [PMID: 29029137 PMCID: PMC5812500 DOI: 10.1093/femsec/fix128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 09/29/2017] [Indexed: 11/13/2022] Open
Abstract
The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. These findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.
Collapse
Affiliation(s)
- Stephen M Techtman
- Department of Biological Sciences, Michigan Technological University, Houghton MI 49931-1295, USA
| | - Nagissa Mahmoudi
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Kendall T Whitt
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Maria Fernanda Campa
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Julian L Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Dominique C Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN 37916, USA.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
28
|
Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight. ISME JOURNAL 2018; 12:1473-1485. [PMID: 29445129 PMCID: PMC5956005 DOI: 10.1038/s41396-018-0066-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/26/2017] [Accepted: 01/13/2018] [Indexed: 11/08/2022]
Abstract
Mid-summer peaks in the abundance of Thaumarchaeota and nitrite concentration observed on the Georgia, USA, coast could result from in situ activity or advection of populations from another source. We collected data on the distribution of Thaumarchaeota, ammonia-oxidizing betaproteobacteria (AOB), Nitrospina, environmental variables and rates of ammonia oxidation during six cruises in the South Atlantic Bight (SAB) from April to November 2014. These data were used to examine seasonality of nitrification in offshore waters and to test the hypothesis that the bloom was localized to inshore waters. The abundance of Thaumarchaeota marker genes (16S rRNA and amoA) increased at inshore and nearshore stations starting in July and peaked in August at >107 copies L-1. The bloom did not extend onto the mid-shelf, where Thaumarchaeota genes ranged from 103 to 105 copies L-1. Ammonia oxidation rates (AO) were highest at inshore stations during summer (to 840 nmol L-1 d-1) and were always at the limit of detection at mid-shelf stations. Nitrite concentrations were correlated with AO (R = 0.94) and were never elevated at mid-shelf stations. Gene sequences from samples collected at mid-shelf stations generated using Archaea 16S rRNA primers were dominated by Euryarchaeota; sequences from inshore and nearshore stations were dominated by Thaumarchaeota. Thaumarchaeota were also abundant at depth at the shelf-break; however, this population was phylogenetically distinct from the inshore/nearshore population. Our analysis shows that the bloom is confined to inshore waters during summer and suggests that Thaumarchaeota distributions in the SAB are controlled primarily by photoinhibition and secondarily by water temperature.
Collapse
|
29
|
Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, Hedlund BP, Wang P, Fang H, Deng M, Zhang CL. Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environ Microbiol 2017; 20:734-754. [PMID: 29235710 DOI: 10.1111/1462-2920.14004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 11/29/2022]
Abstract
Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/l), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments. 10‰ salinity appeared to be a threshold value for these MGII because MGII abundance decreased sharply below it. Above 10‰ salinity, the abundance of MGII on the particles was positively correlated with phototrophs and MGII in the surface water was negatively correlated with irradiance. However, the abundances of those free-living MGII showed positive correlations with salinity and temperature, suggesting the different physiological characteristics between particle-attached and free-living MGIIs. A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binning methods. Compared with the other two MGII genomes from surface ocean, MGIIa_P contained higher proportions of glycoside hydrolases, indicating the ability of MGIIa_P to hydrolyse glycosidic bonds in complex sugars in PRE. MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be involved in scavenging reactive oxygen species generated by the abundant phototrophs in the eutrophic PRE. Our study presented the widespread and high abundance of MGII in the water columns of PRE, and characterized the determinant abiotic factors affecting their distribution. Their association with heterotrophs, preference for particles and resourceful metabolic traits indicate MGII might play a significant role in metabolising organic matters in the PRE and other temperate estuarine systems.
Collapse
Affiliation(s)
- Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.,MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Songze Chen
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Huaying Fang
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| |
Collapse
|
30
|
Bertagnolli AD, Ulloa O. Hydrography shapes community composition and diversity of amoA-containing Thaumarchaeota in the coastal waters off central Chile. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:717-728. [PMID: 28836743 DOI: 10.1111/1758-2229.12579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Thaumarchaea are often abundant in low oxygen marine environments, and recent kinetic studies indicate a capacity for aerobic ammonia oxidation at vanishingly low oxygen levels (nM). However, molecular diversity surveys targeting this group to high sequencing coverage are limited, and how these populations are coupled to changes in dissolved oxygen remains unknown. In this study, the ammonia monooxygenase subunit A (amoA) gene was sequenced from samples collected in the Chilean coast (36.5 °S), a system prone to recurrent seasonal hypoxia and anoxia, at several depths over one year, to read depths that saturated coverage statistics. Temperature, salinity and depth displayed a stronger impact on community composition than chemical and biological variables, such as dissolved oxygen. The Nitrosopumilus water-column A clade (WCA) displayed high proportional representation in all samples (42%-100% of all amoA OTUs). The two dominant WCA OTUs displayed differences in their distributions that were inversely correlated with one another, providing the first evidence for intra-subgroup specific differences in the distributions among closely related WCA Thaumarcheota. Nitrosopumilus water-column B (WCB) representatives displayed increased proportional abundances (42%) at deeper depths during the spring and summer, were highly coupled to decreased dissolved oxygen conditions and were non-detectable during the austral winter. The depth of sequencing also enabled observation of lower abundance taxa that are typically not observed in marine environments, such as members of the genus Nitrosotalea amid austral winter surface waters. This study highlights a strong coupling between Thaumarchaeal community diversity and hydrographic variables, is the first to highlight intra-subclade depth specific shifts in community diversity amongst members of the WCA clade, and links the WCB clade to upwelling conditions associated with seasonal oxygen depletion.
Collapse
Affiliation(s)
- Anthony D Bertagnolli
- Department of Oceanography and Millennium Institute of Oceanography, Universidad de Concepción, Concepción, P.O. Box 160 C, Chile
| | - Osvaldo Ulloa
- Department of Oceanography and Millennium Institute of Oceanography, Universidad de Concepción, Concepción, P.O. Box 160 C, Chile
| |
Collapse
|
31
|
Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. ISME JOURNAL 2017; 12:508-519. [PMID: 29053148 PMCID: PMC5776466 DOI: 10.1038/ismej.2017.186] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 11/08/2022]
Abstract
High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu stress was downregulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.
Collapse
|
32
|
Tolar BB, Herrmann J, Bargar JR, van den Bedem H, Wakatsuki S, Francis CA. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:484-491. [PMID: 28677304 DOI: 10.1111/1758-2229.12567] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/01/2017] [Accepted: 06/25/2017] [Indexed: 06/07/2023]
Abstract
Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK).
Collapse
Affiliation(s)
- Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Herrmann
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - John R Bargar
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Henry van den Bedem
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | |
Collapse
|
33
|
Abstract
Microbial communities adjust the chemical structure of their cell membranes in response to environmental temperature. This enables the development of lipid-based paleothermometers such as the glycerol dialkyl glycerol tetraether (GDGT) proxies described here. Surface-sediment calibrations establish a strong empirical relationship between the relative distribution of GDGTs and temperature. GDGT proxies can be used in marine, lacustrine, and paleosol sequences as long as the organic material is not thermally mature. Thus far, GDGT proxies have been applied to sediments dating back to the middle Jurassic. Many of the key uncertainties of these proxies are related to our emerging understanding of archaeal (and for the branched GDGTs, bacterial) ecology.
Collapse
|
34
|
Schaefer SC, Hollibaugh JT. Temperature Decouples Ammonium and Nitrite Oxidation in Coastal Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3157-3164. [PMID: 28225262 DOI: 10.1021/acs.est.6b03483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nitrification is a two-step process linking the reduced and oxidized sides of the nitrogen cycle. These steps are typically tightly coupled with the primary intermediate, nitrite, rarely accumulating in coastal environments. Nitrite concentrations can exceed 10 μM during summer in estuarine waters adjacent to Sapelo Island, Georgia, U.S.A. Similar peaks at other locations have been attributed to decoupling of the two steps of nitrification by hypoxia; however, the waters around Sapelo Island are aerobic and well-mixed. Experiments examining the response to temperature shifts of a nitrifying assemblage composed of the same organisms found in the field indicate that ammonia- and nitrite-oxidation become uncoupled between 20 and 30 °C, leading to nitrite accumulation. This suggests that nitrite peaks in coastal waters might be explained by differences in the responses of ammonia- and nitrite-oxidizers to increased summer temperatures. Analysis of field data from 270 stations in 29 temperate and subtropical estuaries and lagoons show transient accumulation of nitrite driven primarily by water temperatures, rather than by hypoxia. Increased climate variability and warming coastal waters may therefore increase the frequency of these nitrite peaks, with potential ecosystem consequences that include increased N2O production, NO2- toxicity, and shifts in phytoplankton community composition.
Collapse
Affiliation(s)
- Sylvia C Schaefer
- Department of Marine Sciences, University of Georgia , Athens, Georgia 30602-3636, United States
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia , Athens, Georgia 30602-3636, United States
| |
Collapse
|
35
|
Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, Weckwerth W, Schleper C. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proc Natl Acad Sci U S A 2016; 113:E7937-E7946. [PMID: 27864514 PMCID: PMC5150414 DOI: 10.1073/pnas.1601212113] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile "Ca. Nitrosotalea devanaterra" revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and "Ca Nitrosopelagicus brevis" proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
Collapse
Affiliation(s)
- Melina Kerou
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Pierre Offre
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Luis Valledor
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Sophie S Abby
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Michael Melcher
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Wolfram Weckwerth
- Vienna Metabolomics Center, University of Vienna, A-1090 Vienna, Austria
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria;
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Luo H, Sun Y, Hollibaugh JT, Moran MA. Low genome content diversity of marine planktonic Thaumarchaeota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:501-507. [PMID: 27120311 DOI: 10.1111/1758-2229.12417] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 04/02/2016] [Indexed: 06/05/2023]
Abstract
Members of Thaumarchaeota are responsible for much of the ammonia oxidation occurring in the ocean. Recent studies showed that marine Thaumarchaeota have versatile metabolic capabilities, but sequencing additional genomes has not significantly increased the gene content ascribed to this group. We used the assembly-free dN pipeline software in combination with phylogenetic analyses to interrogate shotgun metagenomic data sets to gain a better understanding of the genomic diversity of Thaumarchaeota populations. The program confidently assigned ∼3,000 paired-end reads to Thaumarchaeota, independent of homologies to any known Thaumarchaeota genome sequence. Only 2% of these reads potentially harbor new genes that were absent from the genome of 'Candidatus Nitrosopumilus maritimus' str. SCM1, even though this strain was isolated from a marine aquarium rather than directly from the ocean. One of these novel genes encode proteins associated with the CRISPR/Cas system, Cas1, suggesting that phage defense through CRISPR may be also present in planktonic Thaumarchaeota lineages. Our results suggest that marine Thaumarchaeota populations have very low diversity in genome content, which is corroborated using computer simulation analyses of two bacterial lineages with known genome content diversity.
Collapse
Affiliation(s)
- Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| |
Collapse
|
38
|
Kozlowski JA, Kits KD, Stein LY. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria. Front Microbiol 2016; 7:1090. [PMID: 27462312 PMCID: PMC4940428 DOI: 10.3389/fmicb.2016.01090] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.
Collapse
Affiliation(s)
- Jessica A Kozlowski
- Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada
| | - K Dimitri Kits
- Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada
| | - Lisa Y Stein
- Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada
| |
Collapse
|
39
|
Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra". Appl Environ Microbiol 2016; 82:2608-2619. [PMID: 26896134 PMCID: PMC4836417 DOI: 10.1128/aem.04031-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/13/2016] [Indexed: 01/11/2023] Open
Abstract
Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer “Candidatus Nitrosotalea devanaterra” provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of “Ca. Nitrosotalea devanaterra” reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that “Ca. Nitrosotalea devanaterra” contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography–mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of “Ca. Nitrosotalea devanaterra” were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization.
Collapse
|
40
|
Shiozaki T, Ijichi M, Isobe K, Hashihama F, Nakamura KI, Ehama M, Hayashizaki KI, Takahashi K, Hamasaki K, Furuya K. Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean. ISME JOURNAL 2016; 10:2184-97. [PMID: 26918664 PMCID: PMC4989309 DOI: 10.1038/ismej.2016.18] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 11/29/2022]
Abstract
We examined nitrification in the euphotic zone, its impact on the nitrogen cycles, and the controlling factors along a 7500 km transect from the equatorial Pacific Ocean to the Arctic Ocean. Ammonia oxidation occurred in the euphotic zone at most of the stations. The gene and transcript abundances for ammonia oxidation indicated that the shallow clade archaea were the major ammonia oxidizers throughout the study regions. Ammonia oxidation accounted for up to 87.4% (average 55.6%) of the rate of nitrate assimilation in the subtropical oligotrophic region. However, in the shallow Bering and Chukchi sea shelves (bottom ⩽67 m), the percentage was small (0–4.74%) because ammonia oxidation and the abundance of ammonia oxidizers were low, the light environment being one possible explanation for the low activity. With the exception of the shallow bottom stations, depth-integrated ammonia oxidation was positively correlated with depth-integrated primary production. Ammonia oxidation was low in the high-nutrient low-chlorophyll subarctic region and high in the Bering Sea Green Belt, and primary production in both was influenced by micronutrient supply. An ammonium kinetics experiment demonstrated that ammonia oxidation did not increase significantly with the addition of 31–1560 nm ammonium at most stations except in the Bering Sea Green Belt. Thus, the relationship between ammonia oxidation and primary production does not simply indicate that ammonia oxidation increased with ammonium supply through decomposition of organic matter produced by primary production but that ammonia oxidation might also be controlled by micronutrient availability as with primary production.
Collapse
Affiliation(s)
- Takuhei Shiozaki
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Minoru Ijichi
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Kazuo Isobe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fuminori Hashihama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ken-Ichi Nakamura
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Makoto Ehama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Koji Hamasaki
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Ken Furuya
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
41
|
Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota. ISME JOURNAL 2016; 10:1836-45. [PMID: 26882267 DOI: 10.1038/ismej.2016.2] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 12/14/2015] [Accepted: 12/24/2015] [Indexed: 11/08/2022]
Abstract
Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76(T) exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196(T). In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions.
Collapse
|
42
|
Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Front Microbiol 2015; 6:998. [PMID: 26441925 PMCID: PMC4585252 DOI: 10.3389/fmicb.2015.00998] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.
Collapse
Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA ; School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Cecilia B Kretz
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | | | - Kristen N Buck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - William M Landing
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University Tallahassee, FL, USA
| | - Peter L Morton
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University Tallahassee, FL, USA
| | - James W Moffett
- Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | | | - Kevin L Vergin
- Department of Microbiology, Oregon State University Corvallis, OR, USA
| | - Frank J Stewart
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA ; School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| |
Collapse
|
43
|
Hong JK, Cho JC. Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects. PLoS One 2015; 10:e0133763. [PMID: 26241328 PMCID: PMC4524719 DOI: 10.1371/journal.pone.0133763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/01/2015] [Indexed: 11/18/2022] Open
Abstract
To find environmental variables (EVs) shaping the ecological niche of the archaeal phylum Thaumarchaeota in terrestrial environments, we determined the abundance of Thaumarchaeota in various soil samples using real-time PCR targeting thaumarchaeotal 16S rRNA gene sequences. We employed our previously developed primer, THAUM-494, which had greater coverage for Thaumarchaeota and lower tolerance to nonthaumarchaeotal taxa than previous Thaumarchaeota-directed primers. The relative abundance estimates (RVs) of Thaumarchaeota (RTHAUM), Archaea (RARCH), and Bacteria (RBACT) were subjected to a series of statistical analyses. Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs. Negative causal relationships between RTHAUM and nutrient level-related EVs were observed in an RDA biplot. These negative relationships were further confirmed by correlation and regression analyses. Total nitrogen content (TN) appeared to be the EV that affected RTHAUM most strongly, and total carbon content (TC), which reflected the content of organic matter (OM), appeared to be the EV that affected it least. However, in the path analysis, a path model indicated that TN might be a mediator EV that could be controlled directly by the OM. Additionally, another path model implied that water content (WC) might also indirectly affect RTHAUM by controlling ammonium nitrogen (NH4+-N) level through ammonification. Thus, although most directly affected by NH4+-N, RTHAUM could be ultimately determined by OM content, suggesting that Thaumarchaeota could prefer low-OM or low-WC conditions, because either of these EVs could subsequently result in low levels of NH4+-N in soil.
Collapse
Affiliation(s)
- Jin-Kyung Hong
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Jae-Chang Cho
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
- * E-mail:
| |
Collapse
|
44
|
Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean. Proc Natl Acad Sci U S A 2015; 112:1173-8. [PMID: 25587132 DOI: 10.1073/pnas.1416223112] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.
Collapse
|
45
|
Long A, Song B, Fridey K, Silva A. Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils. FEMS Microbiol Ecol 2014; 91:1-9. [PMID: 25764542 DOI: 10.1093/femsec/fiu004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.
Collapse
Affiliation(s)
- Andrew Long
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Bongkeun Song
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403 Department of Biological Sciences, Virginia Institute of Marine Sciences, Gloucester Point, VA 23062, USA Department of Life Science, Dongguk University-Seoul, Seoul 100-715, South Korea
| | - Kelly Fridey
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Amy Silva
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| |
Collapse
|
46
|
Tsementzi D, Poretsky R, Rodriguez-R LM, Luo C, Konstantinidis KT. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:640-655. [PMID: 25756118 DOI: 10.1111/1758-2229.12180] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead-beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year-round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcriptional activity compared with other abundant taxa. Our results provide a practical guide to the analysis of metatranscriptomes and advance understanding of the activity and ecology of abundant and rare members of temperate freshwater microbial communities.
Collapse
|
47
|
Huang Q, Briggs BR, Dong H, Jiang H, Wu G, Edwardson C, De Vlaminck I, Quake S. Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China. PLoS One 2014; 9:e111681. [PMID: 25365331 PMCID: PMC4218802 DOI: 10.1371/journal.pone.0111681] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022] Open
Abstract
Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.
Collapse
Affiliation(s)
- Qiuyuan Huang
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, United States of America
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Brandon R. Briggs
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, United States of America
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, United States of America
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Christian Edwardson
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Iwijn De Vlaminck
- Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Stephen Quake
- Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, United States of America
| |
Collapse
|
48
|
Smith JM, Chavez FP, Francis CA. Ammonium uptake by phytoplankton regulates nitrification in the sunlit ocean. PLoS One 2014; 9:e108173. [PMID: 25251022 PMCID: PMC4177112 DOI: 10.1371/journal.pone.0108173] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/23/2014] [Indexed: 11/18/2022] Open
Abstract
Nitrification, the microbial oxidation of ammonium to nitrate, is a central part of the nitrogen cycle. In the ocean’s surface layer, the process alters the distribution of inorganic nitrogen species available to phytoplankton and produces nitrous oxide. A widely held idea among oceanographers is that nitrification is inhibited by light in the ocean. However, recent evidence that the primary organisms involved in nitrification, the ammonia-oxidizing archaea (AOA), are present and active throughout the surface ocean has challenged this idea. Here we show, through field experiments coupling molecular genetic and biogeochemical approaches, that competition for ammonium with phytoplankton is the strongest regulator of nitrification in the photic zone. During multiday experiments at high irradiance a single ecotype of AOA remained active in the presence of rapidly growing phytoplankton. Over the course of this three day experiment, variability in the intensity of competition with phytoplankton caused nitrification rates to decline from those typical of the lower photic zone (60 nmol L−1 d−1) to those in well-lit layers (<1 nmol L−1 d−1). During another set of experiments, nitrification rates exhibited a diel periodicity throughout much of the photic zone, with the highest rates occurring at night when competition with phytoplankton is lowest. Together, the results of our experiments indicate that nitrification rates in the photic zone are more strongly regulated by competition with phytoplankton for ammonium than they are by light itself. This finding advances our ability to model the impact of nitrification on estimates of new primary production, and emphasizes the need to more strongly consider the effects of organismal interactions on nutrient standing stocks and biogeochemical cycling in the surface of the ocean.
Collapse
Affiliation(s)
- Jason M. Smith
- Research Division, Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
- Department of Environmental Earth System Science, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Francisco P. Chavez
- Research Division, Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Christopher A. Francis
- Department of Environmental Earth System Science, Stanford University, Stanford, California, United States of America
| |
Collapse
|
49
|
Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. Proc Natl Acad Sci U S A 2014; 111:12504-9. [PMID: 25114236 DOI: 10.1073/pnas.1324115111] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are now implicated in exerting significant control over the form and availability of reactive nitrogen species in marine environments. Detailed studies of specific metabolic traits and physicochemical factors controlling their activities and distribution have not been well constrained in part due to the scarcity of isolated AOA strains. Here, we report the isolation of two new coastal marine AOA, strains PS0 and HCA1. Comparison of the new strains to Nitrosopumilus maritimus strain SCM1, the only marine AOA in pure culture thus far, demonstrated distinct adaptations to pH, salinity, organic carbon, temperature, and light. Strain PS0 sustained nearly 80% of ammonia oxidation activity at a pH as low as 5.9, indicating that coastal strains may be less sensitive to the ongoing reduction in ocean pH. Notably, the two novel isolates are obligate mixotrophs that rely on uptake and assimilation of organic carbon compounds, suggesting a direct coupling between chemolithotrophy and organic matter assimilation in marine food webs. All three isolates showed only minor photoinhibition at 15 µE ⋅ m(-2) ⋅ s(-1) and rapid recovery of ammonia oxidation in the dark, consistent with an AOA contribution to the primary nitrite maximum and the plausibility of a diurnal cycle of archaeal ammonia oxidation activity in the euphotic zone. Together, these findings highlight an unexpected adaptive capacity within closely related marine group I Archaea and provide new understanding of the physiological basis of the remarkable ecological success reflected by their generally high abundance in marine environments.
Collapse
|
50
|
Abstract
We investigated expression of genes mediating elemental cycling at the microspatial scale in the ocean's largest river plume using, to our knowledge, the first fully quantitative inventory of genes and transcripts. The bacterial and archaeal communities associated with a phytoplankton bloom in Amazon River Plume waters at the outer continental shelf in June 2010 harbored ∼ 1.0 × 10(13) genes and 4.7 × 10(11) transcripts per liter that mapped to several thousand microbial genomes. Genomes from free-living cells were more abundant than those from particle-associated cells, and they generated more transcripts per liter for carbon fixation, heterotrophy, nitrogen and phosphorus uptake, and iron acquisition, although they had lower expression ratios (transcripts ⋅ gene(-1)) overall. Genomes from particle-associated cells contributed more transcripts for sulfur cycling, aromatic compound degradation, and the synthesis of biologically essential vitamins, with an overall twofold up-regulation of expression compared with free-living cells. Quantitatively, gene regulation differences were more important than genome abundance differences in explaining why microenvironment transcriptomes differed. Taxa contributing genomes to both free-living and particle-associated communities had up to 65% of their expressed genes regulated differently between the two, quantifying the extent of transcriptional plasticity in marine microbes in situ. In response to patchiness in carbon, nutrients, and light at the micrometer scale, Amazon Plume microbes regulated the expression of genes relevant to biogeochemical processes at the ecosystem scale.
Collapse
|