101
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Gao ZM, Huang JM, Cui GJ, Li WL, Li J, Wei ZF, Chen J, Xin YZ, Cai DS, Zhang AQ, Wang Y. In situ meta-omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench. Environ Microbiol 2019; 21:4092-4108. [PMID: 31344308 DOI: 10.1111/1462-2920.14759] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 07/06/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023]
Abstract
The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles.
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Affiliation(s)
- Zhao-Ming Gao
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Jiao-Mei Huang
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Guo-Jie Cui
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wen-Li Li
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Li
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Zhan-Fei Wei
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Chen
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yong-Zhi Xin
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Du-Si Cai
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Ai-Qun Zhang
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Yong Wang
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
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102
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Sánchez-Quinto A, Falcón LI. Metagenome of Acropora palmata coral rubble: Potential metabolic pathways and diversity in the reef ecosystem. PLoS One 2019; 14:e0220117. [PMID: 31394568 PMCID: PMC6687439 DOI: 10.1371/journal.pone.0220117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/09/2019] [Indexed: 01/24/2023] Open
Abstract
Over the past 30 years, the stony coral Acropora palmata has experienced an excessive loss of individuals showing few signs of recovery throughout the Mexican Caribbean, resulting in long stretches of coral rubble structures. When the coral dies, the skeleton begins to be colonized by algae, sponges, virus, bacteria and other microorganisms, forming a new community. Here we analyze, using a metagenomic approach, the diversity and biogeochemical cycles associated to coral rubble in La Bocana (Puerto Morelos, QRoo, Mexico). This study provides the first broad characterization of coral rubble associated communities and their role in biogeochemical cycling, suggesting a potential view of a world where coral reefs are no longer dominated by corals.
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Affiliation(s)
- Andrés Sánchez-Quinto
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, UNAM, Ciudad de México, México
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, UNAM, CDMX, México
| | - Luisa I. Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, UNAM, CDMX, México
- * E-mail:
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103
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Analysis of Soil Properties, Bacterial Community Composition, and Metabolic Diversity in Fluvisols of a Floodplain Area. SUSTAINABILITY 2019. [DOI: 10.3390/su11143929] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The quality of a soil environment affects the microbial community that inhabits it. We decided to examine whether soils formed from river sediments, located in an area of high biodiversity of organisms, are fertile and microbiologically diverse. Fluvisols are considered to be one of the most fertile soils. In this research, bacterial and metabolic diversity, as well as physico–chemical parameters, in three Fluvisols from the Vistula River Gorge of Lesser Poland was investigated. The analysis of physico–chemical and biological parameters demonstrated statistically significant differences between the three Fluvisols examined. While determining the metabolic potential of soil microbiomes with the use of the EcoPlate™ Biolog® technique, we also noted variation between the Fluvisols; however, they were arranged in a significantly different manner from other properties. The next generation sequencing method enabled us to determine the microorganisms common to three Fluvisols, and we identified bacteria specific to individual soils. These results corresponded with the data obtained through EcoPlate™, indicating that the structural diversity and metabolic potential of the microbiome does not always depend on soil quality parameters. Meanwhile, the increased structural diversity of the microbiome was found to improve the metabolic potential of soil microorganisms.
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104
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Zhang H, Sun H, Zhou S, Bai N, Zheng X, Li S, Zhang J, Lv W. Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems. Sci Rep 2019; 9:9367. [PMID: 31249385 PMCID: PMC6597706 DOI: 10.1038/s41598-019-45877-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/11/2019] [Indexed: 01/27/2023] Open
Abstract
Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.
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Affiliation(s)
- Hanlin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Huifeng Sun
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Sheng Zhou
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Naling Bai
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Xianqing Zheng
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Shuangxi Li
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Juanqin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Weiguang Lv
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China. .,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China. .,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China. .,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China.
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105
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Nitrifier abundance and diversity peak at deep redox transition zones. Sci Rep 2019; 9:8633. [PMID: 31201353 PMCID: PMC6572806 DOI: 10.1038/s41598-019-44585-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/17/2019] [Indexed: 11/08/2022] Open
Abstract
More than half of the global ocean floor is draped by nutrient-starved sediments characterized by deep oxygen penetration and a prevalence of oxidized nitrogen. Despite low energy availability, this habitat hosts a vast microbial population, and geochemical characteristics suggest that nitrogen compounds are an energy source critical to sustaining this biomass. However, metabolic rates of nitrogen transformation and their link to microbial survival in this global-scale ecosystem remain virtually unknown. Here we provide quantitative constraints on microbial nitrogen cycling in open ocean oligotrophic sediments from seafloor to basement, spanning approximately 8 million years. We find active microbial nitrogen transformation throughout the sediment column but at very low rates. Local peaks in diversity and abundance of nitrifiers and denitrifiers occur at redox transition zones deep within the sediments, strongly indicating that these microbes are revived from their maintenance state and start growing again after millions of years of attrition.
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106
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Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A. Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes (Basel) 2019; 10:E424. [PMID: 31163637 PMCID: PMC6627896 DOI: 10.3390/genes10060424] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe-plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant-growth-promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.
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Affiliation(s)
- Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Christian Henke
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Timo Wentong Lin
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Wiebke Pätzold
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Sebastian Jaenicke
- Justus-Liebig-University Gießen, Bioinformatics & Systems Biology, Heinrich-Buff-Ring 58, 35392 Gießen, Germany.
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ) Großbeeren/Erfurt eV, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
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107
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Vuillemin A, Wankel SD, Coskun ÖK, Magritsch T, Vargas S, Estes ER, Spivack AJ, Smith DC, Pockalny R, Murray RW, D’Hondt S, Orsi WD. Archaea dominate oxic subseafloor communities over multimillion-year time scales. SCIENCE ADVANCES 2019; 5:eaaw4108. [PMID: 31223656 PMCID: PMC6584578 DOI: 10.1126/sciadv.aaw4108] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/10/2019] [Indexed: 05/31/2023]
Abstract
Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Scott D. Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ömer K. Coskun
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Tobias Magritsch
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Emily R. Estes
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Arthur J. Spivack
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - David C. Smith
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Robert Pockalny
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Richard W. Murray
- Department of Earth and Environment, Boston University, Boston, MA 02215, USA
| | - Steven D’Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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108
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Grießmeier V, Leberecht K, Gescher J. NO 3 - removal efficiency in field denitrification beds: key controlling factors and main implications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:316-329. [PMID: 30977281 DOI: 10.1111/1758-2229.12758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Nitrate pollution is a growing environmental threat that affects both ground- and surface-water. The typically used technique for nitrate elimination in wastewater treatment plants cannot be applied for all water streams as it necessitates a highly developed technical infrastructure. Field denitrification beds comprise one strategy to treat surface water containing high nitrate loads, which typically is due to the increasing agricultural land use. Here, the water passes through a basin containing a cheap carbon material as electron donor that provides the environmental niche for a complex microbial biocenosis. The microorganisms catalyse the hydrolysis of the polymeric organic carbon substrate and a variety of fermentative and respiratory pathways that are in the end supposed to lead to an efficient denitrification process. This review article integrates our current knowledge on environmental and operating parameters of and within denitrification beds including biotic and abiotic factors influencing the nitrate removal efficiency. Steering of these two factors can allow to minimise pollution swapping and the formation of greenhouse gases.
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Affiliation(s)
- Victoria Grießmeier
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Kerstin Leberecht
- Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Johannes Gescher
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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109
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Lau E, Frame CH, Nolan EJ, Stewart FJ, Dillard ZW, Lukich DP, Mihalik NE, Yauch KE, Kinker MA, Waychoff SL. Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone. PLoS One 2019; 14:e0217136. [PMID: 31112557 PMCID: PMC6529010 DOI: 10.1371/journal.pone.0217136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2-) and NO2- to nitrate (NO3-), plays a vital role in ocean nitrogen cycling. Characterizing the distribution of nitrifying organisms over environmental gradients can help predict how nitrogen availability may change with shifting ocean conditions, for example, due to loss of dissolved oxygen (O2). We characterized the distribution of nitrifiers at 5 depths spanning the oxic to hypoxic zone of the offshore Benguela upwelling system above the continental slope off Namibia. Based on 16S rRNA gene amplicon sequencing, the proportional abundance of nitrifiers (ammonia and nitrite oxidizers) increased with depth, driven by an increase in ammonia-oxidizing archaea (AOA; Thaumarchaeota) to up to 33% of the community at hypoxic depths where O2 concentrations fell to ~25 μM. The AOA community transitioned from being dominated by a few members at oxic depths to a more even representation of taxa in the hypoxic zone. In comparison, the community of NO2--oxidizing bacteria (NOB), composed primarily of Nitrospinae, was far less abundant and exhibited higher evenness at all depths. The AOA:NOB ratio declined with depth from 41:1 in the oxic zone to 27:1 under hypoxia, suggesting potential variation in the balance between NO2- production and consumption via nitrification. Indeed, in contrast to prior observations from more O2-depleted sites closer to shore, NO2- did not accumulate at hypoxic depths near this offshore site, potentially due in part to a tightened coupling between AOA and NOB.
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Affiliation(s)
- Evan Lau
- Department of Biology, Menlo College, Atherton, California, United States of America
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
- * E-mail:
| | - Caitlin H. Frame
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - E. Joseph Nolan
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zachary W. Dillard
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Daniel P. Lukich
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Nicole E. Mihalik
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Katelyn E. Yauch
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Marcus A. Kinker
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Samantha L. Waychoff
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
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110
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Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol. Appl Environ Microbiol 2019; 85:AEM.02957-18. [PMID: 30952661 DOI: 10.1128/aem.02957-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/19/2019] [Indexed: 11/20/2022] Open
Abstract
The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO2 emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO2 production.
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111
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Miranda ARL, Mendes LW, Lemos LN, Antunes JEL, Amorim MR, Melo VMM, de Melo WJ, Van den Brink PJ, Araujo ASF. Dynamics of archaeal community in soil with application of composted tannery sludge. Sci Rep 2019; 9:7347. [PMID: 31089146 PMCID: PMC6517401 DOI: 10.1038/s41598-019-43478-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Application of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7th year by using different rates (0, 2.5, 5, 10 and 20 ton ha−1). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.
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Affiliation(s)
- Ana Roberta Lima Miranda
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil.
| | | | | | - Jadson Emanuel Lopes Antunes
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | - Marineide Rodrigues Amorim
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | | | - Wanderley Jose de Melo
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Path of Access Prof. Paulo Donato Castellane, Km 5, Postal Code: 14884-900, Jaboticabal, SP, Brazil.,University of Brazil: University campus Descalvado - Hilário da Silva Passos Avenue, 950 - University park, Descalvado, SP, Brazil
| | - Paul J Van den Brink
- Wageningen University, Aquatic Ecology and Water Quality Management Group, P.O. Box 47, 6700 AA, Wageningen, The Netherlands.,Wageningen Environmental Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
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112
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Potts LD, Perez Calderon LJ, Gubry-Rangin C, Witte U, Anderson JA. Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations. MARINE POLLUTION BULLETIN 2019; 142:169-177. [PMID: 31232291 DOI: 10.1016/j.marpolbul.2019.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/03/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.
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Affiliation(s)
- Lloyd D Potts
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom.
| | - Luis J Perez Calderon
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
| | - Cecile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ursula Witte
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - James A Anderson
- Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
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113
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Jensen EL, Clement R, Kosta A, Maberly SC, Gontero B. A new widespread subclass of carbonic anhydrase in marine phytoplankton. ISME JOURNAL 2019; 13:2094-2106. [PMID: 31024153 PMCID: PMC6776030 DOI: 10.1038/s41396-019-0426-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/28/2019] [Accepted: 03/30/2019] [Indexed: 11/09/2022]
Abstract
Most aquatic photoautotrophs depend on CO2-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO2, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn2+ to Zn2+ as a cofactor, which is potentially of ecological relevance since Mn2+ is more abundant than Zn2+ in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO2. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.
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Affiliation(s)
- Erik L Jensen
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, FR3479, 31 Chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Romain Clement
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, FR3479, 31 Chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Artemis Kosta
- Microscopy Core Facility, Aix Marseille Univ, CNRS, IMM, FR3479, 31 Chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Stephen C Maberly
- Lake Ecosystems Group, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, FR3479, 31 Chemin J. Aiguier, 13402, Marseille Cedex 20, France.
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114
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Remarkable N 2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities. Sci Rep 2019; 9:2550. [PMID: 30796347 PMCID: PMC6384938 DOI: 10.1038/s41598-019-39465-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/23/2019] [Indexed: 11/08/2022] Open
Abstract
Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N2O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N2O concentrations in the soil and N2O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N2O concentrations in the soil and N2O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N2O net production and emissions after draining. Moreover, we observed that N2O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH4+-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N2O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N2O emissions as shorter distance of gas diffusion to the soil surface.
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115
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Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria. mSphere 2019; 4:4/1/e00043-19. [PMID: 30787117 PMCID: PMC6382968 DOI: 10.1128/msphere.00043-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with “live rocks” through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment. Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate the hypotheses that newly established aquaria show clear microbial successional patterns over time and that common marine aquarium-conditioning practices, such as the addition of ocean-derived “live rocks” (defined as any “dead coral skeleton covered with crustose coralline algae” transferred into an aquarium from open ocean habitats) impact the diversity of microbial populations as well as nitrogen cycling in aquaria. We collected water chemistry data alongside water and sediment samples from two independent and newly established saltwater aquaria over a 3-month period. Microbial communities in samples were assessed by DNA extraction, amplification of the 16S rRNA gene, and Illumina MiSeq sequencing. Our results showed clear and replicable patterns of community succession in both aquaria, with the existence of multiple stable states for aquarium microbial assemblages. Notably, our results show that changes in aquarium microbial communities do not always correlate with water chemistry measurements and that operational taxonomic unit (OTU)-level patterns relevant to nitrogen cycling were not reported as statistically significant. Overall, our results demonstrate that aquarium perturbations have a substantial impact on microbial community profiles of aquarium water and sediment and that the addition of live rocks improves nutrient cycling by shifting aquarium communities toward a more typical saltwater assemblage of microbial taxa. IMPORTANCE Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with “live rocks” through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment.
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116
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Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, Tang C, Franks AE, Jin J, Liu X, Wang G. Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China. Front Microbiol 2019; 10:23. [PMID: 30740093 PMCID: PMC6355713 DOI: 10.3389/fmicb.2019.00023] [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: 09/04/2018] [Accepted: 01/09/2019] [Indexed: 11/18/2022] Open
Abstract
Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 107 to 26.18 × 107 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions.
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Affiliation(s)
- Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia.,Research Centre for Future Landscapes, La Trobe University, Melbourne, VIC, Australia
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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117
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Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows. BMC Vet Res 2019; 15:7. [PMID: 30606162 PMCID: PMC6318914 DOI: 10.1186/s12917-018-1745-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
Background Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows’ production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows. Results HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment. Conclusions HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine’s function in dairy cows and provided new strategies to improve dairy cows’ health under high-concentrate feeding regime. Electronic supplementary material The online version of this article (10.1186/s12917-018-1745-0) contains supplementary material, which is available to authorized users.
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118
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The human archaeome: methodological pitfalls and knowledge gaps. Emerg Top Life Sci 2018; 2:469-482. [PMID: 33525835 DOI: 10.1042/etls20180037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023]
Abstract
Forty years ago, archaea were described as a separate domain of life, distinct from bacteria and eukarya. Although it is known for quite a long time that methanogenic archaea are substantial components of the human gastrointestinal tract (GIT) and the oral cavity, the knowledge on the human archaeome is very limited. Various methodological problems contribute to the invisibility of the human archaeome, resulting in severe knowledge gaps and contradictory information. Similar to the bacteriome, the archaeal biogeography was found to be site-specific, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT landscape, (iii) a mixed skin/GIT landscape in nose, and (iv) a woesearchaeal lung landscape, including numerous unknown archaeal clades. Compared with so-called universal microbiome approaches, archaea-specific protocols reveal a wide diversity and high quantity of archaeal signatures in various human tissues, with up to 1 : 1 ratios of bacteria and archaea in appendix and nose samples. The archaeome interacts closely with the bacteriome and the human body cells, whereas the roles of the human-associated archaea with respect to human health are only sparsely described. Methanogenic archaea and methane production were correlated with many health issues, including constipation, periodontitis and multiple sclerosis. However, one of the most burning questions - do archaeal pathogens exist? - still remains obscure to date.
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119
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Hao Y, Zhao L, Sun Y, Li X, Weng L, Xu H, Li Y. Enhancement effect of earthworm (Eisenia fetida) on acetochlor biodegradation in soil and possible mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:728-737. [PMID: 30029172 DOI: 10.1016/j.envpol.2018.07.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Acetochlor is a widely used chloroacetanilide herbicide and has posed environmental risks in soil and water due to its toxicity and high leaching capacity. Earthworm represents the dominant invertebrate in soil and can promote the decomposition of organic pollutants. The effect of earthworm on acetochlor degradation in soil was studied by soil column experiment with or without acetochlor and earthworm in sterile and natural soils. The degradation capacities of drilosphere components to acetochlor were investigated by microcosm experiments. Bacterial and fungal acetochlor degraders stimulated by earthworm were identified by high-throughput sequencing. The degradation kinetics of acetochlor suggested that both indigenous microorganisms and earthworm played important roles in acetochlor degradation. Acetochlor degradation was quicker in soil with earthworms than without earthworms, with the degradation rates increased by 62.3 ± 15.2% and 9.7 ± 1.7% in sterile and natural treatments respectively. The result was related to the neutralized pH, higher enzyme activities and enhanced soil microbial community diversity and richness in the presence of earthworms. Earthworm cast was the degradation hotpot in drilosphere and exhibited better anaerobic degradation capacity in microcosm experiments. The acetochlor degradation rate of cast in anaerobic environment was 12.0 ± 0.1% quicker than that in aerobic environment. Residual acetochlor in soil conferred a long-term impairment on fungal community, and this inhibition could be repaired by earthworm. Earthworm stimulated indigenous degraders like Sphingomonas and Microascales and carried suspected intestinal degraders like Mortierella and Escherichia_coli to degradation process. Cometabolism between nutrition cycle species and degraders in casts also contributed to its faster degradation rates. The study also presented some possible anaerobic degradation species like Rhodococcus, Pseudomonas_fulva and Methylobacillus.
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Affiliation(s)
- Yueqi Hao
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Tianjin 300191, China
| | - Lixia Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Tianjin 300191, China.
| | - Yang Sun
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Tianjin 300191, China
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Tianjin 300191, China
| | - Liping Weng
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Tianjin 300191, China
| | - Huijuan Xu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yongtao Li
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Tianjin 300191, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Kimble JC, Winter AS, Spilde MN, Sinsabaugh RL, Northup DE. A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA. FEMS Microbiol Ecol 2018; 94:5079639. [PMID: 30165514 PMCID: PMC6669814 DOI: 10.1093/femsec/fiy173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/23/2018] [Indexed: 01/03/2023] Open
Abstract
Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected. We hypothesized that within FMD samples we would find the presence of microbial N cycling genes and taxonomy related to N cycling microorganisms. Community DNA were sequenced using Illumina shotgun metagenomics and 16S rRNA gene sequencing. Results suggest a diverse N cycle encompassing several energetic pathways including nitrification, dissimilatory nitrate reduction and denitrification. N cycling genes associated with assimilatory nitrate reduction were also identified. Functional gene sequences and taxonomic findings suggest several bacterial and archaeal phyla potentially play a role in nitrification pathways in FSC and FMD. Thaumarchaeota, a deep-branching archaeal division, likely play an essential and possibly dominant role in the oxidation of ammonia. Our results provide genomic evidence for understanding how microbes are potentially able to acquire and cycle N in a low-nutrient subterranean environment.
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Affiliation(s)
- Jason C Kimble
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Ara S Winter
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael N Spilde
- Institute of Meteoritics, MSC03-2050, University of New Mexico, Albuquerque, NM 87131, USA
| | - Robert L Sinsabaugh
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Diana E Northup
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
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121
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Tao J, Bai T, Xiao R, Wang P, Wang F, Duryee AM, Wang Y, Zhang Y, Hu S. Vertical distribution of ammonia-oxidizing microorganisms across a soil profile of the Chinese Loess Plateau and their responses to nitrogen inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 635:240-248. [PMID: 29665543 DOI: 10.1016/j.scitotenv.2018.04.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/01/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) oxidize ammonia into nitrite, the first and rate-limiting step of microbial nitrification, and exert major controls over soil nitrogen transformations. The Loess Plateau in northwest China is characterized with deep soils that are often exposed to the surface and reactive nitrogen (N) inputs due to erosion and human removal of the surface soil. However, few have examined the distribution of AOA and AOB along the profile of Loess Plateau soils and their responses to N inputs. We examined the abundance and diversity of AOA and AOB along the soil profile (0-100cm) and their responses to two levels of N inputs (low at 10, and high at 100μgNg-1 soil) in a 55-d incubation experiment. While AOB were most numerous in the surface soil (0-20cm), AOA were most abundant in the subsoils (20-40 and 40-60cm), suggesting a niche differentiation between AOA and AOB along the soil profile. High N input increased AOB nearly ten-fold in the upper two layers of soils (0-20 and 20-40cm) and sixteen to twenty-five fold in the deeper soil layers (40-60, 60-80 and 80-100cm). However, it only increased AOA by 7% (40-60cm) to 48% (20-40cm). In addition, potential nitrification rate and N2O emissions correlated only with AOB. Finally, high N input significantly increased AOB diversity and led to nitrite accumulation in deep soil layers (60-80 and 80-100cm). Together, our results showed that high N input can significantly alter the diversity and function of ammonia-oxidizing microbes in the deep soil of Loess Plateau, suggesting the need to examine the generality of the observed changes and their potential environmental impacts.
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Affiliation(s)
- Jinjin Tao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongshuo Bai
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Xiao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fuwei Wang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Alexander M Duryee
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Yi Wang
- State Key Laboratory of Loess and Quaternary, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Yi Zhang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shuijin Hu
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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122
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Deignan LK, Pawlik JR, Erwin PM. Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata. MICROBIAL ECOLOGY 2018; 76:459-466. [PMID: 29299617 DOI: 10.1007/s00248-017-1135-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
The brown tube sponge Agelas tubulata (cf. Agelas conifera) is an abundant and long-lived sponge on Caribbean reefs. Recently, a disease-like condition, Agelas wasting syndrome (AWS), was described from A. tubulata in the Florida Keys, where prevalence of the syndrome increased from 7 to 35% of the sponge population between 2010 and 2015. In this study, we characterized the prokaryotic symbiont community of A. tubulata for the first time from individuals collected within the same monitoring plots where AWS was described. We also sampled tissue from A. tubulata exhibiting symptoms of AWS to determine its effect on the diversity and structure of prokaryotic symbiont communities. Bacteria from the phyla Chloroflexi and Proteobacteria, particularly the class Gammaproteobacteria, dominated the sponge microbiome in tissue samples of both healthy sponges and those exhibiting AWS. Prokaryotic community structure differed significantly between the diseased and healthy sponge samples, with greater variability among communities in diseased samples compared to healthy samples. These differences in prokaryotic community structure included a shift in relative abundance of the dominant, ammonia-oxidizing (Thaumarchaeota) symbionts present in diseased and healthy sponge samples. Further research is required to determine the functional consequences of this shift in microbial community structure and the causal relationship of dysbiosis and sponge disease in A. tubulata.
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Affiliation(s)
- Lindsey K Deignan
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Joseph R Pawlik
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA.
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123
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Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832. [PMID: 30026532 PMCID: PMC6053391 DOI: 10.1038/s41467-018-05284-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.
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Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yi-Rui Yin
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China. .,College of Fisheries, Henan Normal University, 453007, Xinxiang, China.
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124
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in ‘t Zandt MH, de Jong AEE, Slomp CP, Jetten MSM. The hunt for the most-wanted chemolithoautotrophic spookmicrobes. FEMS Microbiol Ecol 2018; 94:4966976. [PMID: 29873717 PMCID: PMC5989612 DOI: 10.1093/femsec/fiy064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.
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Affiliation(s)
- Michiel H in ‘t Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Anniek EE de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Department of Earth Sciences, Geochemistry, Utrecht University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
| | - Mike SM Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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125
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Gerrity D, Arnold M, Dickenson E, Moser D, Sackett JD, Wert EC. Microbial community characterization of ozone-biofiltration systems in drinking water and potable reuse applications. WATER RESEARCH 2018; 135:207-219. [PMID: 29477059 DOI: 10.1016/j.watres.2018.02.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 05/16/2023]
Abstract
Microbial community structure in the ozone-biofiltration systems of two drinking water and two wastewater treatment facilities was characterized using 16S rRNA gene sequencing. Collectively, these datasets enabled comparisons by facility, water type (drinking water, wastewater), pre-oxidation (ozonation, chlorination), media type (anthracite, activated carbon), media depth, and backwash dynamics. Proteobacteria was the most abundant phylum in drinking water filters, whereas Bacteroidetes, Chloroflexi, Firmicutes, and Planctomycetes were differentially abundant in wastewater filters. A positive correlation was observed between media depth and relative abundance of Cyanobacteria in drinking water filters, but there was only a slight increase in one alpha diversity metric with depth in the wastewater filters. Media type had a significant effect on beta but not alpha diversity in drinking water and wastewater filters. Pre-ozonation caused a significant decrease in alpha diversity in the wastewater filters, but the effect on beta diversity was not statistically significant. An evaluation of backwash dynamics resulted in two notable observations: (1) endosymbionts such as Neochlamydia and Legionella increased in relative abundance following backwashing and (2) nitrogen-fixing Bradyrhizobium dominated the microbial community in wastewater filters operated with infrequent backwashing. Bradyrhizobium is known to generate extracellular polymeric substances (EPS), which may adversely impact biofilter performance and effluent water quality. These findings have important implications for public health and the operation and resiliency of biofiltration systems.
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Affiliation(s)
- Daniel Gerrity
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, Box 454015, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4015, United States.
| | - Mayara Arnold
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, Box 454015, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4015, United States
| | - Eric Dickenson
- Applied Research and Development Center, Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, United States
| | - Duane Moser
- Desert Research Institute, 755 E. Flamingo Rd. Las Vegas, NV 89119, United States
| | - Joshua D Sackett
- Desert Research Institute, 755 E. Flamingo Rd. Las Vegas, NV 89119, United States; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4015, United States
| | - Eric C Wert
- Applied Research and Development Center, Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, United States
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126
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Restrepo-Ortiz CX, Merbt SN, Barrero-Canossa J, Fuchs BM, Casamayor EO. Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives. Syst Appl Microbiol 2018; 41:408-413. [PMID: 29747878 DOI: 10.1016/j.syapm.2018.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/10/2018] [Accepted: 04/18/2018] [Indexed: 11/16/2022]
Abstract
The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra and its relatives in natural environments.
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Affiliation(s)
- C X Restrepo-Ortiz
- Center of Advanced Studies of Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, Blanes, Spain
| | - S N Merbt
- Center of Advanced Studies of Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, Blanes, Spain
| | - J Barrero-Canossa
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany
| | - B M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany
| | - E O Casamayor
- Center of Advanced Studies of Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, Blanes, Spain.
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127
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Zhai Y, Li X, Wang T, Wang B, Li C, Zeng G. A review on airborne microorganisms in particulate matters: Composition, characteristics and influence factors. ENVIRONMENT INTERNATIONAL 2018; 113:74-90. [PMID: 29421410 DOI: 10.1016/j.envint.2018.01.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/08/2018] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Airborne microorganisms (AM), vital components of particulate matters (PM), are widespread in the atmosphere. Since some AM have pathogenicity, they can lead to a wide range of diseases in human and other organisms, meanwhile, some AM act as cloud condensation nuclei and ice nuclei which let them can affect the climate. The inherent characteristics of AM play critical roles in many aspects which, in turn, can decide microbial traits. The uncertain factors bring various influences on AM, which make it difficult to elaborate effect trends as whole. Because of the potential roles of AM in environment and potent effects of factors on AM, detailed knowledge of them is of primary significance. This review highlights the issues of composition and characteristics of AM with size-distribution, species diversity, variation and so on, and summarizes the main factors which affect airborne microbial features. This general information is a knowledge base for further thorough researches of AM and relevant aspects. Besides, current knowledge gaps and new perspectives are offered to roundly understand the impacts and application of AM in nature and human health.
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Affiliation(s)
- Yunbo Zhai
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China.
| | - Xue Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Tengfei Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Bei Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Caiting Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
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128
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Castelle CJ, Banfield JF. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell 2018. [DOI: 10.1016/j.cell.2018.02.016] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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129
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Liu Y, Ma S, Huang L, Wang S, Liu G, Yang H, Zheng D, Cheng J, Xu Z, Deng L. Two-step heating mode with the same energy consumption as conventional heating for enhancing methane production during anaerobic digestion of swine wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 209:301-307. [PMID: 29306839 DOI: 10.1016/j.jenvman.2017.12.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/26/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
With high percentage of washing water, swine wastewater is characterized by large volume and low concentration of total solids. Thus, in treating swine wastewater, it is relatively difficult to heat digesters, resulting in low methane production at low ambient temperatures (ATs). To increase methane production from swine wastewater, this study proposed a novel "two-step heating (TSH)" mode with the same energy consumption as a one-step process for anaerobic digestion. Compared with the traditionally heated digesters (one-step heating), the digestion temperature in TSH digesters increased by 3.50-10.50 °C under the assumption of no heat dissipation and by 3.30-9.25 °C in the actual experiments. Although methane production of the TSH digesters improved by 15% in our experiments, the improvement was far less than theoretically estimated. This was mainly caused by short hydraulic retention time and sludge washout in the digesters. Moreover, the acetoclastic methanogenesis, accomplished by genus Methanosaeta, was the major methanogenesis pathway at low temperatures in both the TSH and conventional heating modes. However, the relative abundance of syntrophic bacteria and hydrogenotrophic methanogens in TSH mode were both higher than in the digesters operation in conventional heating mode when the atmospheric temperature was below 10 °C.
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Affiliation(s)
- Yi Liu
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Shichun Ma
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Liang Huang
- Sichuan University, No. 24 South Section 1, 1st Ring Rd., Chengdu, 610065, PR China
| | - Shiyu Wang
- Leshan Qinli Agricultural Development Co. Ltd., Maershan, Shizhong District, Leshan, 614000, PR China
| | - Gangjin Liu
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Hongnan Yang
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Dan Zheng
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Jingsi Cheng
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Ze Xu
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China
| | - Liangwei Deng
- Biogas Institute of Ministry of Agriculture, No. 13 Section 4, South Renmin Rd., Chengdu, 610041, PR China.
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130
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Techtman SM, Mahmoudi N, Whitt KT, Campa MF, Fortney JL, Joyner DC, Hazen TC. Comparison of Thaumarchaeotal populations from four deep sea basins. FEMS Microbiol Ecol 2018; 93:4331633. [PMID: 29029137 PMCID: PMC5812500 DOI: 10.1093/femsec/fix128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 09/29/2017] [Indexed: 11/13/2022] Open
Abstract
The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. These findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.
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Affiliation(s)
- Stephen M Techtman
- Department of Biological Sciences, Michigan Technological University, Houghton MI 49931-1295, USA
| | - Nagissa Mahmoudi
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Kendall T Whitt
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Maria Fernanda Campa
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Julian L Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Dominique C Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN 37916, USA.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN 37996, USA
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131
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Adam PS, Borrel G, Gribaldo S. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proc Natl Acad Sci U S A 2018; 115:E1166-E1173. [PMID: 29358391 PMCID: PMC5819426 DOI: 10.1073/pnas.1716667115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of uncultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
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Affiliation(s)
- Panagiotis S Adam
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Simonetta Gribaldo
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France;
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132
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Vogt JC, Abed RMM, Albach DC, Palinska KA. Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman. MICROBIAL ECOLOGY 2018; 75:331-347. [PMID: 28736793 DOI: 10.1007/s00248-017-1040-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Hypersaline intertidal zones are highly dynamic ecosystems that are exposed to multiple extreme environmental conditions including rapidly and frequently changing parameters (water, nutrients, temperature) as well as highly elevated salinity levels often caused by high temperatures and evaporation rates. Microbial mats in most extreme settings, as found at the coastline of the subtropical-arid Arabian Peninsula, have been relatively less studied compared to their counterparts around the world. We report, here, for the first time on the diversity of the bacterial and archaeal communities of marine microbial mats along an intertidal transect in a wide salt flat with strongly increased salinity employing Illumina MiSeq technology for amplicon sequencing of 16S rRNA gene fragments. Microbial communities were dominated by typical halotolerant to halophilic microorganisms, with clear shifts in community composition, richness, and diversity along the transect. Highly adapted specialists (e.g., Euhalothece, Salinibacter, Nanohaloarchaeota) were mainly found at the most extreme, upper tidal sites and less specialized organisms with wide tolerance ranges (e.g., Lyngbya, Rhodovibrio, Salisaeta, Halobacteria) in intermediate sites of the transect. The dominating taxa in the lower tidal sites were typical members of well-stabilized mats (e.g., Coleofasciculus, Anaerolineaceae, Thaumarchaeota). Up to 40% of the archaeal sequences per sample represented so far unknown phyla. In conclusion, the bacterial richness and diversity increased from upper towards lower tidal sites in line with increasing mat stabilization and functional diversity, opposed to that of cyanobacteria only and archaea, which showed their highest richness and diversity in upper tidal samples.
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Affiliation(s)
- Janina C Vogt
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl-von-Ossietzky University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany.
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box 36, 123, Al Khoud, Oman
| | - Dirk C Albach
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl-von-Ossietzky University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Katarzyna A Palinska
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl-von-Ossietzky University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
- Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Al. J. Pilsudskiego 46, 80-378, Gdynia, Poland
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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: 54] [Impact Index Per Article: 9.0] [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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134
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Ling J, Lin X, Zhang Y, Zhou W, Yang Q, Lin L, Zeng S, Zhang Y, Wang C, Ahmad M, Long L, Dong J. Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems. Front Microbiol 2018; 9:7. [PMID: 29422885 PMCID: PMC5788956 DOI: 10.3389/fmicb.2018.00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/04/2018] [Indexed: 11/17/2022] Open
Abstract
Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.
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Affiliation(s)
- Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiancheng Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liyun Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Siquan Zeng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China
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135
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Yan L, Yu D, Hui N, Naanuri E, Viggor S, Gafarov A, Sokolov SL, Heinaru A, Romantschuk M. Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination. Front Microbiol 2018; 9:15. [PMID: 29410652 PMCID: PMC5787342 DOI: 10.3389/fmicb.2018.00015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/05/2018] [Indexed: 11/13/2022] Open
Abstract
The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.
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Affiliation(s)
- Lijuan Yan
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Dan Yu
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Nan Hui
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Eve Naanuri
- Faculty of Science and Technology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Signe Viggor
- Faculty of Science and Technology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Arslan Gafarov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Sergei L Sokolov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Ain Heinaru
- Faculty of Science and Technology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Martin Romantschuk
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland.,Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
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136
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Badapanda C, Metha SM. Advancing our understanding of the oxygen minimum zone microbial communities by an integrated metatranscriptomics approach. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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137
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Yu T, Li M, Niu M, Fan X, Liang W, Wang F. Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea. Appl Microbiol Biotechnol 2017; 102:447-459. [DOI: 10.1007/s00253-017-8594-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 11/29/2022]
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138
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Compte-Port S, Subirats J, Fillol M, Sànchez-Melsió A, Marcé R, Rivas-Ruiz P, Rosell-Melé A, Borrego CM. Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula. MICROBIAL ECOLOGY 2017; 74:776-787. [PMID: 28508926 DOI: 10.1007/s00248-017-0989-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/23/2017] [Indexed: 06/07/2023]
Abstract
Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.
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Affiliation(s)
- Sergi Compte-Port
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Rafael Marcé
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Pedro Rivas-Ruiz
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Rosell-Melé
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010, Barcelona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain.
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139
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Qin W, Heal KR, Ramdasi R, Kobelt JN, Martens-Habbena W, Bertagnolli AD, Amin SA, Walker CB, Urakawa H, Könneke M, Devol AH, Moffett JW, Armbrust EV, Jensen GJ, Ingalls AE, Stahl DA. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. Int J Syst Evol Microbiol 2017; 67:5067-5079. [PMID: 29034851 DOI: 10.1099/ijsem.0.002416] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.
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Affiliation(s)
- Wei Qin
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Rasika Ramdasi
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Julia N Kobelt
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Willm Martens-Habbena
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Department of Microbiology and Cell Science and Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Florida, FL, USA
| | - Anthony D Bertagnolli
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shady A Amin
- Department of Chemistry, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Christopher B Walker
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Marine and Ecological Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Martin Könneke
- Marine Archaea Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Allan H Devol
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - James W Moffett
- Departments of Biological Sciences and Earth Sciences and Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | | | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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140
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Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment. Appl Environ Microbiol 2017; 83:AEM.00729-17. [PMID: 28667104 PMCID: PMC5561297 DOI: 10.1128/aem.00729-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/20/2017] [Indexed: 02/06/2023] Open
Abstract
During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.
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141
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Schieffer KM, Sabey K, Wright JR, Toole DR, Drucker R, Tokarev V, Harris LR, Deiling S, Eshelman MA, Hegarty JP, Yochum GS, Koltun WA, Lamendella R, Stewart DB. The Microbial Ecosystem Distinguishes Chronically Diseased Tissue from Adjacent Tissue in the Sigmoid Colon of Chronic, Recurrent Diverticulitis Patients. Sci Rep 2017; 7:8467. [PMID: 28814777 PMCID: PMC5559482 DOI: 10.1038/s41598-017-06787-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 06/19/2017] [Indexed: 02/01/2023] Open
Abstract
Diverticular disease is commonly associated with the older population in the United States. As individual’s age, diverticulae, or herniation of the mucosa through the colonic wall, develop. In 10–25% of individuals, the diverticulae become inflamed, resulting in diverticulitis. The gut ecosystem relies on the interaction of bacteria and fungi to maintain homeostasis. Although bacterial dysbiosis has been implicated in the pathogenesis of diverticulitis, associations between the microbial ecosystem and diverticulitis remain largely unstudied. This study investigated how the cooperative network of bacteria and fungi differ between a diseased area of the sigmoid colon chronically affected by diverticulitis and adjacent non-affected tissue. To identify mucosa-associated microbes, bacterial 16S rRNA and fungal ITS sequencing were performed on chronically diseased sigmoid colon tissue (DT) and adjacent tissue (AT) from the same colonic segment. We found that Pseudomonas and Basidiomycota OTUs were associated with AT while Microbacteriaceae and Ascomycota were enriched in DT. Bipartite co-occurrence networks were constructed for each tissue type. The DT and AT networks were distinct for each tissue type, with no microbial relationships maintained after intersection merge of the groups. Our findings indicate that the microbial ecosystem distinguishes chronically diseased tissue from adjacent tissue.
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Affiliation(s)
- Kathleen M Schieffer
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Kate Sabey
- Department of Biology, Juniata College, Huntingdon, PA, USA
| | - Justin R Wright
- Department of Biology, Juniata College, Huntingdon, PA, USA.,Wright Labs LLC., Huntingdon, PA, USA
| | - David R Toole
- Department of Biology, Juniata College, Huntingdon, PA, USA
| | | | - Vasily Tokarev
- Department of Biology, Juniata College, Huntingdon, PA, USA
| | - Leonard R Harris
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Sue Deiling
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Melanie A Eshelman
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA.,Department of Biochemistry & Molecular Biology, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - John P Hegarty
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Gregory S Yochum
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA.,Department of Biochemistry & Molecular Biology, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Walter A Koltun
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, PA, USA.,Wright Labs LLC., Huntingdon, PA, USA
| | - David B Stewart
- Division of Colon and Rectal Surgery, Department of Surgery, The Pennsylvania State University, College of Medicine, Hershey, PA, USA.
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142
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Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 2017; 357:357/6351/eaaf3883. [DOI: 10.1126/science.aaf3883] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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143
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The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME JOURNAL 2017; 11:2407-2425. [PMID: 28777382 DOI: 10.1038/ismej.2017.122] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/07/2017] [Accepted: 06/07/2017] [Indexed: 01/19/2023]
Abstract
The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.
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144
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Black EM, Chimenti MS, Just CL. Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment. PeerJ 2017; 5:e3536. [PMID: 28717594 PMCID: PMC5510576 DOI: 10.7717/peerj.3536] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/13/2017] [Indexed: 01/03/2023] Open
Abstract
Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.
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Affiliation(s)
- Ellen M Black
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States of America
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, United States of America
| | - Craig L Just
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States of America
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145
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Leuko S, Koskinen K, Sanna L, D’Angeli IM, De Waele J, Marcia P, Moissl-Eichinger C, Rettberg P. The influence of human exploration on the microbial community structure and ammonia oxidizing potential of the Su Bentu limestone cave in Sardinia, Italy. PLoS One 2017; 12:e0180700. [PMID: 28704427 PMCID: PMC5507542 DOI: 10.1371/journal.pone.0180700] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/20/2017] [Indexed: 01/20/2023] Open
Abstract
The bacterial diversity in the Su Bentu Cave in Sardinia was investigated by means of 16S rRNA gene-based analysis. This 15 km long cave, carved in Jurassic limestone, hosts a variety of calcite speleothems, and a long succession of subterranean lakes with mixed granite and carbonate sands. The lower level is occasionally flooded by a rising groundwater level, but with only scarce input of organic remains (leaves and charcoal fragments). On the quiet cave pools there are visible calcite rafts, whereas walls are locally coated with manganese deposits. In the drier upper levels, where organic input is much more subdued, moonmilk—a hydrated calcium-magnesium carbonate speleothem—can be found. Relative humidity approaches 100% and the measured mean annual cave air temperature is 14.8°C. Samples were obtained in 2014 from calcite rafts, moonmilk, manganese oxide deposits and soil (limestone and granite grains). Microclimatic conditions in the cave near the sampling sites, sample properties, physico-chemical parameters of water, and sediment composition were determined. The microbial community of this system is predominately composed of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Nitrospirae, and Firmicutes. Sampling sites near the entrance of the cave and in close proximity of the underground campsite–located 500 meters deep into the cave—revealed the highest diversity as well as the highest number of human associated microorganisms. Two samples obtained in very close proximity of each other near the campsite, indicate that the human impact is localized and is not distributed freely within the system. Analysis of the abundance of bacterial and archaeal amoA genes revealed a far greater abundance of archaeal amoA genes compared to bacterial representatives. The results of this study highlight that human impact is confined to locations that are utilized as campsites and that exploration leaves little microbial trails. Furthermore, we uncovered a highly specialized microbiome, which is perfectly adapted to survive and thrive in an environment with low nutrient availability.
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Affiliation(s)
- Stefan Leuko
- German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine, Radiation Biology Department, Research Group 'Astrobiology', Linder Höhe, Cologne (Köln), Germany
- * E-mail:
| | - Kaisa Koskinen
- Medical University of Graz, Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, BioTechMed, Krenngasse, Graz, Austria
| | - Laura Sanna
- Institute for Biometeorology, National Research Council of Italy, Sassari, Italy
| | | | - Jo De Waele
- Italian Institute of Speleology, University of Bologna, Bologna, Italy
| | - Paolo Marcia
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Christine Moissl-Eichinger
- Medical University of Graz, Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, BioTechMed, Krenngasse, Graz, Austria
| | - Petra Rettberg
- German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine, Radiation Biology Department, Research Group 'Astrobiology', Linder Höhe, Cologne (Köln), Germany
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146
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Tait AW, Gagen EJ, Wilson S, Tomkins AG, Southam G. Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers. Front Microbiol 2017; 8:1227. [PMID: 28713354 PMCID: PMC5492697 DOI: 10.3389/fmicb.2017.01227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/16/2017] [Indexed: 11/13/2022] Open
Abstract
Finding fresh, sterilized rocks provides ecologists with a clean slate to test ideas about first colonization and the evolution of soils de novo. Lava has been used previously in first colonizer studies due to the sterilizing heat required for its formation. However, fresh lava typically falls upon older volcanic successions of similar chemistry and modal mineral abundance. Given enough time, this results in the development of similar microbial communities in the newly erupted lava due to a lack of contrast between the new and old substrates. Meteorites, which are sterile when they fall to Earth, provide such contrast because their reduced and mafic chemistry commonly differs to the surfaces on which they land; thus allowing investigation of how community membership and structure respond to this new substrate over time. We conducted 16S rRNA gene analysis on meteorites and soil from the Nullarbor Plain, Australia. We found that the meteorites have low species richness and evenness compared to soil sampled from directly beneath each meteorite. Despite the meteorites being found kilometers apart, the community structure of each meteorite bore more similarity to those of other meteorites (of similar composition) than to the community structure of the soil on which it resided. Meteorites were dominated by sequences that affiliated with the Actinobacteria with the major Operational Taxonomic Unit (OTU) classified as Rubrobacter radiotolerans. Proteobacteria and Bacteroidetes were the next most abundant phyla. The soils were also dominated by Actinobacteria but to a lesser extent than the meteorites. We also found OTUs affiliated with iron/sulfur cycling organisms Geobacter spp. and Desulfovibrio spp. This is an important finding as meteorites contain abundant metal and sulfur for use as energy sources. These ecological findings demonstrate that the structure of the microbial community in these meteorites is controlled by the substrate, and will not reach homeostasis with the Nullarbor community, even after ca. 35,000 years. Our findings show that meteorites provide a unique, sterile substrate with which to test ideas relating to first-colonizers. Although meteorites are colonized by microorganisms, the microbial population is unlikely to match the community of the surrounding soil on which they fall.
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Affiliation(s)
- Alastair W. Tait
- School of Earth, Atmosphere and Environment, Monash University, MelbourneVIC, Australia
| | - Emma J. Gagen
- School of Earth and Environmental Sciences, The University of Queensland, St. LuciaQLD, Australia
| | - Sasha Wilson
- School of Earth, Atmosphere and Environment, Monash University, MelbourneVIC, Australia
| | - Andrew G. Tomkins
- School of Earth, Atmosphere and Environment, Monash University, MelbourneVIC, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St. LuciaQLD, Australia
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147
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Abstract
The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or younger than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. Amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.
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148
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Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM. Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci U S A 2017; 114:E4602-E4611. [PMID: 28533395 PMCID: PMC5468678 DOI: 10.1073/pnas.1618463114] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
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Affiliation(s)
- Tom A Williams
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom;
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Gergely J Szöllősi
- MTA-ELTE Lendület Evolutionary Genomics Research Group, 1117 Budapest, Hungary
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Sarah E Heaps
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Bastien Boussau
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622 Villeurbanne, France
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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149
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Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 2017; 19:2681-2700. [PMID: 28419726 DOI: 10.1111/1462-2920.13759] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany.,Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | | | - Barbara Bayer
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria
| | - Eva Spieck
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, 22609, Germany
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, 93053, Germany
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
| | | | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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150
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Argiroff WA, Zak DR, Lanser CM, Wiley MJ. Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils. MICROBIAL ECOLOGY 2017; 73:630-644. [PMID: 27807645 DOI: 10.1007/s00248-016-0883-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/17/2016] [Indexed: 05/12/2023]
Abstract
Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.
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Affiliation(s)
- William A Argiroff
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA.
| | - Donald R Zak
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI, 48109, USA
| | - Christine M Lanser
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
| | - Michael J Wiley
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
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