51
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Kataoka T, Suzuki K, Irino T, Yamamoto M, Higashi S, Liu H. Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring. Arch Microbiol 2017; 200:329-342. [PMID: 29143851 DOI: 10.1007/s00203-017-1442-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/28/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
Microbial nitrification is a key process in the nitrogen cycle in the continental shelf ecosystems. The genotype compositions and abundance of the ammonia monooxygenase gene, amoA, derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) in two size fractions (2-10 and 0.2-2 µm), were investigated in the East China Sea (ECS) in May 2008 using PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Four sites were selected across the continental shelf edge: continental shelf water (CSW), Kuroshio branch water (KBW), transition between CSW and KBW (TCSKB) and coastal KBW (CKBW). The gene copy numbers of AOA-amoA were higher than those of AOB-amoA in ECS. The relative abundance of amoA to the total 16S rRNA gene level reached approximately 15% in KBW and CKBW for the free-living fraction of AOA, whereas the level was less than 0.01% throughout ECS for the AOB. A cluster analysis of the AOA-amoA-DGGE band pattern showed distinct genotype compositions in CSW in both the size fractions and in the surface of the TCSKB and KBW. Sequences of the DGGE bands were assigned to two clades. One of the clades exclusively consisted of sequences derived from the 2-10-µm fraction. This study revealed that AOA-amoA abundance dominated over AOB-amoA throughout the ECS, whereas the genotype composition of AOA-amoA were distributed heterogeneously across the water masses. Additionally, this is the first report showing the distribution of AOA-amoA genotypes characteristic to particle-associated AOA in the offshore of the East China Sea.
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Affiliation(s)
- Takafumi Kataoka
- Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, Hong Kong. .,Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan. .,Faculty of Marine Science and Technology, Fukui Prefectural University, Gakuen-cho 1-1, Obama, 917-0003, Japan.
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan
| | - Tomohisa Irino
- Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan
| | - Masanobu Yamamoto
- Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan
| | - Seigo Higashi
- Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan
| | - Hongbin Liu
- Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, Hong Kong
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52
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Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. Archaea and the origin of eukaryotes. Nat Rev Microbiol 2017; 15:711-723. [DOI: 10.1038/nrmicro.2017.133] [Citation(s) in RCA: 279] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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53
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Ham B, Choi BY, Chae GT, Kirk MF, Kwon MJ. Geochemical Influence on Microbial Communities at CO 2-Leakage Analog Sites. Front Microbiol 2017; 8:2203. [PMID: 29170659 PMCID: PMC5684959 DOI: 10.3389/fmicb.2017.02203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/26/2017] [Indexed: 01/22/2023] Open
Abstract
Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites.
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Affiliation(s)
- Baknoon Ham
- KU-KIST Green School, Korea University, Seoul, South Korea
| | - Byoung-Young Choi
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Gi-Tak Chae
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Matthew F Kirk
- Department of Geology, Kansas State University, Manhattan, KS, United States
| | - Man Jae Kwon
- KU-KIST Green School, Korea University, Seoul, South Korea.,Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
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54
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Qin W, Heal KR, Ramdasi R, Kobelt JN, Martens-Habbena W, Bertagnolli AD, Amin SA, Walker CB, Urakawa H, Könneke M, Devol AH, Moffett JW, Armbrust EV, Jensen GJ, Ingalls AE, Stahl DA. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. Int J Syst Evol Microbiol 2017; 67:5067-5079. [PMID: 29034851 DOI: 10.1099/ijsem.0.002416] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.
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Affiliation(s)
- Wei Qin
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Rasika Ramdasi
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Julia N Kobelt
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Willm Martens-Habbena
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Department of Microbiology and Cell Science and Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Florida, FL, USA
| | - Anthony D Bertagnolli
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shady A Amin
- Department of Chemistry, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Christopher B Walker
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Marine and Ecological Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Martin Könneke
- Marine Archaea Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Allan H Devol
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - James W Moffett
- Departments of Biological Sciences and Earth Sciences and Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | | | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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55
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Wang S, Wang L, Deng L, Zheng D, Zhang Y, Jiang Y, Yang H, Lei Y. Performance of autotrophic nitrogen removal from digested piggery wastewater. BIORESOURCE TECHNOLOGY 2017; 241:465-472. [PMID: 28599225 DOI: 10.1016/j.biortech.2017.05.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 05/21/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
The performance of an autotrophic nitrogen removal process to treat digested piggery wastewater (DPW) was investigated by gradually shortening the HRT and enhancing the DPW concentration during 390days of operation. The results showed that the total nitrogen removal rate and efficiency reached 3.9kg-Nm-3day-1 and 73%, which were significantly higher than the levels reported previously. A high relative abundance of Nitrosomonas (4.2%) and functional microbes (12.15%) resulted in a high aerobic ammonium oxidizing activity (1.25±0.1g-NgVSS-1d-1), and a good settling ability (SVI, 78.42mLg-1SS) resulted in a high sludge concentration (VSS, 11.01gL-1), which laid a solid foundation for the excellent performance. High-throughput pyrosequencing indicated that, compared with synthetic wastewater, the DPW decreased the relative abundances of every functional group of nitrogen removal microbes, and increased relative abundances of anaerobes (15.7%), sulfur-oxidizing bacteria (9.4%) and methanogens (40.8%).
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Affiliation(s)
- Shuang Wang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Lan Wang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China.
| | - Liangwei Deng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Dan Zheng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Yunhong Zhang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Yiqi Jiang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Hongnan Yang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Yunhui Lei
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
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56
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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.
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57
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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58
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Eva S. Longterm Monitoring of Nitrification and Nitrifying Communities during Biofilter Activation of Two Marine Recirculation Aquaculture Systems (RAS). ACTA ACUST UNITED AC 2017. [DOI: 10.17352/2455-8400.000029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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59
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Hollibaugh JT. Oxygen and the activity and distribution of marine Thaumarchaeota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:186-188. [PMID: 28401690 DOI: 10.1111/1758-2229.12534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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60
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Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 2017; 19:2681-2700. [PMID: 28419726 DOI: 10.1111/1462-2920.13759] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany.,Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | | | - Barbara Bayer
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria
| | - Eva Spieck
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, 22609, Germany
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, 93053, Germany
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
| | | | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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61
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Rush D, Sinninghe Damsté JS. Lipids as paleomarkers to constrain the marine nitrogen cycle. Environ Microbiol 2017; 19:2119-2132. [PMID: 28142226 PMCID: PMC5516240 DOI: 10.1111/1462-2920.13682] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 11/30/2022]
Abstract
Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past.
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Affiliation(s)
- Darci Rush
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, P.O. Box 59 1790 AB, The Netherlands.,School of Civil Engineering and Geosciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, P.O. Box 59 1790 AB, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, TA Utrecht, P.O. Box 80.121, 3508, The Netherlands
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62
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Shi Y, Adams JM, Ni Y, Yang T, Jing X, Chen L, He JS, Chu H. The biogeography of soil archaeal communities on the eastern Tibetan Plateau. Sci Rep 2016; 6:38893. [PMID: 27958324 PMCID: PMC5153633 DOI: 10.1038/srep38893] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022] Open
Abstract
The biogeographical distribution of soil bacterial communities has been widely investigated. However, there has been little study of the biogeography of soil archaeal communities on a regional scale. Here, using high-throughput sequencing, we characterized the archaeal communities of 94 soil samples across the eastern Tibetan Plateau. Thaumarchaeota was the predominant archael phylum in all the soils, and Halobacteria was dominant only in dry soils. Archaeal community composition was significantly correlated with soil moisture content and C:N ratio, and archaeal phylotype richness was negatively correlated with soil moisture content (r = −0.47, P < 0.01). Spatial distance, a potential measure of the legacy effect of evolutionary and dispersal factors, was less important than measured environmental factors in determining the broad scale archaeal community pattern. These results indicate that soil moisture and C:N ratio are the key factors structuring soil archaeal communities on the eastern Tibetan Plateau. Our findings suggest that archaeal communities have adjusted their distributions rapidly enough to reach range equilibrium in relation to past environmental changes e.g. in water availability and soil nutrient status. This responsiveness may allow better prediction of future responses of soil archaea to environmental change in these sensitive ecosystems.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Jonathan M Adams
- Department of Biological Sciences, Seoul National University, Gwanak, Seoul 151, Republic of Korea
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Xin Jing
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Litong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining 810008, China
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 5 Yiheyuan Road, Beijing 100871, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining 810008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
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63
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The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:9278929. [PMID: 28070167 PMCID: PMC5187460 DOI: 10.1155/2016/9278929] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/23/2016] [Accepted: 08/09/2016] [Indexed: 11/17/2022]
Abstract
Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p < 0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.
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64
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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.
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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;
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65
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Wang K, Ye X, Zhang H, Chen H, Zhang D, Liu L. Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea. Sci Rep 2016; 6:38709. [PMID: 27917954 PMCID: PMC5137025 DOI: 10.1038/srep38709] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/11/2016] [Indexed: 12/21/2022] Open
Abstract
Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies.
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Affiliation(s)
- Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiansen Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo, 315012, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Heping Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo, 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Lian Liu
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo, 315012, China
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66
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Ammonium removal from high-salinity oilfield-produced water: assessing the microbial community dynamics at increasing salt concentrations. Appl Microbiol Biotechnol 2016; 101:859-870. [DOI: 10.1007/s00253-016-7902-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022]
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67
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Shakoor A, Abdullah M, Yousaf B, Amina, Ma Y. Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016:10.1007/s11356-016-7823-6. [PMID: 27771880 DOI: 10.1007/s11356-016-7823-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.
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Affiliation(s)
- Awais Shakoor
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- State-Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Balal Yousaf
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Amina
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Youhua Ma
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China.
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68
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Insights into microbial diversity in wastewater treatment systems: How far have we come? Biotechnol Adv 2016; 34:790-802. [DOI: 10.1016/j.biotechadv.2016.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/15/2016] [Accepted: 04/07/2016] [Indexed: 11/16/2022]
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69
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Wang J, Xue C, Song Y, Wang L, Huang Q, Shen Q. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity. Front Microbiol 2016; 7:1207. [PMID: 27536292 PMCID: PMC4971054 DOI: 10.3389/fmicb.2016.01207] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/20/2016] [Indexed: 11/13/2022] Open
Abstract
Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.
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Affiliation(s)
- Jichen Wang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Chao Xue
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Yang Song
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Lei Wang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
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70
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Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy. Proc Natl Acad Sci U S A 2016; 113:7762-7. [PMID: 27357675 DOI: 10.1073/pnas.1518534113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R(2) = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol·cell(-1)·d(-1) increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86 Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature.
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71
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Florio A, Felici B, Migliore M, Dell'Abate MT, Benedetti A. Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:2440-2450. [PMID: 26249321 DOI: 10.1002/jsfa.7364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/26/2015] [Accepted: 07/30/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. RESULTS While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. CONCLUSION The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Alessandro Florio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per lo studio delle relazioni tra pianta e suolo, Via della Navicella 2, 4-00184, Rome, Italy
| | - Barbara Felici
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per lo studio delle relazioni tra pianta e suolo, Via della Navicella 2, 4-00184, Rome, Italy
| | - Melania Migliore
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per lo studio delle relazioni tra pianta e suolo, Via della Navicella 2, 4-00184, Rome, Italy
| | - Maria Teresa Dell'Abate
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per lo studio delle relazioni tra pianta e suolo, Via della Navicella 2, 4-00184, Rome, Italy
| | - Anna Benedetti
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per lo studio delle relazioni tra pianta e suolo, Via della Navicella 2, 4-00184, Rome, Italy
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72
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Braker G, Conrad R. Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning? ADVANCES IN APPLIED MICROBIOLOGY 2016; 75:33-70. [PMID: 21807245 DOI: 10.1016/b978-0-12-387046-9.00002-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.
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Affiliation(s)
- Gesche Braker
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, Germany.
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73
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Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:3762159. [PMID: 27006640 PMCID: PMC4783532 DOI: 10.1155/2016/3762159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/14/2015] [Accepted: 01/10/2016] [Indexed: 12/28/2022]
Abstract
This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.
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74
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Dahmane N, Gadelle D, Delmas S, Criscuolo A, Eberhard S, Desnoues N, Collin S, Zhang H, Pommier Y, Forterre P, Sezonov G. topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB. Nucleic Acids Res 2016; 44:2795-805. [PMID: 26908651 PMCID: PMC4824112 DOI: 10.1093/nar/gkw097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/08/2016] [Indexed: 11/28/2022] Open
Abstract
Type IB DNA topoisomerases can eliminate torsional stresses produced during replication and transcription. These enzymes are found in all eukaryotes and a short version is present in some bacteria and viruses. Among prokaryotes, the long eukaryotic version is only observed in archaea of the phylum Thaumarchaeota. However, the activities and the roles of these topoisomerases have remained an open question. Here, we demonstrate that all available thaumarchaeal genomes contain a topoisomerase IB gene that defines a monophyletic group closely related to the eukaryotic enzymes. We show that the topIB gene is expressed in the model thaumarchaeon Nitrososphaera viennensis and we purified the recombinant enzyme from the uncultivated thaumarchaeon Candidatus Caldiarchaeum subterraneum. This enzyme is active in vitro at high temperature, making it the first thermophilic topoisomerase IB characterized so far. We have compared this archaeal type IB enzyme to its human mitochondrial and nuclear counterparts. The archaeal enzyme relaxes both negatively and positively supercoiled DNA like the eukaryotic enzymes. However, its pattern of DNA cleavage specificity is different and it is resistant to camptothecins (CPTs) and non-CPT Top1 inhibitors, LMP744 and lamellarin D. This newly described thermostable topoisomerases IB should be a promising new model for evolutionary, mechanistic and structural studies.
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Affiliation(s)
- Narimane Dahmane
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France
| | - Danièle Gadelle
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Stéphane Delmas
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France
| | - Alexis Criscuolo
- Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, Institut Pasteur, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Stephan Eberhard
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France
| | - Nicole Desnoues
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylvie Collin
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Guennadi Sezonov
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France
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75
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Mateos-Rivera A, Yde JC, Wilson B, Finster KW, Reigstad LJ, Øvreås L. The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway). FEMS Microbiol Ecol 2016; 92:fnw038. [DOI: 10.1093/femsec/fiw038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 11/14/2022] Open
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76
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Liu Y, Priscu JC, Xiong J, Conrad R, Vick-Majors T, Chu H, Hou J. Salinity drives archaeal distribution patterns in high altitude lake sediments on the Tibetan Plateau. FEMS Microbiol Ecol 2016; 92:fiw033. [DOI: 10.1093/femsec/fiw033] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 11/13/2022] Open
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77
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Sintes E, De Corte D, Haberleitner E, Herndl GJ. Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean. Front Microbiol 2016; 7:77. [PMID: 26903961 PMCID: PMC4746290 DOI: 10.3389/fmicb.2016.00077] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Abstract
In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization.
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Affiliation(s)
- Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Ecology, University of ViennaVienna, Austria
| | - Daniele De Corte
- Department of Limnology and Bio-Oceanography, Center of Ecology, University of ViennaVienna, Austria
| | - Elisabeth Haberleitner
- Department of Limnology and Bio-Oceanography, Center of Ecology, University of ViennaVienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Ecology, University of ViennaVienna, Austria
- Department of Biological Oceanography, Royal Netherlands Institute for Sea ResearchDen Burg, Netherlands
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78
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Mikucki JA, Lee PA, Ghosh D, Purcell AM, Mitchell AC, Mankoff KD, Fisher AT, Tulaczyk S, Carter S, Siegfried MR, Fricker HA, Hodson T, Coenen J, Powell R, Scherer R, Vick-Majors T, Achberger AA, Christner BC, Tranter M. Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2014.0290. [PMID: 26667908 DOI: 10.1098/rsta.2014.0290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.
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Affiliation(s)
- J A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - P A Lee
- Hollings Marine Lab, College of Charleston, Charleston, SC 29412, USA
| | - D Ghosh
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - A M Purcell
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - A C Mitchell
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK
| | - K D Mankoff
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - A T Fisher
- Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - S Tulaczyk
- Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - S Carter
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - M R Siegfried
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - H A Fricker
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - T Hodson
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - J Coenen
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - R Powell
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - R Scherer
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - T Vick-Majors
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
| | - A A Achberger
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - B C Christner
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Tranter
- Bristol Glaciology Centre, Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
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79
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Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes. Appl Microbiol Biotechnol 2016; 100:4685-98. [PMID: 26810199 DOI: 10.1007/s00253-016-7318-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities.
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80
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Elling FJ, Becker KW, Könneke M, Schröder JM, Kellermann MY, Thomm M, Hinrichs KU. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environ Microbiol 2015; 18:692-707. [PMID: 26472620 DOI: 10.1111/1462-2920.13086] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/28/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022]
Abstract
The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Jan M Schröder
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, 93053, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
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81
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Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau. Sci Rep 2015; 5:18071. [PMID: 26666501 PMCID: PMC4678299 DOI: 10.1038/srep18071] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022] Open
Abstract
Integration of DNA derived from ancient phototrophs with their characteristic lipid biomarkers has been successfully employed to reconstruct paleoenvironmental conditions. However, it is poorly known that whether the DNA and lipids of microbial functional aerobes (such as ammonia-oxidizing archaea: AOA) can be used for reconstructing past environmental conditions. Here we identify and quantify the AOA amoA genes (encoding the alpha subunit of ammonia monooxygenases) preserved in a 5.8-m sediment core (spanning the last 18,500 years) from Qinghai Lake. Parallel analyses revealed that low amoA gene abundance corresponded to high total organic carbon (TOC) and salinity, while high amoA gene abundance corresponded to low TOC and salinity. In the Qinghai Lake region, TOC can serve as an indicator of paleo-productivity and paleo-precipitation, which is related to historic nutrient input and salinity. So our data suggest that temporal variation of AOA amoA gene abundance preserved in Qinghai Lake sediment may reflect the variations of nutrient level and salinity throughout the late Pleistocene and Holocene in the Qinghai Lake region.
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82
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Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. ISME JOURNAL 2015; 10:1051-63. [PMID: 26528837 PMCID: PMC4839502 DOI: 10.1038/ismej.2015.200] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 11/09/2022]
Abstract
Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel Nitrosopumilus strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems.
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83
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Zhou L, Wang S, Zou Y, Xia C, Zhu G. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China. Sci Rep 2015; 5:15969. [PMID: 26522086 PMCID: PMC4629152 DOI: 10.1038/srep15969] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/06/2015] [Indexed: 12/28/2022] Open
Abstract
Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.
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Affiliation(s)
- Leiliu Zhou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Yuxuan Zou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Chao Xia
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China.,Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Breme, Germany
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84
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Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment. Appl Microbiol Biotechnol 2015; 100:1479-1488. [DOI: 10.1007/s00253-015-7072-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 09/30/2015] [Accepted: 10/06/2015] [Indexed: 01/29/2023]
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85
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Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process. Appl Microbiol Biotechnol 2015; 100:729-42. [DOI: 10.1007/s00253-015-6969-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/13/2015] [Accepted: 08/27/2015] [Indexed: 11/26/2022]
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86
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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.
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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:
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87
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The influence of salinity on the abundance, transcriptional activity, and diversity of AOA and AOB in an estuarine sediment: a microcosm study. Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6804-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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88
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Abstract
Biologists used to draw schematic “universal” trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese’s universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.
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Affiliation(s)
- Patrick Forterre
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur , Paris, France ; Institut de Biologie Intégrative de la cellule, Université Paris-Saclay , Paris, France
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89
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Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc Natl Acad Sci U S A 2015; 112:9370-5. [PMID: 26170282 DOI: 10.1073/pnas.1419329112] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum.
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90
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Long XE, Yao H, Wang J, Huang Y, Singh BK, Zhu YG. Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7152-7160. [PMID: 25989872 DOI: 10.1021/acs.est.5b00506] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.
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Affiliation(s)
- Xi-En Long
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Huaiying Yao
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Juan Wang
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Ying Huang
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Brajesh K Singh
- §Hawkesbury Institute for the Environment, University of Western Sydney, Penrith South DC, NSW 2751, Australia
| | - Yong-Guan Zhu
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
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91
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Ma Y, Hu A, Yu CP, Yan Q, Yan X, Wang Y, Deng F, Xiong H. Response of microbial communities to bioturbation by artificially introducing macrobenthos to mudflat sediments for in situ bioremediation in a typical semi-enclosed bay, southeast China. MARINE POLLUTION BULLETIN 2015; 94:114-122. [PMID: 25783451 DOI: 10.1016/j.marpolbul.2015.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/01/2015] [Indexed: 06/04/2023]
Abstract
Although microbes play important roles during the bioremediation process using macrobenthos in degraded environments, their response to macrobenthos bioturbation remains poorly understood. This study used 16S rRNA gene-Illumina Miseq sequencing to investigate the microbial communities and their response to bioturbation by artificially introducing macrobenthos to the mudflat of Sansha Bay, southeast China. A total of 56 phyla were identified, dominated by δ- and γ-Proteobacteria, with a total percentage of over 50%. Others, such as Acidobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Alphaproteobacteria occupied 4-7% respectively. Eighteen genera indicating the microbial communities response to bioturbation and seasonal change were identified. Bioturbated samples contained more ecologically important genera, and untreated samples contained more genera ubiquitous in marine environments. The physicochemical characteristics did not change significantly probably due to the short time of bioremediation and low survival rate of macrobenthos, confirming that microbial communities are more sensitive and can serve as sentinels for environmental changes.
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Affiliation(s)
- Ying Ma
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College of Jimei University, Xiamen 361021, China
| | - Anyi Hu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chang-Ping Yu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingpi Yan
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College of Jimei University, Xiamen 361021, China
| | - Xizhu Yan
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College of Jimei University, Xiamen 361021, China
| | - Yongzhong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College of Jimei University, Xiamen 361021, China
| | - Fei Deng
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College of Jimei University, Xiamen 361021, China
| | - Hejian Xiong
- Bioengineering College of Jimei University, Xiamen 361021, China.
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92
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Auyeung DSN, Martiny JBH, Dukes JS. Nitrification kinetics and ammonia-oxidizing community respond to warming and altered precipitation. Ecosphere 2015. [DOI: 10.1890/es14-00481.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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93
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Bang C, Schmitz RA. Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol Rev 2015; 39:631-48. [DOI: 10.1093/femsre/fuv010] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 12/18/2022] Open
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94
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Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment. PLoS One 2015; 10:e0119465. [PMID: 25742617 PMCID: PMC4351183 DOI: 10.1371/journal.pone.0119465] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/29/2015] [Indexed: 12/21/2022] Open
Abstract
Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world's largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.
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95
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Shi Y, Huang Z, Han S, Fan S, Yang H. Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages. J Basic Microbiol 2015; 55:1021-8. [DOI: 10.1002/jobm.201400678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/22/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Yu Shi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Institute of Entomology; School of Life Sciences; Central China Normal University; Wuhan P.R. China
| | - Zhou Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Institute of Entomology; School of Life Sciences; Central China Normal University; Wuhan P.R. China
| | - Shuai Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Institute of Entomology; School of Life Sciences; Central China Normal University; Wuhan P.R. China
| | - Shuo Fan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Institute of Entomology; School of Life Sciences; Central China Normal University; Wuhan P.R. China
| | - Hong Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Institute of Entomology; School of Life Sciences; Central China Normal University; Wuhan P.R. China
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96
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Dong K, Kim WS, Tripathi BM, Adams J. Generalized soil Thaumarchaeota community in weathering rock and saprolite. MICROBIAL ECOLOGY 2015; 69:356-360. [PMID: 25370886 DOI: 10.1007/s00248-014-0526-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
Relatively little is known of the archaeal communities associated with endolithic environments, compared to other microbial groups such as bacteria and fungi. Analyzing the pyrosequenced archaeal 16S ribosomal RNA (rRNA) gene V1-V3 region, we investigated the archaeal community associated with aboveground-exfoliated weathering layers of a granite gneiss, and of the saprolite derived from this rock at 1 m depth below the soil surface, in a forested hilly area south of Seoul, South Korea. In both these sites, an archaeal community dominated by the phylum Thaumarchaeota was identified. The archaeal community in all cases closely resembled that of the surface layer of acidic soils in temperate climates of Korea. It appears that there is no clear distinction in archaeal community composition between a soil and a rock and a saprolite despite a tremendous difference in the concentration of total nitrogen and organic carbon. Of the chemical properties we measured, pH was the best predictor of the archaeal community composition and relative abundance of thaumarchaeal subphyla. These findings reinforce the view that soil archaea are mostly generalists, whose ecology is not closely dependent on nitrogen concentration or soil organic matter status, the presence of living roots, or the abundant presence of any other biota.
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Affiliation(s)
- Ke Dong
- College of Natural Sciences, Seoul National University, Seoul, 151-742, South Korea
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97
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Martens-Habbena W, Qin W, Horak REA, Urakawa H, Schauer AJ, Moffett JW, Armbrust EV, Ingalls AE, Devol AH, Stahl DA. The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger. Environ Microbiol 2015; 17:2261-74. [DOI: 10.1111/1462-2920.12677] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/14/2014] [Accepted: 10/16/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Willm Martens-Habbena
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA 98195 USA
| | - Wei Qin
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA 98195 USA
| | | | - Hidetoshi Urakawa
- Department of Marine and Ecological Sciences; Florida Gulf Coast University; Fort Myers FL 33965 USA
| | - Andrew J. Schauer
- Department of Earth and Space Sciences; University of Washington; Seattle WA 98195 USA
| | - James W. Moffett
- Department of Biological Sciences; University of Southern California; Los Angeles CA 90089 USA
| | | | - Anitra E. Ingalls
- School of Oceanography; University of Washington; Seattle WA 98195 USA
| | - Allan H. Devol
- School of Oceanography; University of Washington; Seattle WA 98195 USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA 98195 USA
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98
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Berg C, Listmann L, Vandieken V, Vogts A, Jürgens K. Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea. Front Microbiol 2015; 5:786. [PMID: 25642221 PMCID: PMC4295551 DOI: 10.3389/fmicb.2014.00786] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/21/2014] [Indexed: 11/15/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 107 cells mL−1. Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA) gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO2 fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based 13C and 15N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy.
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Affiliation(s)
- Carlo Berg
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
| | - Luisa Listmann
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
| | - Verona Vandieken
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany ; Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Angela Vogts
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
| | - Klaus Jürgens
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
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99
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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.
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100
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Tago K, Okubo T, Shimomura Y, Kikuchi Y, Hori T, Nagayama A, Hayatsu M. Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil. Microbes Environ 2014; 30:21-8. [PMID: 25736866 PMCID: PMC4356460 DOI: 10.1264/jsme2.me14137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers’ fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers’ sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 105–9.2 × 106 and 1.7 × 106–5.3 × 107 gene copies g dry soil−1, respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences
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