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Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
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Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
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Sasi R, Suchithra TV. Wastewater microbial diversity versus molecular analysis at a glance: a mini-review. Braz J Microbiol 2023; 54:3033-3039. [PMID: 37723328 PMCID: PMC10689596 DOI: 10.1007/s42770-023-01130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023] Open
Abstract
Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.
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Affiliation(s)
- R Sasi
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601
| | - T V Suchithra
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601.
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3
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Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior. Microorganisms 2023; 11:microorganisms11020504. [PMID: 36838469 PMCID: PMC9963676 DOI: 10.3390/microorganisms11020504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
Despite being the largest freshwater lake system in the world, relatively little is known about the sestonic microbial community structure in the Laurentian Great Lakes. The goal of this research was to better understand this ecosystem using high-throughput sequencing of microbial communities as a function of water depth at six locations in the westernmost Great Lakes of Superior and Michigan. The water column was characterized by gradients in temperature, dissolved oxygen (DO), pH, and other physicochemical parameters with depth. Mean nitrate concentrations were 32 μmol/L, with only slight variation within and between the lakes, and with depth. Mean available phosphorus was 0.07 μmol/L, resulting in relatively large N:P ratios (97:1) indicative of P limitation. Abundances of the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Thaumarchaeota, and Verrucomicrobia differed significantly among the Lakes. Candidatus Nitrosopumilus was present in greater abundance in Lake Superior compared to Lake Michigan, suggesting the importance of ammonia-oxidating archaea in water column N cycling in Lake Superior. The Shannon diversity index was negatively correlated with pH, temperature, and salinity, and positively correlated with DO, latitude, and N2 saturation. Results of this study suggest that DO, pH, temperature, and salinity were major drivers shaping the community composition in the Great Lakes.
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Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management. mSystems 2022; 7:e0057122. [PMID: 36445691 PMCID: PMC9765229 DOI: 10.1128/msystems.00571-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic units (vOTUs) in samples collected from soil taken from four nitrogen fertilization (N-fertilization) and cover-cropping practices at an experimental site under continuous cotton production evaluating conservation agricultural management systems for more than 40 years. Only ~6% of the vOTUs identified were clustered with known viruses in the RefSeq database using a gene-sharing network. We found that 14% of 260 vOTUs could be linked to microbial hosts that cover key carbon and nitrogen cycling taxa, including Acidobacteriota, Proteobacteria, Verrucomicrobiota, Firmicutes, and ammonia-oxidizing archaea, i.e., Nitrososphaeria (phylum Thermoproteota). Viral diversity, community structure, and the positive correlation between abundance of a virus and its host indicate that viruses and microbes are more sensitive to N-fertilization than cover-cropping treatment. Viruses may influence key carbon and nitrogen cycling through control of microbial function and host populations (e.g., Chthoniobacterales and Nitrososphaerales). These findings provide an initial view of soil viral ecology and how it is influenced by long-term conservation agricultural management. IMPORTANCE Bacterial viruses are extremely small and abundant particles that can control the microbial abundance and community composition through infection, which gradually showed their vital roles in the ecological process to influence the nutrient flow. Compared to the substrate control, less is known about the influence of soil viruses on microbial community function, and even less is known about microbial and viral diversity in the soil system. To obtain a more complete knowledge of microbial function dynamics, the interaction between microbes and viruses cannot be ignored. To fully understand this process, it is fundamental to get insight into the correlation between the diversity of viral communities and bacteria which could induce these changes.
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Kohtz AJ, Jay ZJ, Lynes MM, Krukenberg V, Hatzenpichler R. Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME COMMUNICATIONS 2022; 2:86. [PMID: 37938354 PMCID: PMC9723716 DOI: 10.1038/s43705-022-00175-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2023]
Abstract
Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.
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Affiliation(s)
- Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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6
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The Prokaryotic Complex of Modern and Buried Soils on the Kamchatka Peninsula. FORESTS 2022. [DOI: 10.3390/f13071066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A prokaryotic heterotrophic mesophilic community was studied in volcanic soil samples from Kamchatka. A phylogenetic and physiological characterization of the prokaryotic complex of modern and buried soils of the Kamchatka Peninsula is given. Volcanic Paleolithic soils (2500 and 11,300 years old) and their modern equivalents were investigated. It was found that the biomass of metabolically active prokaryotes in modern volcanic and Paleolithic soils reached 50 and 40 µg/g, respectively. The proportion of archaea in the metabolically active prokaryotic complex varied from 20% to 30% and increased in variants with the application of the nitrogen-containing biopolymer chitin. The application of the additional resource to paleovolcanic soils led to an incremental increase in the proportion of metabolically active prokaryotes, which reached 50% of the total prokaryotic biomass detected, indicating the high metabolic potential of the considered soils. Phylogenetic structure characteristics of the prokaryotic metabolically active component of modern and buried volcanic soil were established by molecular biology methods (metagenomic analysis, FISH method). The phylum Proteobacteria (74%), Acidobacteria, and Actinobacteria (14% combined) were dominant in modern soils; phylum Acidobacteria (51.8%) was dominant in paleosoils, whereas Chloroflexi (21%) and Proteobacteria (9%) were subdominant. It was determined that the potential activity of the microbial hydrolytic community, as measured by the relative response to the added resource (chitin), was found to increase in a series from modern to paleovolcanic soil. It was demonstrated that several key genes of the nitrogen cycle responsible for the processes of molecular nitrogen fixation, nitrification, and denitrification (nifH, amoA, nirK) were present in both modern and buried horizons.
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Fisk LM, Barton L, Maccarone LD, Jenkins SN, Murphy DV. Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil. Sci Rep 2022; 12:7299. [PMID: 35508560 PMCID: PMC9068766 DOI: 10.1038/s41598-022-10711-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.
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Affiliation(s)
- L M Fisk
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - L Barton
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - L D Maccarone
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - S N Jenkins
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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8
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Natalicchio M, Birgel D, Dela Pierre F, Ziegenbalg S, Hoffmann-Sell L, Gier S, Peckmann J. Messinian bottom-grown selenitic gypsum: An archive of microbial life. GEOBIOLOGY 2022; 20:3-21. [PMID: 34296807 DOI: 10.1111/gbi.12464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Primary gypsum deposits, which accumulated in the Mediterranean Basin during the so-called Messinian salinity crisis (5.97-5.33 Ma), represent an excellent archive of microbial life. We investigated the molecular fossil inventory and the corresponding compound-specific δ13 C values of bottom-grown gypsum formed during the first stage of the crisis in four marginal basins across the Mediterranean (Nijar, Spain; Vena del Gesso, Italy; Heraklion, Crete; and Psematismenos, Cyprus). All studied gypsum samples contain intricate networks of filamentous microfossils, whose phylogenetic affiliation has been debated for a long time. Petrographic analysis, molecular fossil inventories (hydrocarbons, alcohols, and carboxylic acids), and carbon stable isotope patterns suggest that the mazes of filamentous fossils represent benthic microbial assemblages dominated by chemotrophic sulfide-oxidizing bacteria; in some of the samples, the body fossils are accompanied by lipids produced by sulfate-reducing bacteria. Abundant isoprenoid alcohols including diphytanyl glycerol diethers (DGDs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), typified by highly variable carbon stable isotope composition with δ13 C values spanning from -40 to -14‰, reveal the presence of planktic and benthic archaeal communities dwelling in Messinian paleoenvironments. The compound inventory of archaeal lipids indicates the existence of a stratified water column, with a normal marine to diluted upper water column and more saline deeper waters. This study documents the lipid biomarker inventory of microbial life preserved in ancient gypsum deposits, helping to reconstruct the widely debated conditions under which Messinian gypsum formed.
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Affiliation(s)
- Marcello Natalicchio
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
| | - Daniel Birgel
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
| | - Francesco Dela Pierre
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
| | | | | | - Susanne Gier
- Institut für Geologie, Universität Wien, Wien, Austria
| | - Jörn Peckmann
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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Ban Q, Zhang L, Li J. Correlating bacterial and archaeal community with efficiency of a coking wastewater treatment plant employing anaerobic-anoxic-oxic process in coal industry. CHEMOSPHERE 2022; 286:131724. [PMID: 34388873 DOI: 10.1016/j.chemosphere.2021.131724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Coking wastewater (CWW) contains various complex pollutants, and biological treatment processes are frequently applied in the coking wastewater treatment plants (CWWTPs). The present work is to evaluate the contaminants removal of a full-scale CWWTP with an anaerobic-anoxic-oxic process (A/A/O), to reveal function of bacterial and archaeal community involved in different bioreactors, and to clarify the relationship between the performance and microbial community. Illumina Miseq sequencing of bacteria showed that β-proteobacteria dominated in three bioreactors with relative abundance of 60.2%~81.7%. 75.2% of sequences were assigned to Petrobacter in the bioreactor A1, while Thiobacillus dominated in A2 and O with relative abundance of 31.8% and 38.7%, respectively. Illumina Miseq sequencing of archaea revealed a high diversity of methanogens existed in A1 and A2 activated sludge. Moreover, Halostagnicola was the dominant archaea in A1 and A2 activated sludge with relative abundance of 41.8% and 66.5%, respectively. Function predicted analysis explored that function of bacteria was similar to that of archaea but the relative abundance differed from each other. A putative biodegradation model of CWW treatment in A/A/O process indicated that A1 and A2 activated sludge mainly reduced carbohydrate, protein, TN, phenol and cyanide, as well as methane production. Bacteria in the bioreactor O were responsible for aerobic biotransformation of residual carbohydrates, refractory organics and nitrification. The redundancy analysis (RDA) further revealed that removal of COD, TN, and NO3--N, phenol and cyanides were highly correlated with some anaerobic bacteria and archaea, whereas the transformation of NH4+-N was positively correlated with some aerobic bacteria.
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Affiliation(s)
- Qiaoying Ban
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, PR China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China
| | - Liguo Zhang
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, PR China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
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10
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Li F, Leu A, Poff K, Carlson LT, Ingalls AE, DeLong EF. Planktonic Archaeal Ether Lipid Origins in Surface Waters of the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:610675. [PMID: 34589060 PMCID: PMC8473941 DOI: 10.3389/fmicb.2021.610675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Thaumarchaeota and Thermoplasmatota are the most abundant planktonic archaea in the sea. Thaumarchaeota contain tetraether lipids as their major membrane lipids, but the lipid composition of uncultured planktonic Thermoplasmatota representatives remains unknown. To address this knowledge gap, we quantified archaeal cells and ether lipids in open ocean depth profiles (0–200 m) of the North Pacific Subtropical Gyre. Planktonic archaeal community structure and ether lipid composition in the water column partitioned into two separate clusters: one above the deep chlorophyll maximum, the other within and below it. In surface waters, Thermoplasmatota densities ranged from 2.11 × 106 to 6.02 × 106 cells/L, while Thaumarchaeota were undetectable. As previously reported for Thaumarchaeota, potential homologs of archaeal tetraether ring synthases were present in planktonic Thermoplasmatota metagenomes. Despite the absence of Thaumarchaeota in surface waters, measurable amounts of intact polar ether lipids were found there. Based on cell abundance estimates, these surface water archaeal ether lipids contributed only 1.21 × 10–9 ng lipid/Thermoplasmatota cell, about three orders of magnitude less than that reported for Thaumarchaeota cells. While these data indicate that even if some tetraether and diether lipids may be derived from Thermoplasmatota, they would only comprise a small fraction of Thermoplasmatota total biomass. Therefore, while both MGI Thaumarchaeota and MGII/III Thermoplasmatota are potential biological sources of archaeal GDGTs, the Thaumarchaeota appear to be the major contributors of archaeal tetraether lipids in planktonic marine habitats. These results extend and confirm previous reports of planktonic archaeal lipid sources, and further emphasize the need for Thermoplasmatota cultivation, to better characterize the membrane lipid constituents of marine planktonic Thermoplasmatota, and more precisely define the sources and patterns of archaeal tetraether lipid distributions in marine plankton.
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Affiliation(s)
- Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Andy Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Kirsten Poff
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
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11
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Wang H, Bagnoud A, Ponce-Toledo RI, Kerou M, Weil M, Schleper C, Urich T. Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils. mSystems 2021; 6:e0054621. [PMID: 34463572 DOI: 10.1128/msystems.00546-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023] Open
Abstract
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Alexandre Bagnoud
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Micha Weil
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
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12
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Zheng Y, Yu S, Wang G, Xie F, Xu H, Du S, Zhao H, Sang X, Lu J, Jiang W. Comparative microbial antibiotic resistome between urban and deep forest environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:503-508. [PMID: 33751816 DOI: 10.1111/1758-2229.12942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
A paradoxical result of using antibiotics to eradicate microbial pathogens is the emergence of a vast number of resistant microbes in various environments. The concern that environmental microbes will inevitably become resistant to virtually every clinically usable antibiotics has been exacerbated by the spread of these resistance genes across different environments and the emergence of multidrug resistant phenotypes. Here, we provide metagenomic insights into the microbiomes and resistomes of 16 soil samples collected from hospitals, residential areas, and forest parks in the megacity of Beijing and deep forests in the Yunnan province. Using Illumina HiSeq sequencing, we investigated the microbial diversity within the metagenomic shotgun reads and identified 486 antibiotic-resistant genes (ARGs) classified into 30 types from these samples, among which multidrug resistance genes were the most abundant. Our results present an important reference and direct comparison of microbial antibiotic resistomes of soil samples from a megacity and deep forests and extend our understanding of the spread of ARGs in modern urban and natural environments.
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Affiliation(s)
- Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Si Yu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guanqun Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fucun Xie
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Haifeng Xu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jizhou Lu
- Department of Liver Surgery, The Third People's Hospital of Gansu Province, Lanzhou, 730020, China
| | - Wenjun Jiang
- Department of Plant Pathology and Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
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13
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Song Y, Li F, Fischer-Tlustos AJ, Neves ALA, He Z, Steele MA, Guan LL. Metagenomic analysis revealed the individualized shift in ileal microbiome of neonatal calves in response to delaying the first colostrum feeding. J Dairy Sci 2021; 104:8783-8797. [PMID: 34024606 DOI: 10.3168/jds.2020-20068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/13/2021] [Indexed: 01/14/2023]
Abstract
The aim of this study was to explore the effect of colostrum feeding time on the ileal microbiome of neonatal calves. In this study, 22 male Holstein calves were randomly assigned to different colostrum feeding time treatments: after birth (at 45 min, n = 7); at 6 h after birth (n = 8); and at 12 h after birth (TRT12h; n = 7). At 51 h after birth, calves were killed and ileum digesta was collected for microbiome analysis using shotgun metagenomic sequencing. Bacteria, archaea, eukaryotes, and viruses were identified from the ileum microbiome. For the bacteriome, Firmicutes and Proteobacteria were the predominant phyla, and Escherichia, Streptococcus, Lactobacillus were the 3 most abundant genera. For the archaeal community, Euryarchaeota and Crenarchaeota were the 2 major phyla, and Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the 3 most abundant genera. In total, 116 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified from the ileal microbiome, with "biosynthesis of vancomycin group antibiotics," "biosynthesis of ansamycins," "valine, leucine, and isoleucine biosynthesis," "ribosome," and "d-alanine metabolism" as the top 5 functions. When the ileal microbiomes were compared among the 3 treatments, the relative abundance of Enterococcus was higher in TRT12h calves, suggesting that calves may have a higher abundance of opportunistic pathogens when the feeding of colostrum is delayed for 12 h. Moreover, among all KEGG pathways, the enriched "taurine and hypotaurine metabolism" (KO00430) pathway was identified in the ileal microbiome of TRT12h calves; however, future studies are needed to understand the effect on the host. Additionally, 2 distinct ileal microbial profiles were identified across all samples, indicating that that host factors may play a significant role in driving varied microbiome changes in response to colostrum feeding time. Whether such microbiome shifts affect long-term gut function and calf performance warrants future studies.
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Affiliation(s)
- Y Song
- College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, P. R. China 028000; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G2P5; Brucellosis Prevention and Treatment Engineering Research Center of Inner Mongolia Autonomous region, Tongliao, P. R. China 028000
| | - F Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G2P5
| | - A J Fischer-Tlustos
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G2W1
| | - A L A Neves
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G2P5; Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Gr⊘nnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Z He
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Changsha, Hunan, P. R. China 410125
| | - M A Steele
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G2W1.
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G2P5.
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14
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Yang Y, Zhang C, Lenton TM, Yan X, Zhu M, Zhou M, Tao J, Phelps TJ, Cao Z. The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Mol Biol Evol 2021; 38:3637-3648. [PMID: 33993308 PMCID: PMC8382903 DOI: 10.1093/molbev/msab129] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth’s early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928–880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767–554 Ma) before diversifying into marine settings at ∼509 Ma (629–412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.
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Affiliation(s)
- Yiyan Yang
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, 201602, China
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Exeter, EX4 4QE, United Kingdom
| | - Xinmiao Yan
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, P.R. China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Mengdi Zhou
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China
| | - Tommy J Phelps
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China
| | - Zhiwei Cao
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
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15
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Luo ZH, Narsing Rao MP, Chen H, Hua ZS, Li Q, Hedlund BP, Dong ZY, Liu BB, Guo SX, Shu WS, Li WJ. Genomic Insights of " Candidatus Nitrosocaldaceae" Based on Nine New Metagenome-Assembled Genomes, Including " Candidatus Nitrosothermus" Gen Nov. and Two New Species of " Candidatus Nitrosocaldus". Front Microbiol 2021; 11:608832. [PMID: 33488549 PMCID: PMC7819960 DOI: 10.3389/fmicb.2020.608832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 01/11/2023] Open
Abstract
“Candidatus Nitrosocaldaceae” are globally distributed in neutral or slightly alkaline hot springs and geothermally heated soils. Despite their essential role in the nitrogen cycle in high-temperature ecosystems, they remain poorly understood because they have never been isolated in pure culture, and very few genomes are available. In the present study, a metagenomics approach was employed to obtain “Ca. Nitrosocaldaceae” metagenomic-assembled genomes (MAGs) from hot spring samples collected from India and China. Phylogenomic analysis placed these MAGs within “Ca. Nitrosocaldaceae.” Average nucleotide identity and average amino acid identity analysis suggested the new MAGs represent two novel species of “Candidatus Nitrosocaldus” and a novel genus, herein proposed as “Candidatus Nitrosothermus.” Key genes responsible for chemolithotrophic ammonia oxidation and a thaumarchaeal 3HP/4HB cycle were detected in all MAGs. Furthermore, genes coding for urea degradation were only present in “Ca. Nitrosocaldus,” while biosynthesis of the vitamins, biotin, cobalamin, and riboflavin were detected in almost all MAGs. Comparison of “Ca. Nitrosocaldales/Nitrosocaldaceae” with other AOA revealed 526 specific orthogroups. This included genes related to thermal adaptation (cyclic 2,3-diphosphoglycerate, and S-adenosylmethionine decarboxylase), indicating their importance for life at high temperature. In addition, these MAGs acquired genes from members from archaea (Crenarchaeota) and bacteria (Firmicutes), mainly involved in metabolism and stress responses, which might play a role to allow this group to adapt to thermal habitats.
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Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
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16
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Song D, Liu C, Sun Z, Liu Q, Wang P, Sun S, Cheng W, Qiu L, Ma J, Qi J. Tailoring the distribution of microbial communities and gene expressions to achieve integrating nitrogen transformation in a gravity-driven submerged membrane bioreactor. WATER RESEARCH 2020; 187:116382. [PMID: 32947113 DOI: 10.1016/j.watres.2020.116382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
A pilot-scale upgraded gravity-driven submerged membrane (GDSM) reactor was constructed to enhance nitrogen removal. It was artificially formed multiple stratified environments (dissolved oxygen (DO) and substrate supply (TOC, TN, COD, NH4+-N, NO2--N, and NO3--N)) by embedding moving water baffles to control water-flow process in bulk liquid with slow-flowing liquid state. Significant diversity and relative abundance of microorganisms associated with nitrogen transformation paths (i.e., ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite oxidizing bacteria, and denitrifying bacteria) were tailored to distribute on different spatial and temporal regions, and performed their dominant functions. The process simultaneously integrated diverse and effective nitrogen transformation paths (i.e., nitrification, partial nitrification, denitrification, anammox, and dissimilatory nitrate reduction) to achieve high nitrogen removal, with NH4+-N, TN, and COD eliminated by 94.68 ± 2.55%, 55.16 ± 5.53%, and 80.17 ± 6.75%, respectively. Gene expressions involved in the nitrogen transformations were estimated by qPCR to explore the shifts of dominant nitrogen transforming bioreactions in multiple stratified environments. Pearson correlation coefficients supported that the functional genes had more stable and active ability by complementing each other. As a result, an endogenous integration of diverse nitrogen transformation paths was achieved in a single system by artificially tailoring the distributions of microbial communities and gene expressions with enhanced nitrogen removal.
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Affiliation(s)
- Dan Song
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Caihong Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Zhiqiang Sun
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Qianliang Liu
- Key Laboratory of Green Chemical Engineering and Technology of College of Heilongjiang Province, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Panpan Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Shaofang Sun
- School of Civil Engineering and Architecture, University of Jinan, Jinan 250022, China
| | - Wei Cheng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liping Qiu
- School of Civil Engineering and Architecture, University of Jinan, Jinan 250022, China.
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China.
| | - Jingyao Qi
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China.
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17
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Kato S, Ohnishi M, Nagamori M, Yuki M, Takashina T, Ohkuma M, Itoh T. Conexivisphaera calida gen. nov., sp. nov., a thermophilic sulfur- and iron-reducing archaeon, and proposal of Conexivisphaeraceae fam. nov., Conexivisphaerales ord. nov., and Conexivisphaeria class. nov. in the phylum Thaumarchaeota. Int J Syst Evol Microbiol 2020; 71. [PMID: 33295866 DOI: 10.1099/ijsem.0.004595] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermoacidophilic, anaerobic, and iron- and sulfur-reducing archaeon, strain NAS-02T, was isolated from a terrestrial hot spring in Japan, as previously reported. This organism is the first non-ammonia-oxidizing isolate in the phylum Thaumarchaeota. Here, we propose Conexivisphaera calida gen. nov., sp. nov. to accommodate this strain. The type strain of the type species is NAS-02T (=JCM 31663T=DSM 105898T). The values of 16S rRNA gene similarity and average amino acid identity between NAS-02T and its closest relatives are <86 and <42 %, respectively. Based on the phylogeny and physiology, we propose the family Conexivisphaeraceae fam. nov., the order Conexivisphaerales ord. nov. and the class Conexivisphaeria class. nov. to accommodate the novel genus.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masafumi Ohnishi
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Mai Nagamori
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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18
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Sillen WMA, Thijs S, Abbamondi GR, De La Torre Roche R, Weyens N, White JC, Vangronsveld J. Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis. MICROBIOME 2020; 8:127. [PMID: 32907632 PMCID: PMC7488162 DOI: 10.1186/s40168-020-00904-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver's effects on this environment is lacking because the impact on the natural soil microbiome is not known. In a study assessing the use of nanosilver for phytopathogen control with maize, we analyzed the metatranscriptome of the maize rhizosphere and observed multiple unintended effects of exposure to 100 mg kg-1 nanosilver in soil during a growth period of 117 days. RESULTS We found several unintended effects of nanosilver which could interfere with agricultural systems in the long term. Firstly, the archaea community was negatively impacted with a more than 30% decrease in relative abundance, and as such, their involvement in nitrogen cycling and specifically, nitrification, was compromised. Secondly, certain potentially phytopathogenic fungal groups showed significantly increased abundances, possibly due to the negative effects of nanosilver on bacteria exerting natural biocontrol against these fungi as indicated by negative interactions in a network analysis. Up to 5-fold increases in relative abundance have been observed for certain possibly phytopathogenic fungal genera. Lastly, nanosilver exposure also caused a direct physiological impact on maize as illustrated by increased transcript abundance of aquaporin and phytohormone genes, overall resulting in a stress level with the potential to yield hormetically stimulated plant root growth. CONCLUSIONS This study indicates the occurrence of significant unintended effects of nanosilver use on corn, which could turn out to be negative to crop productivity and ecosystem health in the long term. We therefore highlight the need to include the microbiome when assessing the risk associated with nano-enabled agriculture. Video Abstract.
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Affiliation(s)
- Wouter M. A. Sillen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Gennaro Roberto Abbamondi
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, Pozzuoli, 80078 Napoli, Italy
| | - Roberto De La Torre Roche
- Department Analytical Chemistry, Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT USA
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Jason C. White
- Department Analytical Chemistry, Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT USA
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
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19
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Fuller AJ, Leary P, Gray ND, Davies HS, Mosselmans JFW, Cox F, Robinson CH, Pittman JK, McCann CM, Muir M, Graham MC, Utsunomiya S, Bower WR, Morris K, Shaw S, Bots P, Livens FR, Law GTW. Organic complexation of U(VI) in reducing soils at a natural analogue site: Implications for uranium transport. CHEMOSPHERE 2020; 254:126859. [PMID: 32957279 DOI: 10.1016/j.chemosphere.2020.126859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/07/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Understanding the long-term fate, stability, and bioavailability of uranium (U) in the environment is important for the management of nuclear legacy sites and radioactive wastes. Analysis of U behavior at natural analogue sites permits evaluation of U biogeochemistry under conditions more representative of long-term equilibrium. Here, we have used bulk geochemical and microbial community analysis of soils, coupled with X-ray absorption spectroscopy and μ-focus X-ray fluorescence mapping, to gain a mechanistic understanding of the fate of U transported into an organic-rich soil from a pitchblende vein at the UK Needle's Eye Natural Analogue site. U is highly enriched in the Needle's Eye soils (∼1600 mg kg-1). We show that this enrichment is largely controlled by U(VI) complexation with soil organic matter and not U(VI) bioreduction. Instead, organic-associated U(VI) seems to remain stable under microbially-mediated Fe(III)-reducing conditions. U(IV) (as non-crystalline U(IV)) was only observed at greater depths at the site (>25 cm); the soil here was comparatively mineral-rich, organic-poor, and sulfate-reducing/methanogenic. Furthermore, nanocrystalline UO2, an alternative product of U(VI) reduction in soils, was not observed at the site, and U did not appear to be associated with Fe-bearing minerals. Organic-rich soils appear to have the potential to impede U groundwater transport, irrespective of ambient redox conditions.
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Affiliation(s)
- Adam J Fuller
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK
| | - Peter Leary
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Neil D Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Helena S Davies
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | | | - Filipa Cox
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Clare H Robinson
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Jon K Pittman
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Clare M McCann
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Michael Muir
- School of Geoscience, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Margaret C Graham
- School of Geoscience, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Satoshi Utsunomiya
- School of Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - William R Bower
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK; Radiochemistry Unit, Department of Chemistry, The University of Helsinki, 00014, Finland
| | - Katherine Morris
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Samuel Shaw
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Pieter Bots
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Francis R Livens
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK; Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Gareth T W Law
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK; Radiochemistry Unit, Department of Chemistry, The University of Helsinki, 00014, Finland.
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20
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Ma C, Coffinet S, Lipp JS, Hinrichs KU, Zhang C. Marine Group II Euryarchaeota Contribute to the Archaeal Lipid Pool in Northwestern Pacific Ocean Surface Waters. Front Microbiol 2020; 11:1034. [PMID: 32582055 PMCID: PMC7291766 DOI: 10.3389/fmicb.2020.01034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Planktonic archaea include predominantly Marine Group I Thaumarchaeota (MG I) and Marine Group II Euryarchaeota (MG II), which play important roles in the oceanic carbon cycle. MG I produce specific lipids called isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs), which are being used in the sea surface temperature proxy named TEX86. Although MG II may be the most abundant planktonic archaeal group in surface water, their lipid composition remains poorly characterized because of the lack of cultured representatives. Circumstantial evidence from previous studies of marine suspended particulate matter suggests that MG II may produce both GDGTs and archaeol-based lipids. In this study, integration of the 16S rRNA gene quantification and sequencing and lipid analysis demonstrated that MG II contributed significantly to the pool of archaeal tetraether lipids in samples collected from MG II-dominated surface waters of the Northwestern Pacific Ocean (NWPO). The archaeal lipid composition in MG II-dominated NWPO waters differed significantly from that of known MG I cultures, containing relatively more 2G-OH-, 2G- and 1G- GDGTs, especially in their acyclic form. Lipid composition in NWPO waters was also markedly different from MG I-dominated surface water samples collected in the East China Sea. GDGTs from MG II-dominated samples seemed to respond to temperature similarly to GDGTs from the MG I-dominated samples, which calls for further study using pure cultures to determine the exact impact of MG II on GDGT-based proxies.
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Affiliation(s)
- Cenling Ma
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Sarah Coffinet
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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21
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Maruyama H, Prieto EI, Nambu T, Mashimo C, Kashiwagi K, Okinaga T, Atomi H, Takeyasu K. Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis. Front Microbiol 2020; 11:1247. [PMID: 32655523 PMCID: PMC7325993 DOI: 10.3389/fmicb.2020.01247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/15/2020] [Indexed: 12/15/2022] Open
Abstract
Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30–40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa and Rad50 in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Eloise I Prieto
- National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Kosuke Kashiwagi
- Department of Fixed Prosthodontics, Osaka Dental University, Hirakata, Japan
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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22
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Diversity, ecology and evolution of Archaea. Nat Microbiol 2020; 5:887-900. [PMID: 32367054 DOI: 10.1038/s41564-020-0715-z] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/30/2020] [Indexed: 12/23/2022]
Abstract
Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.
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23
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Wang Y, Wang C. Comparative study on archaeal diversity in the sediments of two urban landscape water bodies. PLoS One 2020; 15:e0229097. [PMID: 32069312 PMCID: PMC7028264 DOI: 10.1371/journal.pone.0229097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022] Open
Abstract
Urban lake sediment plays a very important role in waterbody ecosystems. It is the basis of nutrient cycling and material exchange between microorganisms and lake ecosystems. In this study, Illumina high-throughput sequencing technology was employed to detect the structure and species richness of Archaea in anoxic sediments of urban waterbodies (Aohai Lake and Kunming Lake) in Beijing, and the environmental factors (pH level, organic matter, available nitrogen and total nitrogen) affecting the structure and succession of archaeal communities were also investigated. The results showed that there were 13 classified archaeal phyla, and the most frequent archaeal species in the lakes were Bathyarchaeota (MCG), Euryarchaeota, Thaumarchaeota, Aenigmarchaeota, Hadesarchaea, Lokiarchaeota, and Parvarchaeota. The top ten most abundant genera in the two lakes were significantly associated with at least one environmental factor. The results of this study enrich the understanding of microbial diversity in urban eutrophic lake sediments in northern China.
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Affiliation(s)
- Yuxin Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
- * E-mail:
| | - Chaonan Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
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24
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Pinto OHB, Silva TF, Vizzotto CS, Santana RH, Lopes FAC, Silva BS, Thompson FL, Kruger RH. Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. BMC Microbiol 2020; 20:13. [PMID: 31941452 PMCID: PMC6964070 DOI: 10.1186/s12866-020-1698-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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Affiliation(s)
- Otávio H B Pinto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Thais F Silva
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Carla S Vizzotto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.,Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil
| | | | - Fabyano A C Lopes
- Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil
| | - Bruno S Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Ricardo H Kruger
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.
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25
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Thouin H, Battaglia-Brunet F, Norini MP, Joulian C, Hellal J, Le Forestier L, Dupraz S, Gautret P. Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134108. [PMID: 32380607 DOI: 10.1016/j.scitotenv.2019.134108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/30/2019] [Accepted: 08/24/2019] [Indexed: 06/11/2023]
Abstract
The burning of chemical weapons in the 1926-1928 period produced polluted technosols with elevated levels of arsenic, zinc, lead and copper. During an eight-month mesocosm experiment, these soils were submitted to two controlled environmental changes, namely the alternation of dry and water-saturated conditions and the addition of fragmented organic forest litter to the surface soil. We investigated, by sequencing the gene coding 16S rRNA and 18S rRNA, (1) the structure of the prokaryotic and eukaryotic community in this polluted technosol and (2) their response to the simulated environmental changes, in the four distinct layers of the mesocosm. In spite of the high concentrations of toxic elements, microbial diversity was found to be similar to that of non-polluted soils. The bacterial community was dominated by Proteobacteria, Acidobacteria and Bacteroidetes, while the fungal community was dominated by Ascomicota. Amongst the most abundant bacterial Operational Taxonomic Units (OTUs), including Sphingomonas as a major genus, some were common to soil environments in general whereas a few, such as organisms related to Leptospirillum and Acidiferrobacter, seemed to be more specific to the geochemical context. Evolution of the microbial abundance and community structures shed light on modifications induced by water saturation and the addition of forest litter to the soil surface. Co-inertia analysis suggests a relationship between the physico-chemical parameters total organic carbon, Zn, NH4+ and As(III) concentrations and the bacterial community structure. Both these results imply that microbial community dynamics linked to environmental changes should be considered as factors influencing the behavior of toxic elements on former ammunition burning sites.
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Affiliation(s)
- Hugues Thouin
- BRGM, 3 avenue Claude Guillemin, 45060 Orléans, France; Université d'Orléans, CNRS, BRGM, ISTO, UMR 7327, F-45071 Orléans, France.
| | - Fabienne Battaglia-Brunet
- BRGM, 3 avenue Claude Guillemin, 45060 Orléans, France; Université d'Orléans, CNRS, BRGM, ISTO, UMR 7327, F-45071 Orléans, France
| | - Marie-Paule Norini
- Université d'Orléans, CNRS, BRGM, ISTO, UMR 7327, F-45071 Orléans, France
| | | | | | - Lydie Le Forestier
- Université d'Orléans, CNRS, BRGM, ISTO, UMR 7327, F-45071 Orléans, France
| | | | - Pascale Gautret
- Université d'Orléans, CNRS, BRGM, ISTO, UMR 7327, F-45071 Orléans, France
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26
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Zhou A, Weber Y, Chiu BK, Elling FJ, Cobban AB, Pearson A, Leavitt WD. Energy flux controls tetraether lipid cyclization in Sulfolobus acidocaldarius. Environ Microbiol 2019; 22:343-353. [PMID: 31696620 DOI: 10.1111/1462-2920.14851] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
Abstract
Microorganisms regulate the composition of their membranes in response to environmental cues. Many Archaea maintain the fluidity and permeability of their membranes by adjusting the number of cyclic moieties within the cores of their glycerol dibiphytanyl glycerol tetraether (GDGT) lipids. Cyclized GDGTs increase membrane packing and stability, which has been shown to help cells survive shifts in temperature and pH. However, the extent of this cyclization also varies with growth phase and electron acceptor or donor limitation. These observations indicate a relationship between energy metabolism and membrane composition. Here we show that the average degree of GDGT cyclization increases with doubling time in continuous cultures of the thermoacidophile Sulfolobus acidocaldarius (DSM 639). This is consistent with the behavior of a mesoneutrophile, Nitrosopumilus maritimus SCM1. Together, these results demonstrate that archaeal GDGT distributions can shift in response to electron donor flux and energy availability, independent of pH or temperature. Paleoenvironmental reconstructions based on GDGTs thus capture the energy available to microbes, which encompasses fluctuations in temperature and pH, as well as electron donor and acceptor availability. The ability of Archaea to adjust membrane composition and packing may be an important strategy that enables survival during episodes of energy stress.
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Affiliation(s)
- Alice Zhou
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Yuki Weber
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - Beverly K Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Felix J Elling
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - Alec B Cobban
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Ann Pearson
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA.,Department of Chemistry, Dartmouth College, Hanover, New Hampshire, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
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27
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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28
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Lehtovirta-Morley LE. Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together. FEMS Microbiol Lett 2019; 365:4931719. [PMID: 29668934 DOI: 10.1093/femsle/fny058] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022] Open
Abstract
Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 -) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.
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Affiliation(s)
- Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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29
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Mamuad LL, Kim SH, Biswas AA, Yu Z, Cho KK, Kim SB, Lee K, Lee SS. Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation. AMB Express 2019; 9:123. [PMID: 31363877 PMCID: PMC6667549 DOI: 10.1186/s13568-019-0848-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Supplementation of appropriate probiotics can improve the health and productivity of ruminants while mitigating environmental methane production. Hence, this study was conducted to determine the effects of Enterococcus faecium SROD on in vitro rumen fermentation, methane concentration, and microbial population structure. Ruminal samples were collected from ruminally cannulated Holstein–Friesian cattle, and 40:60 rice straw to concentrate ratio was used as substrate. Fresh culture of E. faecium SROD at different inclusion rates (0, 0.1%, 0.5%, and 1.0%) were investigated using in vitro rumen fermentation system. Addition of E. faecium SROD had a significant effect on total gas production with the greatest effect observed with 0.1% supplementation; however, there was no significant influence on pH. Supplementation of 0.1% E. faecium SROD resulted in the highest propionate (P = 0.005) but the lowest methane concentration (P = 0.001). In addition, acetate, butyrate, and total VFA concentrations in treatments were comparatively higher than control. Bioinformatics analysis revealed the predominance of the bacterial phyla Bacteroidetes and Firmicutes and the archaeal phylum Euryarchaeota. At the genus level, Prevotella (15–17%) and Methanobrevibacter (96%) dominated the bacterial and archaeal communities of the in vitro rumen fermenta, respectively. Supplementation of 0.1% E. faecium SROD resulted in the highest quantities of total bacteria and Ruminococcus flavefaciens, whereas 1.0% E. faecium SROD resulted in the highest contents of total fungi and Fibrobacter succinogenes. Overall, supplementation of 0.1% E. faecium SROD significantly increased the propionate and total volatile fatty acids concentrations but decreased the methane concentration while changing the microbial community abundance and composition.
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30
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Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. mSystems 2019; 4:4/4/e00181-19. [PMID: 31239395 PMCID: PMC6593220 DOI: 10.1128/msystems.00181-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms. Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2. However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments. IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.
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Wang S, Zheng X, Xia H, Shi D, Fan J, Wang P, Yan Z. Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing. PLoS One 2019; 14:e0218611. [PMID: 31226149 PMCID: PMC6588238 DOI: 10.1371/journal.pone.0218611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.
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Affiliation(s)
- Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Huijuan Xia
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Di Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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Liu F, Zhang Y, Liang H, Gao D. Specific quorum sensing molecules of ammonia oxidizers and their role during ammonium metabolism in Zhalong wetland, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:1106-1113. [PMID: 30970476 DOI: 10.1016/j.scitotenv.2019.02.261] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/14/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
The primary challenge of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) surviving in wetlands are the rapid and unpredictable environmental changes. To adapt to a fluctuant environment, ammonia oxidizers have to communicate with each other via acyl-homoserine lactones (AHLs). In this study, AOA and AOB in the soil samples taken from Zhalong wetland were incubated. Dynamics of AHLs during the incubation of ammonia oxidizers were measured. Then, the specific AHLs of AOA and AOB were identified, respectively. The results showed that AOA secreted N-butyryl-dl-homoserine lactone (C4-HSL) and N-octanoyl-l-homoserine lactone (C8-HSL) to cope with nitrite accumulation, while they secreted N-(3-oxododecanoyl)-dl-homoserine lactone (OXOC12-HSL) to regulate their ammonium metabolism activity. AOB secreted N-hexanoyl-dl-homoserine lactone (C6-HSL), N-dodecanoyl-l-homoserine lactone (C12-HSL), N-tetradecanoyl-dl-homoserine lactone (C14-HSL) and N-(3-oxododecanoyl)-tetradecanoyl-dl-homoserine lactone (OXOC14-HSL) only to enhance the metabolism activity. The dominant AOA belonged to the Nitrososphaera lineage, while the dominant AOB grouped into the Nitrosomonas lineage. The AHLs receptor homologs were identified in both AOA and AOB, which confirmed that AOA and AOB had the QS system. The present work was the first study that elucidated the QS system of AOA and AOB in multidimensional, and confirmed the role of QS system in ammonia oxidizers' metabolism.
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Affiliation(s)
- Fengqin Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yupeng Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hong Liang
- School of Environment, Harbin Institute of Technology, Harbin, China.
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China; School of Environment, Harbin Institute of Technology, Harbin, China.
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Hernández M, Klose M, Claus P, Bastviken D, Marotta H, Figueiredo V, Enrich‐Prast A, Conrad R. Structure, function and resilience to desiccation of methanogenic microbial communities in temporarily inundated soils of the Amazon rainforest (Cunia Reserve, Rondonia). Environ Microbiol 2019; 21:1702-1717. [DOI: 10.1111/1462-2920.14535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Marcela Hernández
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
| | - David Bastviken
- Department of Thematic Studies ‐ Environmental ChangeLinköping University Linköping Sweden
| | - Humberto Marotta
- Ecosystems and Global Change Laboratory (LEMGUFF)/International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NABUFF), Graduate Program in Geosciences (Environmental Geochemistry), Universidade Federal Fluminense (UFF) Niteroi, Rio de Janeiro Brazil
- Sedimentary and Environmental Processes Laboratory (LAPSA‐UFF), Department of Geography, Graduate Program in GeographyUniversidade Federal Fluminense (UFF) Niteroi, Rio de Janeiro Brazil
| | - Viviane Figueiredo
- Departamento de BotânicaInstituto de Biologia, University Federal do Rio de Janeiro (UFRJ) Rio de Janeiro Brazil
| | - Alex Enrich‐Prast
- Department of Thematic Studies ‐ Environmental ChangeLinköping University Linköping Sweden
- Ecosystems and Global Change Laboratory (LEMGUFF)/International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NABUFF), Graduate Program in Geosciences (Environmental Geochemistry), Universidade Federal Fluminense (UFF) Niteroi, Rio de Janeiro Brazil
- Departamento de BotânicaInstituto de Biologia, University Federal do Rio de Janeiro (UFRJ) Rio de Janeiro Brazil
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
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Tong X, Wang X, He X, Xu K, Mao F. Effects of ofloxacin on nitrogen removal and microbial community structure in constructed wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:503-511. [PMID: 30522033 DOI: 10.1016/j.scitotenv.2018.11.358] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/22/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
Constructed wetlands (CWs) have emerged as a promising technology for the purification of micro-polluted water. However, their nitrogen removal performance can be significantly degraded by design, operational, and environmental factors. The present study investigates the effects of ofloxacin (OFL: 0.1, 10, and 1000 μg L-1) and plants (Cyperus alternifolius L. and Typha angustifolia L.) on nitrogen removal in a micro-polluted CW system over a duration of 12 weeks. The effects were evaluated by investigating NH4-N and NO3-N removal efficiency, nitrification genes (amoA-AOA and amoA-AOB), denitrification genes (nirK and nirS), fungal 18S rRNA gene and microorganism community structure. The results showed that in unplanted CWs, OFL increased the NH4-N removal efficiency (from 72.6% to 80.7-82.1%), the abundances of amoA-AOA, nirS, nirK and fungal 18S rRNA gene, and the bacterial diversity but decreased the abundance of both amoA-AOB and bacterial richness. In contrast, both the nitrogen removal efficiency (83.4-89.5% for NH4-N and 33.8-38.5% for NO3-N) and bacterial diversity/richness were not significantly affected by OFL in planted CWs. In planted systems, OFL increased the relative abundance of Arthrobacter, Pseudomonas, and Enterococcus, which are proven antibiotic-resistant bacteria. This study showed that CWs are able to remove nitrogen from antibiotic-contaminated micro-polluted water, which might primarily be attributed to the presence of plants that protect the microorganism community.
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Affiliation(s)
- Xinnan Tong
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, China
| | - Xinze Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, China.
| | - Xiaojuan He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, China
| | - Kaiqin Xu
- Research Center for Material Cycles and Waste Management, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Feijian Mao
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore117576, Singapore
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Abstract
Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.
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Affiliation(s)
- Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA;
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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Sollai M, Villanueva L, Hopmans EC, Reichart G, Sinninghe Damsté JS. A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. GEOBIOLOGY 2019; 17:91-109. [PMID: 30281902 PMCID: PMC6586073 DOI: 10.1111/gbi.12316] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.
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Affiliation(s)
- Martina Sollai
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Laura Villanueva
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Ellen C. Hopmans
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Gert‐Jan Reichart
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
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Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX. Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox). Appl Environ Microbiol 2018; 84:e01390-18. [PMID: 30315079 PMCID: PMC6275355 DOI: 10.1128/aem.01390-18] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.
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Affiliation(s)
- Fei Xia
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian-Gong Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers. Emerg Top Life Sci 2018; 2:619-628. [PMID: 33525821 DOI: 10.1042/etls20180018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.
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Chow J, Danso D, Ferrer M, Streit WR. The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1. Sci Rep 2018; 8:13823. [PMID: 30218044 PMCID: PMC6138646 DOI: 10.1038/s41598-018-32059-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022] Open
Abstract
Biotin is an essential cofactor required for carboxylation and decarboxylation reactions in all domains of life. While biotin biosynthesis in most Bacteria and Eukarya is well studied, the complete pathway for this vitamer in Archaea is still not known. Detailed genome searches indicated the presence of possible bio gene clusters only in Methanococcales and Thaumarchaeota. Therefore, we analysed the functionality of the predicted genes bioA, bioB, bioD and bioF in the Thaumarchaeon Nitrososphaera gargensis Ga2.9 which are essential for the later steps of biotin synthesis. In complementation tests, the gene cluster-encoded N. gargensis bioABD genes except bioF restored growth of corresponding E. coli Rosetta-gami 2 (DE3) deletion mutants. To find out how biotin biosynthesis is initiated, we searched the genome for a possible bioH analogue encoding a pimeloyl-ACP-methylester carboxylesterase. The respective amino acid sequence of the ORF estN1 showed weak conserved domain similarity to this class of enzymes (e-value 3.70e-42). Remarkably, EstN1 is a promiscuous carboxylesterase that complements E. coli ΔbioH and Mesorhizobium loti ΔbioZ mutants for growth on biotin-free minimal medium. Additional 3D-structural models support the hypothesis that EstN1 is a BioH analogue. Thus, this is the first report providing experimental evidence that Archaea carry functional bio genes.
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Affiliation(s)
- Jennifer Chow
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Dominik Danso
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
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Jung MY, Islam MA, Gwak JH, Kim JG, Rhee SK. Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil. Int J Syst Evol Microbiol 2018; 68:3084-3095. [PMID: 30124400 DOI: 10.1099/ijsem.0.002926] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, chemolithoautotrophic, neutrophilic and aerobic ammonia-oxidizing archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3-0.5 µm and length of 0.6-1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically oxidizing ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2-0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceaeof the phylum Thaumarchaeota, sharing the highest 16S rRNA gene sequence similarity (96.6-97.1 %) with marine isolates of the genus Nitrosopumilus. The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).
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Affiliation(s)
- Man-Young Jung
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea.,2Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Md Arafat Islam
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Jong-Geol Kim
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Sung-Keun Rhee
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
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Zhang X, Hu BX, Ren H, Zhang J. Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:518-528. [PMID: 29579663 DOI: 10.1016/j.scitotenv.2018.03.158] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 05/25/2023]
Abstract
The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity.
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Affiliation(s)
- Xiaoying Zhang
- Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; Department of Ecology, Jinan University, 510632 Guangzhou, China.
| | - Bill X Hu
- Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; School of Water Resources and Environment, China University of Geosciences (Beijing), 100083 Beijing, China.
| | - Hejun Ren
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of Environment and Resources, Jilin University, 130021 Changchun, China
| | - Jin Zhang
- Institute of Urban Water Management, Technische Universität Dresden, 01062 Dresden, Germany
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43
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Temporal and spatial distribution of ammonia-oxidizing organisms of two types of wetlands in Northeast China. Appl Microbiol Biotechnol 2018; 102:7195-7205. [DOI: 10.1007/s00253-018-9152-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
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44
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Li Y, Jing H, Xia X, Cheung S, Suzuki K, Liu H. Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean. Front Microbiol 2018; 9:623. [PMID: 29670596 PMCID: PMC5894113 DOI: 10.3389/fmicb.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/19/2018] [Indexed: 01/05/2023] Open
Abstract
The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP.
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Affiliation(s)
- Yingdong Li
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xiaomin Xia
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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Da Cunha V, Gaia M, Nasir A, Forterre P. Asgard archaea do not close the debate about the universal tree of life topology. PLoS Genet 2018; 14:e1007215. [PMID: 29596428 PMCID: PMC5875737 DOI: 10.1371/journal.pgen.1007215] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/22/2018] [Indexed: 11/24/2022] Open
Affiliation(s)
- Violette Da Cunha
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Morgan Gaia
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Paris, France
| | - Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Patrick Forterre
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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46
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Zhang ST, Song XN, Li N, Zhang K, Liu GS, Li XD, Wang ZZ, He XB, Wang GF, Shao HF. Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation. Res Microbiol 2018; 169:115-126. [PMID: 29122672 DOI: 10.1016/j.resmic.2017.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 11/17/2022]
Abstract
Soil microorganisms play a crucial role in cycling soil nutrients and providing organic nutrients for plant growth and development. Fertilisation balances soil fertility and quality, and affects soil microbial communities. Fertilisation is a frontier subject in agricultural and environmental sciences. Here we showed that the application of high-carbon basal fertiliser treatment could improve the tobacco yield and quality when compared to chemical fertiliser, high-carbon basal fertiliser and mixed high-carbon chemical fertiliser. The potential reason is that different fertiliser treatments influence soil fertility, such as nitrogen, phosphorus, and other contents, besides soil organic matter. Further experiments revealed that populations of bacteria, fungi and actinomycetes fluctuated during tobacco development under different fertilisation treatments. Then we performed high-throughput sequencing of the 16S rRNA gene, and the results showed that the fertilisation treatments had significant effects on the microbial community, particularly within the finer taxonomic divisions or non-dominant taxa. Moreover, proteobacteria and fungal genera had significantly different relative abundances during tobacco growth under various tobacco developmental stages and fertilisation treatments. These results indicated that mixed high-carbon chemical fertiliser could improve soil fertility by influencing the soil microorganism, and that the fertilisation treatments impacted on the structure and composition of the microbial community, and especially the diversity of non-dominant taxa. However, more studies are needed to confirm their reliability.
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Affiliation(s)
- Song-Tao Zhang
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou 450002, China.
| | - Xiao-Ning Song
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou 450002, China
| | - Ning Li
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou 450002, China
| | - Ke Zhang
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou 450002, China
| | - Guo-Shun Liu
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou 450002, China
| | - Xue-Dong Li
- China Tobacco Chongqing Industrial Corporation, Chongqing 400000, China
| | - Zhi-Zhong Wang
- Wuyang County Tobacco Branch of Luohe Tobacco Company, Luohe 462000, China
| | - Xiao-Bing He
- China Tobacco Chongqing Industrial Corporation, Chongqing 400000, China
| | - Guo-Feng Wang
- Wuyang County Tobacco Branch of Luohe Tobacco Company, Luohe 462000, China
| | - Hui-Fang Shao
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou 450002, China.
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Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. Front Microbiol 2018; 9:28. [PMID: 29434576 PMCID: PMC5797428 DOI: 10.3389/fmicb.2018.00028] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.
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Affiliation(s)
- Sophie S Abby
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Centre National de la Recherche Scientifique, Université Grenoble Alpes, Grenoble, France
| | - Michael Melcher
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Michaela Stieglmeier
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Claudia Rossel
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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48
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Southern Ocean warming and Wilkes Land ice sheet retreat during the mid-Miocene. Nat Commun 2018; 9:317. [PMID: 29358604 PMCID: PMC5778126 DOI: 10.1038/s41467-017-02609-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/13/2017] [Indexed: 01/20/2023] Open
Abstract
Observations and model experiments highlight the importance of ocean heat in forcing ice sheet retreat during the present and geological past, but past ocean temperature data are virtually missing in ice sheet proximal locations. Here we document paleoceanographic conditions and the (in)stability of the Wilkes Land subglacial basin (East Antarctica) during the mid-Miocene (~17-13.4 million years ago) by studying sediment cores from offshore Adélie Coast. Inland retreat of the ice sheet, temperate vegetation, and warm oligotrophic waters characterise the mid-Miocene Climatic Optimum (MCO; 17-14.8 Ma). After the MCO, expansion of a marine-based ice sheet occurs, but remains sensitive to melting upon episodic warm water incursions. Our results suggest that the mid-Miocene latitudinal temperature gradient across the Southern Ocean never resembled that of the present day. We demonstrate that a strong coupling of oceanic climate and Antarctic continental conditions existed and that the East Antarctic subglacial basins were highly sensitive to ocean warming.
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49
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50
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Rodrigues-Oliveira T, Belmok A, Vasconcellos D, Schuster B, Kyaw CM. Archaeal S-Layers: Overview and Current State of the Art. Front Microbiol 2017; 8:2597. [PMID: 29312266 PMCID: PMC5744192 DOI: 10.3389/fmicb.2017.02597] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 01/01/2023] Open
Abstract
In contrast to bacteria, all archaea possess cell walls lacking peptidoglycan and a number of different cell envelope components have also been described. A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. S-layers are composed of only one or two proteins and form different lattice structures. In this review, we summarize current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. The hexagonal lattice type is dominant within the phylum Euryarchaeota, while in the Crenarchaeota this feature is mainly associated with specific orders. S-layers exclusive to the Crenarchaeota have also been described, which are composed of two proteins. Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. Despite the numerous applied studies using bacterial S-layers, few reports have employed archaea as a study model. As such, archaeal S-layers represent an area for exploration in both basic and applied research.
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Affiliation(s)
- Thiago Rodrigues-Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Aline Belmok
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Deborah Vasconcellos
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Bernhard Schuster
- Department of NanoBiotechnology, Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cynthia M. Kyaw
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
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