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Sarkar J, Mondal M, Bhattacharya S, Dutta S, Chatterjee S, Mondal N, N S, Peketi A, Mazumdar A, Ghosh W. Extremely oligotrophic and complex-carbon-degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments. Arch Microbiol 2024; 206:179. [PMID: 38498215 DOI: 10.1007/s00203-024-03875-y] [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: 10/30/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024]
Abstract
Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2 limitation, obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a ~ 3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates' genomes and the habitat's metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains' survival in the critically carbon-depleted layers below the explored sediment depths (core-bottom organic carbon: 0.5-1.0% w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously reported sources such as Nitrosopumilus species.
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Affiliation(s)
- Jagannath Sarkar
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India.
| | - Mahamadul Mondal
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Sabyasachi Bhattacharya
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Subhajit Dutta
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Sumit Chatterjee
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Nibendu Mondal
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
- International Institute of Innovation and Technology, Kolkata, West Bengal, India
| | - Saran N
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Aditya Peketi
- Geological Oceanography, CSIR National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Aninda Mazumdar
- Geological Oceanography, CSIR National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Wriddhiman Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India.
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2
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
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3
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Caffrey JM, Bonaglia S, Conley DJ. Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments. FEMS Microbiol Lett 2019; 366:5266299. [PMID: 30596977 PMCID: PMC6343015 DOI: 10.1093/femsle/fny288] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 02/03/2023] Open
Abstract
Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm−3 d−1) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm−3 d−1 and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm−3 d−1. This was significantly higher than all oxygen treatments that were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.
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Affiliation(s)
- Jane M Caffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
| | - Stefano Bonaglia
- Department of Geology, Lund University, Solvegatan 12, SE-223 62 Lund, Sweden
| | - Daniel J Conley
- Department of Geology, Lund University, Solvegatan 12, SE-223 62 Lund, Sweden
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4
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He H, Zhen Y, Mi T, Fu L, Yu Z. Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China. Front Microbiol 2018; 9:116. [PMID: 29456526 PMCID: PMC5801408 DOI: 10.3389/fmicb.2018.00116] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.
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Affiliation(s)
- Hui He
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, China
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5
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Reyes C, Schneider D, Lipka M, Thürmer A, Böttcher ME, Friedrich MW. Nitrogen Metabolism Genes from Temperate Marine Sediments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:175-190. [PMID: 28283802 PMCID: PMC5405112 DOI: 10.1007/s10126-017-9741-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 02/05/2017] [Indexed: 05/26/2023]
Abstract
In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO3- was present in the top 5 cm below the sediment-water interface at both sites. NH4+ increased with depth below 5 cm where it overlapped with the NO3- zone. Steady-state modelling of NO3- and NH4+ porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amo, hao), denitrification (nir, nor), dissimilatory NO3- reduction to NH4+ (nfr and otr) and in both of the latter two pathways (nar, nap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO3- reduction to NO2- or NH4+ as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.
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Affiliation(s)
- Carolina Reyes
- Microbial Ecophysiology, University of Bremen, Leobener Strasse, D-28359, Bremen, Germany.
- Department of Environmental Geosciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Marko Lipka
- Geochemistry and Stable Isotope Biogeochemistry Group, Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, D-18119, Warnemünde, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Michael E Böttcher
- Geochemistry and Stable Isotope Biogeochemistry Group, Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, D-18119, Warnemünde, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology, University of Bremen, Leobener Strasse, D-28359, Bremen, Germany
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6
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Wang J, Kan J, Zhang X, Xia Z, Zhang X, Qian G, Miao Y, Leng X, Sun J. Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal. Front Microbiol 2017; 8:415. [PMID: 28360898 PMCID: PMC5352681 DOI: 10.3389/fmicb.2017.00415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.
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Affiliation(s)
- Jing Wang
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Jinjun Kan
- Stroud Water Research Center Avondale, PA, USA
| | - Xiaodong Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Zhiqiang Xia
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Xuecheng Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Gang Qian
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Yanyi Miao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Xiaoyun Leng
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
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7
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Diepens NJ, Dimitrov MR, Koelmans AA, Smidt H. Molecular Assessment of Bacterial Community Dynamics and Functional End Points during Sediment Bioaccumulation Tests. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:13586-13595. [PMID: 26466173 DOI: 10.1021/acs.est.5b02992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in artificial sediment during a 28 day bioaccumulation test with polychlorinated biphenyls, chlorpyrifos, and four marine benthic invertebrates. DGGE and 454-pyrosequencing of PCR-amplified 16S rRNA genes were used to characterize bacterial community composition. Abundance of total bacteria and selected genes encoding enzymes involved in important microbially mediated ecosystem functions were measured by qPCR. Community composition and diversity responded most to the time course of the experiment, whereas organic matter (OM) content showed a low but significant effect on community composition, biodiversity and two functional genes tested. Moreover, OM content had a higher influence on bacterial community composition than invertebrate species. Medium OM content led to the highest gene abundance and is preferred for standard testing. Our results also indicated that a pre-equilibration period is essential for growth and stabilization of the bacterial community. The observed changes in microbial community composition and functional gene abundance may imply actual changes in such functions during tests, with consequences for exposure and toxicity assessment.
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Affiliation(s)
- Noël J Diepens
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
| | - Mauricio R Dimitrov
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Albert A Koelmans
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
- IMARES, Institute for Marine Resources & Ecosystem Studies, Wageningen UR , P.O. Box 68, 1970 AB IJmuiden, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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Lagostina L, Goldhammer T, Røy H, Evans TW, Lever MA, Jørgensen BB, Petersen DG, Schramm A, Schreiber L. Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:404-413. [PMID: 25581373 PMCID: PMC5008181 DOI: 10.1111/1758-2229.12264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/22/2014] [Accepted: 01/01/2015] [Indexed: 05/31/2023]
Abstract
Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle.
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Affiliation(s)
- Lorenzo Lagostina
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Tobias Goldhammer
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Hans Røy
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Thomas W Evans
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Mark A Lever
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Dorthe G Petersen
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
- Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
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9
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Ward BB, Jensen MM. The microbial nitrogen cycle. Front Microbiol 2014; 5:553. [PMID: 25386170 PMCID: PMC4208395 DOI: 10.3389/fmicb.2014.00553] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/03/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Bess B Ward
- Geosciences, Princeton University Princeton, NJ, USA
| | - Marlene M Jensen
- Department of Environmental Engineering, Technical University of Denmark Lyngby, Denmark
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10
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Lipsewers YA, Bale NJ, Hopmans EC, Schouten S, Sinninghe Damsté JS, Villanueva L. Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea). Front Microbiol 2014; 5:472. [PMID: 25250020 PMCID: PMC4155873 DOI: 10.3389/fmicb.2014.00472] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/20/2014] [Indexed: 11/13/2022] Open
Abstract
Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.
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Affiliation(s)
- Yvonne A Lipsewers
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Nicole J Bale
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Ellen C Hopmans
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Stefan Schouten
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
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11
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Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 2012; 78:7501-10. [PMID: 22923400 DOI: 10.1128/aem.01960-12] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.
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