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Liu S, Liu J, She J, Xie Z, Zhou L, Dai Q, Zhang X, Wan Y, Yin M, Dong X, Zhao M, Chen D, Wang J. Microbial features with uranium pollution in artificial reservoir sediments at different depths under drought stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170694. [PMID: 38325477 DOI: 10.1016/j.scitotenv.2024.170694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/22/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
The uranium (U) containing leachate from uranium tailings dam into the natural settings, may greatly affect the downstream environment. To reveal such relationship between uranium contamination and microbial communities in the most affected downstream environment under drought stress, a 180 cm downstream artificial reservoir depth sediment profile was collected, and the microbial communities and related genes were analyzed by 16S rDNA and metagenomics. Besides, the sequential extraction scheme was employed to shed light on the distinct role of U geochemical speciations in shaping microbial community structures. The results showed that U content ranged from 28.1 to 70.1 mg/kg, with an average content of 44.9 mg/kg, significantly exceeding the value of background sediments. Further, U in all the studied sediments was related to remarkably high portions of mobile fractions, and U was likely deposited layer by layer depending on the discharge/leachate inputs from uranium-involving anthoropogenic facilities/activities upstream. The nexus between U speciation, physico-chemical indicators and microbial composition showed that Fe, S, and N metabolism played a vital role in microbial adaptation to U-enriched environment; meanwhile, the fraction of Ureducible and the Fe and S contents had the most significant effects on microbial community composition in the sediments under drought stress.
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Affiliation(s)
- Siyu Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Juan Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Jingye She
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Zhenyu Xie
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Lei Zhou
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycling, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Qunwei Dai
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycling, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Xing Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Yuebing Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Meiling Yin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Xinjiao Dong
- School of Life & Environmental Science, Wenzhou University, Wenzhou, China
| | - Min Zhao
- School of Life & Environmental Science, Wenzhou University, Wenzhou, China
| | - Diyun Chen
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, Guangzhou, China
| | - Jin Wang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, Guangzhou, China.
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VanderRoest JP, Fowler JA, Rhoades CC, Roth HK, Broeckling CD, Fegel TS, McKenna AM, Bechtold EK, Boot CM, Wilkins MJ, Borch T. Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4167-4180. [PMID: 38385432 DOI: 10.1021/acs.est.3c09797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Global wildfire activity has increased since the 1970s and is projected to intensify throughout the 21st century. Wildfires change the composition and biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms of SOM often increase postfire, the response of more biodegradable SOM remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach to identify biodegradable sources of SOM and characterize the soil metabolome immediately postfire. Using microbial amplicon (16S/ITS) sequencing and gas chromatography-mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, and Protobacteria) and specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating that burned soils contain a variety of substrates that support microbial metabolism. Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed that SOM in burned soil was lower in molecular weight and featured 20 to 43% more nitrogen-containing molecular formulas than unburned soil. We also measured higher water extractable organic carbon concentrations and higher CO2 efflux in burned soils. The observed enrichment of biodegradable SOM and microbial heterotrophs demonstrates the resilience of these soils to severe burning, providing important implications for postfire soil microbial and plant recolonization and ecosystem recovery.
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Affiliation(s)
- Jacob P VanderRoest
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Julie A Fowler
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Holly K Roth
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Corey D Broeckling
- Bioanalysis and Omics Center, Analytical Resources Core, Colorado State University, Fort Collins, 80521, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Emily K Bechtold
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Claudia M Boot
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
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Beeckman F, Drozdzecki A, De Knijf A, Corrochano-Monsalve M, Bodé S, Blom P, Goeminne G, González-Murua C, Lücker S, Boeckx P, Stevens CV, Audenaert D, Beeckman T, Motte H. Drug discovery-based approach identifies new nitrification inhibitors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118996. [PMID: 37725864 DOI: 10.1016/j.jenvman.2023.118996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/24/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Andrzej Drozdzecki
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Samuel Bodé
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Pascal Boeckx
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Christian V Stevens
- Synthesis, Bioresources and Bioorganic Chemistry Research Group (SynBioC), Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dominique Audenaert
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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Gusmão ACB, Peres FV, Paula FS, Pellizari VH, Kolm HE, Signori CN. Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean. Int Microbiol 2023; 26:1041-1051. [PMID: 37093322 DOI: 10.1007/s10123-023-00358-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.
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Affiliation(s)
- Ana Carolina Bercini Gusmão
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil.
| | - Francielli Vilela Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Hedda Elisabeth Kolm
- Department of Oceanography, Center for Marine Studies, Federal University of Paraná, Pontal do Paraná, Brazil
| | - Camila Negrão Signori
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
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He P, Wang H, Shi J, Xin M, Wang W, Xie L, Wei Q, Huang M, Shi X, Fan Y, Chen H. Prokaryote Distribution Patterns along a Dissolved Oxygen Gradient Section in the Tropical Pacific Ocean. Microorganisms 2023; 11:2172. [PMID: 37764016 PMCID: PMC10534896 DOI: 10.3390/microorganisms11092172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
Oceanic oxygen levels are decreasing significantly in response to global climate change; however, the microbial diversity and ecological functional responses to dissolved oxygen (DO) in the open ocean are largely unknown. Here, we present prokaryotic distribution coupled with physical and biogeochemical variables and DO gradients from the surface to near the bottom of a water column along an approximately 12,000-km transect from 13° N to 18° S in the Tropical Pacific Ocean. Nitrate (11.42%), temperature (10.90%), pH (10.91%), silicate (9.34%), phosphate (4.25%), chlorophyll a (3.66%), DO (3.50%), and salinity (3.48%) significantly explained the microbial community variations in the studied area. A distinct microbial community composition broadly corresponding to the water masses formed vertically. Additionally, distinct ecotypes of Thaumarchaeota and Nitrospinae belonging to diverse phylogenetic clades that coincided with specific vertical niches were observed. Moreover, the correlation analysis revealed large-scale natural feedback in which chlorophyll a (organic matter) promoted Thaumarchaeotal biomass at depths that subsequently coupled with Nitrospina, produced and replenished nitrate for phytoplankton productivity at the surface. Low DO also favored Thaumarchaeota growth and fueled nitrate production.
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Affiliation(s)
- Peiqing He
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Huan Wang
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Jie Shi
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Ming Xin
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Weimin Wang
- Center for Ocean and Climate Research, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China;
| | - Linping Xie
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Qinsheng Wei
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Mu Huang
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Xuefa Shi
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Yaqin Fan
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Hao Chen
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
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Zhao W, Bi X, Bai M, Wang Y. Research advances of ammonia oxidation microorganisms in wastewater: metabolic characteristics, microbial community, influencing factors and process applications. Bioprocess Biosyst Eng 2023; 46:621-633. [PMID: 36988685 DOI: 10.1007/s00449-023-02866-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Ammonia oxidation carried out by ammonia-oxidizing microorganisms (AOMs) is a central step in the global nitrogen cycle. Aerobic AOMs comprise conventional ammonia-oxidizing bacteria (AOB), novel ammonia-oxidizing archaea (AOA), which could exist in complex and extreme conditions, and complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate within a single cell. Anaerobic AOMs mainly comprise anaerobic ammonia-oxidizing bacteria (AnAOB), which can transform NH4+-N and NO2--N into N2 under anaerobic conditions. In this review, the unique metabolic characteristics, microbial community of AOMs and the influencing factors are discussed. Process applications of nitrification/denitrification, nitritation/denitrification, nitritation/anammox and partial denitrification/anammox in wastewater treatment systems are emphasized. The future development of nitrogen removal processes using AOMs is expected, enrichment of comammox facilitates the complete nitrification performance, inhibiting the activity of comammox and NOB could achieve stable nitritation, and additionally, AnAOB conducting the anammox process in municipal wastewater is a promising development direction.
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Affiliation(s)
- Weihua Zhao
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China.
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, People's Republic of China.
- Qingdao University of Technology, Huangdao District, Qingdao, 266525, People's Republic of China.
| | - Xuejun Bi
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Meng Bai
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Yanyan Wang
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
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Bhaduri D, Sihi D, Bhowmik A, Verma BC, Munda S, Dari B. A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Front Microbiol 2022; 13:938481. [PMID: 36060788 PMCID: PMC9428492 DOI: 10.3389/fmicb.2022.938481] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.
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Affiliation(s)
- Debarati Bhaduri
- ICAR-National Rice Research Institute, Cuttack, India
- *Correspondence: Debarati Bhaduri
| | - Debjani Sihi
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States
| | - Arnab Bhowmik
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
- Arnab Bhowmik
| | - Bibhash C. Verma
- Central Rainfed Upland Rice Research Station (ICAR-NRRI), Hazaribagh, India
| | | | - Biswanath Dari
- Agriculture and Natural Resources, Cooperative Extension at North Carolina Agricultural and Technical State University, Greensboro, NC, United States
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8
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Abstract
Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.
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Statistical Learning and Uncommon Soil Microbiota Explain Biogeochemical Responses after Wildfire. Appl Environ Microbiol 2022; 88:e0034322. [PMID: 35703548 DOI: 10.1128/aem.00343-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wildfires are a perennial event globally, and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, United States, across the first and second postfire years and leveraged statistical learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with the hybrid and biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4+). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the "rare biosphere" [existing at <1% mean relative abundance]). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predicts environmental features in postfire soils, although this approach could likely be applied to any biogeochemical system. IMPORTANCE Soil biogeochemical processes are critical to plant growth and water quality and are substantially disturbed by wildfire. However, soil responses to fire are difficult to predict. To address this issue, we developed a large environmental data set that tracks postfire changes in soil and used statistical learning (SL) to build models that exploit complex data to make predictions about biogeochemical responses. Here, we show that SL depends upon uncommon microbiota in soil (the "rare biosphere") to make surprisingly accurate predictions about soil biogeochemical responses to wildfire. Using SL to explain variation in a natively chaotic environmental system is mechanism independent. Likely, the approach that we describe for combining SL with microbiome and biogeochemical parameters has practical applications across a range of issues in the environmental sciences where predicting responses would be useful.
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Alcamán-Arias ME, Cifuentes-Anticevic J, Díez B, Testa G, Troncoso M, Bello E, Farías L. Surface Ammonia-Oxidizer Abundance During the Late Summer in the West Antarctic Coastal System. Front Microbiol 2022; 13:821902. [PMID: 35401462 PMCID: PMC8992545 DOI: 10.3389/fmicb.2022.821902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 01/04/2023] Open
Abstract
Marine ammonia oxidizers that oxidize ammonium to nitrite are abundant in polar waters, especially during the winter in the deeper mixed-layer of West Antarctic Peninsula (WAP) waters. However, the activity and abundance of ammonia-oxidizers during the summer in surface coastal Antarctic waters remain unclear. In this study, the ammonia-oxidation rates, abundance and identity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were evaluated in the marine surface layer (to 30 m depth) in Chile Bay (Greenwich Island, WAP) over three consecutive late-summer periods (2017, 2018, and 2019). Ammonia-oxidation rates of 68.31 nmol N L−1 day−1 (2018) and 37.28 nmol N L−1 day−1 (2019) were detected from illuminated 2 m seawater incubations. However, high ammonia-oxidation rates between 267.75 and 109.38 nmol N L−1 day−1 were obtained under the dark condition at 30 m in 2018 and 2019, respectively. During the late-summer sampling periods both stratifying and mixing events occurring in the water column over short timescales (February–March). Metagenomic analysis of seven nitrogen cycle modules revealed the presence of ammonia-oxidizers, such as the Archaea Nitrosopumilus and the Bacteria Nitrosomonas and Nitrosospira, with AOA often being more abundant than AOB. However, quantification of specific amoA gene transcripts showed number of AOB being two orders of magnitude higher than AOA, with Nitrosomonas representing the most transcriptionally active AOB in the surface waters. Additionally, Candidatus Nitrosopelagicus and Nitrosopumilus, phylogenetically related to surface members of the NP-ε and NP-γ clades respectively, were the predominant AOA. Our findings expand the known distribution of ammonium-oxidizers to the marine surface layer, exposing their potential ecological role in supporting the marine Antarctic system during the productive summer periods.
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Affiliation(s)
- María E Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Center for Climate and Resilience Research (CR)2, Santiago, Chile.,Escuela de Medicina, Universidad Espíritu Santo, Guayaquil, Ecuador
| | | | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Giovanni Testa
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Programa de Postgrado en Oceanografía, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Research Center Dynamics of High Latitude Marine Ecosystems (IDEAL), Punta Arenas, Chile
| | | | - Estrella Bello
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Center for Climate and Resilience Research (CR)2, Santiago, Chile
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11
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Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications. Mar Drugs 2022; 20:md20020108. [PMID: 35200637 PMCID: PMC8874374 DOI: 10.3390/md20020108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Environmental microbes living in communities engage in complex interspecies interactions that are challenging to decipher. Nevertheless, the interactions provide the basis for shaping community structure and functioning, which is crucial for ecosystem service. In addition, microbial interactions facilitate specific adaptation and ecological evolution processes particularly essential for microbial communities dwelling in resource-limiting habitats, such as the deep oceans. Recent technological and knowledge advancements provide an opportunity for the study of interactions within complex microbial communities, such as those inhabiting deep-sea waters and sediments. The microbial interaction studies provide insights into developing new strategies for biotechnical applications. For example, cooperative microbial interactions drive the degradation of complex organic matter such as chitins and celluloses. Such microbiologically-driven biogeochemical processes stimulate creative designs in many applied sciences. Understanding the interaction processes and mechanisms provides the basis for the development of synthetic communities and consequently the achievement of specific community functions. Microbial community engineering has many application potentials, including the production of novel antibiotics, biofuels, and other valuable chemicals and biomaterials. It can also be developed into biotechniques for waste processing and environmental contaminant bioremediation. This review summarizes our current understanding of the microbial interaction mechanisms and emerging techniques for inferring interactions in deep-sea microbial communities, aiding in future biotechnological and therapeutic applications.
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12
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Kajla S, Kumari R, Nagi GK. Microbial CO2 fixation and biotechnology in reducing industrial CO2 emissions. Arch Microbiol 2022; 204:149. [DOI: 10.1007/s00203-021-02677-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
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13
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Sow SLS, Brown MV, Clarke LJ, Bissett A, van de Kamp J, Trull TW, Raes EJ, Seymour JR, Bramucci AR, Ostrowski M, Boyd PW, Deagle BE, Pardo PC, Sloyan BM, Bodrossy L. Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors. Environ Microbiol 2022; 24:2449-2466. [PMID: 35049099 PMCID: PMC9303206 DOI: 10.1111/1462-2920.15906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/13/2022] [Indexed: 11/27/2022]
Abstract
We investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.
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Affiliation(s)
- Swan L S Sow
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, New South Wales, 2308, Australia
| | - Laurence J Clarke
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia.,Australian Antarctic Division, Channel Highway, Kingston, Tasmania, 7050, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Thomas W Trull
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Eric J Raes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Anna R Bramucci
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania, 7050, Australia.,National Collections & Marine Infrastructure, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Paula C Pardo
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Bernadette M Sloyan
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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14
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Li F, Leu A, Poff K, Carlson LT, Ingalls AE, DeLong EF. Planktonic Archaeal Ether Lipid Origins in Surface Waters of the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:610675. [PMID: 34589060 PMCID: PMC8473941 DOI: 10.3389/fmicb.2021.610675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Thaumarchaeota and Thermoplasmatota are the most abundant planktonic archaea in the sea. Thaumarchaeota contain tetraether lipids as their major membrane lipids, but the lipid composition of uncultured planktonic Thermoplasmatota representatives remains unknown. To address this knowledge gap, we quantified archaeal cells and ether lipids in open ocean depth profiles (0–200 m) of the North Pacific Subtropical Gyre. Planktonic archaeal community structure and ether lipid composition in the water column partitioned into two separate clusters: one above the deep chlorophyll maximum, the other within and below it. In surface waters, Thermoplasmatota densities ranged from 2.11 × 106 to 6.02 × 106 cells/L, while Thaumarchaeota were undetectable. As previously reported for Thaumarchaeota, potential homologs of archaeal tetraether ring synthases were present in planktonic Thermoplasmatota metagenomes. Despite the absence of Thaumarchaeota in surface waters, measurable amounts of intact polar ether lipids were found there. Based on cell abundance estimates, these surface water archaeal ether lipids contributed only 1.21 × 10–9 ng lipid/Thermoplasmatota cell, about three orders of magnitude less than that reported for Thaumarchaeota cells. While these data indicate that even if some tetraether and diether lipids may be derived from Thermoplasmatota, they would only comprise a small fraction of Thermoplasmatota total biomass. Therefore, while both MGI Thaumarchaeota and MGII/III Thermoplasmatota are potential biological sources of archaeal GDGTs, the Thaumarchaeota appear to be the major contributors of archaeal tetraether lipids in planktonic marine habitats. These results extend and confirm previous reports of planktonic archaeal lipid sources, and further emphasize the need for Thermoplasmatota cultivation, to better characterize the membrane lipid constituents of marine planktonic Thermoplasmatota, and more precisely define the sources and patterns of archaeal tetraether lipid distributions in marine plankton.
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Affiliation(s)
- Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Andy Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Kirsten Poff
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
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15
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Boey JS, Mortimer R, Couturier A, Worrallo K, Handley KM. Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance. Environ Microbiol 2021; 24:50-65. [PMID: 33973326 DOI: 10.1111/1462-2920.15550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023]
Abstract
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.
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Affiliation(s)
- Jian Sheng Boey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Redmond Mortimer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Agathe Couturier
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Ecole Supérieure de Biologie Biochimie Biotechnologies, Faculté des Sciences, Université Catholique de Lyon, Lyon, France
| | - Katie Worrallo
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Kim M Handley
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
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16
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Dom SP, Ikenaga M, Lau SYL, Radu S, Midot F, Yap ML, Chin MY, Lo ML, Jee MS, Maie N, Melling L. Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia. Sci Rep 2021; 11:6416. [PMID: 33742002 PMCID: PMC7979770 DOI: 10.1038/s41598-021-81865-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80-90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities' composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.
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Affiliation(s)
- Simon Peter Dom
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Frazer Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Lan Yap
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei-Yee Chin
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei Lieng Lo
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Sie Jee
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Nagamitsu Maie
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Lulie Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
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17
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DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
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18
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DeLong EF. Exploring Marine Planktonic Archaea: Then and Now. Front Microbiol 2021; 11:616086. [PMID: 33519774 PMCID: PMC7838436 DOI: 10.3389/fmicb.2020.616086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Mănoa, Honolulu, HI, United States
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19
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Muturi SM, Muthui LW, Njogu PM, Onguso JM, Wachira FN, Opiyo SO, Pelle R. Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PLoS One 2021; 16:e0244755. [PMID: 33395690 PMCID: PMC7781671 DOI: 10.1371/journal.pone.0244755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022] Open
Abstract
The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.
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Affiliation(s)
- Samuel Mwangangi Muturi
- Department of Biological Sciences, University of Eldoret, Eldoret, Kenya
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucy Wangui Muthui
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Paul Mwangi Njogu
- Institute for Energy and Environmental Technology, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Justus Mong’are Onguso
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | | | - Stephen Obol Opiyo
- OARDC, Molecular and Cellular Imaging Center-Columbus, Ohio State University, Columbus, Ohio, United States of America
- The University of Sacread Heart, Gulu, Uganda
| | - Roger Pelle
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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20
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Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
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21
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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22
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Seward J, Carson MA, Lamit LJ, Basiliko N, Yavitt JB, Lilleskov E, Schadt CW, Smith DS, Mclaughlin J, Mykytczuk N, Willims-Johnson S, Roulet N, Moore T, Harris L, Bräuer S. Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient. MICROBIAL ECOLOGY 2020; 80:593-602. [PMID: 32388577 DOI: 10.1007/s00248-020-01510-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/30/2020] [Indexed: 05/20/2023]
Abstract
Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.
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Affiliation(s)
- James Seward
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608-2026, USA.
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada.
| | - Michael A Carson
- Department of Renewable Resources, Earth Sciences Building, University of Alberta, 116 St. and 85 Ave., Edmonton, Alberta, T6G 2R3, Canada
| | - L J Lamit
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Nathan Basiliko
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, 14853, USA
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, 410 MacInnes Dr, Houghton, MI, 49931, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6038, USA
| | - Dave Solance Smith
- Department of Biology, California State University, San Bernardino, CA, 92407, USA
| | - Jim Mclaughlin
- Ontario Forest Research Institute, Sault Ste. Marie, ON, Canada
| | - Nadia Mykytczuk
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Shanay Willims-Johnson
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Nigel Roulet
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Tim Moore
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Lorna Harris
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608-2026, USA
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23
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Dai J, Ye Q, Wu Y, Zhang M, Zhang J. Simulation of Enhanced Growth of Marine Group II Euryarchaeota From the Deep Chlorophyll Maximum of the Western Pacific Ocean: Implication for Upwelling Impact on Microbial Functions in the Photic Zone. Front Microbiol 2020; 11:571199. [PMID: 33013804 PMCID: PMC7516215 DOI: 10.3389/fmicb.2020.571199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
Mesoscale eddies can have a strong impact on regional biogeochemistry and primary productivity. To investigate the effect of the upwelling of seawater by western Pacific eddies on the composition of the active planktonic marine archaeal community composition of the deep chlorophyll maximum (DCM) layer, mesoscale cold-core eddies were simulated in situ by mixing western Pacific DCM layer water with mesopelagic layer (400 m) water. Illumina sequencing of the 16S rRNA gene and 16S rRNA transcripts indicated that the specific heterotrophic Marine Group IIb (MGIIb) taxonomic group of the DCM layer was rapidly stimulated after receiving fresh substrate from 400 m water, which was dominated by uncultured autotrophic Marine Group I (MGI) archaea. Furthermore, niche differentiation of autotrophic ammonia-oxidizing archaea (MGI) was demonstrated by deep sequencing of 16S rRNA, amoA, and accA genes, respectively. Similar distribution patterns of active Marine Group III (MGIII) were observed in the DCM layer with or without vertical mixing, indicating that they are inclined to utilize the substrates already present in the DCM layer. These findings underscore the importance of mesoscale cyclonic eddies in stimulating microbial processes involved in the regional carbon cycle.
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Affiliation(s)
- Jinlong Dai
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Miao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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24
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Sedlacek CJ. It Takes a Village: Discovering and Isolating the Nitrifiers. Front Microbiol 2020; 11:1900. [PMID: 32849473 PMCID: PMC7431685 DOI: 10.3389/fmicb.2020.01900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.
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Affiliation(s)
- Christopher J. Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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25
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Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, Nielsen JL, Mori K, Takahashi R, Virginia Armbrust E, Winkler MKH, DeLong EF, Li M, Lee PH, Zhou J, Zhang C, Zhang T, Stahl DA, Ingalls AE. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME JOURNAL 2020; 14:2595-2609. [PMID: 32636492 PMCID: PMC7490402 DOI: 10.1038/s41396-020-0710-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
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Affiliation(s)
- Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA.
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL, USA
| | - Haodong Liu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Xiaowu Huang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | | | - Baozhan Wang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shady A Amin
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | | | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China.,Department of Civil and Environmental Engineering, Imperial College London, London, UK
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Environment, Tsinghua University, Beijing, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA.
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26
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Cao Q, Najnine F, Han H, Wu B, Cai J. BALOs Improved Gut Microbiota Health in Postlarval Shrimp ( Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment. Front Microbiol 2020; 11:1296. [PMID: 32714290 PMCID: PMC7344170 DOI: 10.3389/fmicb.2020.01296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
Abstract
White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.
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Affiliation(s)
- Qingqing Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Farhana Najnine
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongcao Han
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Bing Wu
- Modern Analysis Centre, South China University of Technology, Guangzhou, China
| | - Junpeng Cai
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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27
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Zhong H, Lehtovirta-Morley L, Liu J, Zheng Y, Lin H, Song D, Todd JD, Tian J, Zhang XH. Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms. MICROBIOME 2020; 8:78. [PMID: 32482169 PMCID: PMC7265257 DOI: 10.1186/s40168-020-00849-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. RESULTS In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. CONCLUSIONS Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.
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Affiliation(s)
- Haohui Zhong
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Laura Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwen Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Heyu Lin
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Delei Song
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China.
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28
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Brin LD, Goyer C, Zebarth BJ, Burton DL, Chantigny MH. Linking changes in snow cover with microbial nitrogen cycling functional gene abundance and expression in agricultural soil. FEMS Microbiol Ecol 2020; 95:5511778. [PMID: 31167230 DOI: 10.1093/femsec/fiz073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/04/2019] [Indexed: 11/12/2022] Open
Abstract
In eastern Canada, climate change-related warming and increased precipitation may alter winter snow cover, with potential consequences for soil conditions, nitrogen (N) cycling, and microbes. We conducted a 2-year field study aimed at determining the influence of snow removal, snow accumulation, and ambient snow in a potato-barley crop system on the abundance and expression of denitrifier (nirS, nirK, nosZ) and nitrifier (ammonium oxidizing archaeal (AOA) and bacterial (AOB) amoA) genes. Denitrifier and nitrifier abundance and expression results were compared to N2O production, soil atmosphere accumulation, and surface fluxes. In the first winter, nirK abundance was lowest while AOB abundance was greatest in snow accumulation treatments. In the second winter, greatest abundances were observed in the ambient snow treatment, which had greatest N2O accumulation and spring thaw fluxes, suggesting a link between microbial populations and biogeochemical functioning. Treatment effects on gene expression were limited, but greatest AOA, AOB, and nosZ expression was measured near 0°C and above 15°C, indicating that activity was promoted by freeze-thaw conditions and at summer temperatures. Overall, effects of changing snow depth on denitrifier and nitrifier abundance were not solely due to change in soil temperature, but also to soil moisture and/or interactions between these parameters.
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Affiliation(s)
- Lindsay D Brin
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Claudia Goyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Bernie J Zebarth
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - David L Burton
- Department of Environmental Sciences, Dalhousie University, Agricultural Campus, PO Box 550, Truro, Nova Scotia, B2N 5E3, Canada
| | - Martin H Chantigny
- Québec Research and Development Centre, Agriculture and Agri-Food Canada, 2560 Hochelaga Boulevard, Québec, Québec, G1V 2J3, Canada
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29
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Pinto OHB, Silva TF, Vizzotto CS, Santana RH, Lopes FAC, Silva BS, Thompson FL, Kruger RH. Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. BMC Microbiol 2020; 20:13. [PMID: 31941452 PMCID: PMC6964070 DOI: 10.1186/s12866-020-1698-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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Affiliation(s)
- Otávio H B Pinto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Thais F Silva
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Carla S Vizzotto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.,Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil
| | | | - Fabyano A C Lopes
- Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil
| | - Bruno S Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Ricardo H Kruger
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.
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30
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Dekas AE, Parada AE, Mayali X, Fuhrman JA, Wollard J, Weber PK, Pett-Ridge J. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Front Microbiol 2019; 10:2682. [PMID: 31920997 PMCID: PMC6927911 DOI: 10.3389/fmicb.2019.02682] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/05/2019] [Indexed: 11/28/2022] Open
Abstract
Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle—chemoautotrophic or heterotrophic—of each cell. Most cells (>90%) were anabolically active during the incubation, and 4–17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.
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Affiliation(s)
- Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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31
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Knobloch S, Jóhannsson R, Marteinsson VÞ. Genome analysis of sponge symbiont 'Candidatus Halichondribacter symbioticus' shows genomic adaptation to a host-dependent lifestyle. Environ Microbiol 2019; 22:483-498. [PMID: 31747724 DOI: 10.1111/1462-2920.14869] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 10/03/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022]
Abstract
The marine sponge Halichondria panicea inhabits coastal areas around the globe and is a widely studied sponge species in terms of its biology, yet the ecological functions of its dominant bacterial symbiont 'Candidatus Halichondribacter symbioticus' remain unknown. Here, we present the draft genome of 'Ca. H. symbioticus' HS1 (2.8 Mbp, ca. 87.6% genome coverage) recovered from the sponge metagenome of H. panicea in order to study functions and symbiotic interactions at the genome level. Functional genome comparison of HS1 against closely related free-living seawater bacteria revealed a reduction of genes associated with carbohydrate transport and transcription regulation, pointing towards a limited carbohydrate metabolism, and static transcriptional dynamics reminiscent of other bacterial symbionts. In addition, HS1 was enriched in sponge symbiont specific gene families related to host-symbiont interactions and defence. Similarity in the functional gene repertoire between HS1 and a phylogenetically more distant symbiont in the marine sponge Aplysina aerophoba, based on COG category distribution, suggest a convergent evolution of symbiont specific traits and general metabolic features. This warrants further investigation into convergent genomic evolution of symbionts across different sponge species and habitats.
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Affiliation(s)
- Stephen Knobloch
- Microbiology Group, Department of Research and Innovation, Matís ohf, 113, Reykjavik, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, 101, Reykjavík, Iceland
| | - Ragnar Jóhannsson
- Marine and Freshwater Research Institute, Hafrannsóknastofnun, 101, Reykjavik, Iceland
| | - Viggó Þór Marteinsson
- Microbiology Group, Department of Research and Innovation, Matís ohf, 113, Reykjavik, Iceland.,Faculty of Food Science and Nutrition, University of Iceland, 101, Reykjavik, Iceland
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32
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Lu Y, Xia X, Cheung S, Jing H, Liu H. Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica. Microorganisms 2019; 7:E453. [PMID: 31618850 PMCID: PMC6843251 DOI: 10.3390/microorganisms7100453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/08/2019] [Accepted: 10/13/2019] [Indexed: 11/17/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40-3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.
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Affiliation(s)
- Yanhong Lu
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen 518061, China.
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510220, China.
| | - Shunyan Cheung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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33
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Santoro AE, Kellom M, Laperriere SM. Contributions of single-cell genomics to our understanding of planktonic marine archaea. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190096. [PMID: 31587640 DOI: 10.1098/rstb.2019.0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- A E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106-9620, USA
| | - M Kellom
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106-9620, USA
| | - S M Laperriere
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106-9620, USA
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34
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Zhang F, Jonas L, Lin H, Hill RT. Microbially mediated nutrient cycles in marine sponges. FEMS Microbiol Ecol 2019; 95:5582607. [DOI: 10.1093/femsec/fiz155] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023] Open
Abstract
ABSTRACTEfficient nutrient cycles mediated by symbiotic microorganisms with their hosts are vital to support the high productivity of coral reef ecosystems. In these ecosystems, marine sponges are important habitat-forming organisms in the benthic community and harbor abundant microbial symbionts. However, few studies have reviewed the critical microbially mediated nutrient cycling processes in marine sponges. To bridge this gap, in this review article, we summarize existing knowledge and recent advances in understanding microbially mediated carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles in sponges, propose a conceptual model that describes potential interactions and constraints in the major nutrient cycles, and suggest that shifting redox state induced by animal behavior like sponge pumping can exert great influence on the activities of symbiotic microbial communities. Constraints include the lack of knowledge on spatial and temporal variations and host behavior; more studies are needed in these areas. Sponge microbiomes may have a significant impact on the nutrient cycles in the world’s coral reef ecosystems.
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Affiliation(s)
- Fan Zhang
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Lauren Jonas
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Hanzhi Lin
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
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35
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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36
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Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, Hall R, Martens-Habbena W, Herbold CW, Rhee SK, Bartlett DH, Huang L, Ingalls AE, Wagner M, Stahl DA, Jia Z. Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME JOURNAL 2019; 13:3067-3079. [PMID: 31462715 PMCID: PMC6863869 DOI: 10.1038/s41396-019-0493-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/01/2019] [Accepted: 07/29/2019] [Indexed: 01/04/2023]
Abstract
Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons.
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Affiliation(s)
- Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Yi Ren
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Xue Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Man-Young Jung
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ping Han
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Emiley A Eloe-Fadrosh
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Lu Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xin Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Junbin Ji
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Linmeng Liu
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | | | | | - Willm Martens-Habbena
- Department of Microbiology and Cell Science & Fort Lauderdale Research and Education Center, University of Florida, Gainesville, FL, USA
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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37
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Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019; 21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, Moss Landing, CA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA
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38
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Yi X, Yi K, Fang K, Gao H, Dai W, Cao L. Microbial Community Structures and Important Associations Between Soil Nutrients and the Responses of Specific Taxa to Rice-Frog Cultivation. Front Microbiol 2019; 10:1752. [PMID: 31440215 PMCID: PMC6693445 DOI: 10.3389/fmicb.2019.01752] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/15/2019] [Indexed: 02/04/2023] Open
Abstract
Rice-frog cultivation is a traditional farming system in China and has been reintroduced as an agricultural practice in China in recent years. The microbial community in paddy rhizospheric soils has attracted much attention because many microorganisms participate in functional processes in soils. In this study, Illumina MiSeq sequencing-based techniques were used to investigate soil microbial communities and functional gene patterns across samples obtained by conventional rice cultivation (CR) and rice-frog cultivation (RF). The results showed that RF significantly affected the microbial community composition and richness, which indicated that the rhizospheric microorganisms responded to the introduction of tiger frogs into the paddy fields. Operational taxonomic units (OTUs) from Sandaracinaceae, Anaerolineaceae, Candidatus Nitrososphaera, Candidatus Nitrosotalea, Candidatus Nitrosoarchaeum and some unclassified OTUs from Euryarchaeota and Agaricomycetes were significantly enriched by RF. The abiotic parameters soil organic carbon (SOC), nitrate nitrogen (NO3 --N), and available phosphorus (AP) changed under RF treatment and played essential roles in establishing the soil bacterial, archaeal, and fungal compositions. Correlations between environmental factors and microbial communities were described using network analysis. SOC was strongly correlated with Anaerolineaceae, Methanosaeta, and Scutellinia. NO3 --N showed strong positive correlations with Opitutus, Geobacter, and Methanosaeta. NH4 ++-N was strongly positively associated with Sideroxydans, and TN was strongly positively correlated with Candidatus Nitrotoga. Compared to conventional CR, RF greatly enriched specific microbial taxa. These taxa may be involved in the decomposition of complex organic matter and the transformation of soil nutrients, thus promoting plant growth by improving nutrient cycling. The unique patterns of microbial taxonomic and functional composition in soil profiles suggested functional redundancy in these paddy soils. RF could significantly affect the bacterial, archaeal, and fungal communities though changing SOC and AP levels.
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Affiliation(s)
- Xiaomei Yi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Yi
- China National Cereals, Oils and Foodstuffs Corporation, Beijing, China
| | - Kaikai Fang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Dai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Linkui Cao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Ijichi M, Itoh H, Hamasaki K. Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan. Arch Microbiol 2019; 201:1141-1146. [DOI: 10.1007/s00203-019-01680-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/14/2019] [Accepted: 05/21/2019] [Indexed: 11/30/2022]
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Sollai M, Villanueva L, Hopmans EC, Keil RG, Sinninghe Damsté JS. Archaeal Sources of Intact Membrane Lipid Biomarkers in the Oxygen Deficient Zone of the Eastern Tropical South Pacific. Front Microbiol 2019; 10:765. [PMID: 31031734 PMCID: PMC6470261 DOI: 10.3389/fmicb.2019.00765] [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: 08/09/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membranes with IPLs in a different relative abundance which could be attributed to the different detected population or to an environmental adaptation. Our study sheds light on the complex archaeal community of one of the most prominent ODZs and on the IPL biomarkers they potentially synthesize.
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Affiliation(s)
- Martina Sollai
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Laura Villanueva
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Ellen C Hopmans
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Richard G Keil
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Jaap S Sinninghe Damsté
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands.,Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Xu HJ, Chen H, Wang XL, Zhang YL, Wang JJ, Li N, Li YT. Earthworms stimulate nitrogen transformation in an acidic soil under different Cd contamination. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 165:564-572. [PMID: 30236918 DOI: 10.1016/j.ecoenv.2018.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/06/2018] [Accepted: 09/08/2018] [Indexed: 06/08/2023]
Abstract
In acidic Cd-contaminated soils, soil nitrogen conversion is inhibited and usually block nitrogen supply for plants. Earthworms are well known for improving soil properties and regulating various soil biogeochemical processes including nitrogen cycling. To figure out the effect and mechanisms of earthworms on soil nitrogen transformation in Cd-contaminated soil, ten treatments with and without A. robustus in five soil Cd concentration gradients were established. The tolerant concentration of A. robustus to Cd in the acidic soil is about 6 mg kg-1. The potential ammonia oxidation of the acidic soils was very low, ranging from 0.05 to 0.1 µg NO2--N g-1 d-1. Although AOA was more abundant in the acidic soil than AOB, AOA was inhibited by Cd pollution, while AOB showed some increase under Cd-stress. AOA may play a dominant role in ammonia oxidation in acidic soil, but the recovery of nitrification in Cd-contaminated acidic soil was probably due to the effect of AOB. Earthworms significantly increased soil pH, DOC, ammonium and PAO, thus promoted soil ammonification and potential nitrification, but had no significant effect on soil net nitrification. Correlation analysis results demonstrate that earthworms may promote soil PAO by increasing soil pH, NH4+-N content, and AOB abundance. This study could provide a theoretical basis for solving the problem of nitrogen-cycling-functional degradation and nitrogen supply in the process of phytoremediation of heavy metals-contaminated soils.
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Affiliation(s)
- Hui-Juan Xu
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Hao Chen
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xue-Li Wang
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Yu-Long Zhang
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jin-Jin Wang
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Ning Li
- Guangxi Zhuang Autonomous Region Environmental Monitoring Centre, Nanning 530028, China
| | - Yong-Tao Li
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Nakagawa T, Tsuchiya Y, Ueda S, Fukui M, Takahashi R. Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan. Microbes Environ 2018; 34:13-22. [PMID: 30504642 PMCID: PMC6440730 DOI: 10.1264/jsme2.me18103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
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Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
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Fan X, Yin C, Yan G, Cui P, Shen Q, Wang Q, Chen H, Zhang N, Ye M, Zhao Y, Li T, Liang Y. The contrasting effects of N-(n-butyl) thiophosphoric triamide (NBPT) on N 2O emissions in arable soils differing in pH are underlain by complex microbial mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:155-167. [PMID: 29894875 DOI: 10.1016/j.scitotenv.2018.05.356] [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: 03/16/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
The urease inhibitor, N-(n-butyl) thiophosphoric triamide (NBPT), has been proposed to reduce synthetic fertilizer-N losses, including nitrous oxide (N2O) emissions from agricultural soils. However, the response of N2O emission to NBPT amendment is inconsistent across soils and associated microbial mechanisms remain largely unknown. Here we performed a meta-analysis of the effects of NBPT on N2O emissions and found NBPT significantly reduced N2O emissions in alkaline soils whereas no obvious effects exhibited in acid soils. Based on the finding of meta-analysis that pH was a key modifier in regulating the effect of NBPT on N2O emissions, we selected two arable soils differing in pH and conducted a microcosm study. In conjunction with measurement of N2O emission, community structure and abundance of functional guilds were assessed using T-RFLP and qPCR. Our results showed NBPT retarded urea hydrolysis and inhibited nitrification, but stimulated N2O emission in alkaline soil, whereas it exhibited no remarkable effects in acid soil, thereby only partly confirming the results of meta-analysis. Abundances of AOB and ureC-containing bacteria decreased, while abundance of AOA increased in both soils with NBPT addition. For acid soil, N2O emissions were significantly correlated with both abundances and community structures of AOA and ureC-containing bacteria, as well as abundance of AOB; for alkaline soil, abundances and community structures of AOB were correlated with N2O emission, as well as community structures of ureC-containing bacteria and archaea, indicating an inconsistent response pattern of community traits of N2O emissions-related functional guilds to NBPT between alkaline soil and acid soil. Our findings suggest that (i) efficacy of NBPT in N2O emission was mainly influenced by soil pH and (ii) variable effects of NBPT on N2O emission might originate not only from the direct effect of NBPT on community traits of urease-positive microbes, but from the indirect effect on ammonia oxidizers.
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Affiliation(s)
- Xiaoping Fan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chang Yin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guochao Yan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peiyuan Cui
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Qi Shen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qun Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Nan Zhang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mujun Ye
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, 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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Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME JOURNAL 2018; 13:618-631. [PMID: 30315316 DOI: 10.1038/s41396-018-0289-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Much of the diversity of prokaryotic viruses has yet to be described. In particular, there are no viral isolates that infect abundant, globally significant marine archaea including the phylum Thaumarchaeota. This phylum oxidizes ammonia, fixes inorganic carbon, and thus contributes to globally significant nitrogen and carbon cycles in the oceans. Metagenomics provides an alternative to culture-dependent means for identifying and characterizing viral diversity. Some viruses carry auxiliary metabolic genes (AMGs) that are acquired via horizontal gene transfer from their host(s), allowing inference of what host a virus infects. Here we present the discovery of 15 new genomically and ecologically distinct Thaumarchaeota virus populations, identified as contigs that encode viral capsid and thaumarchaeal ammonia monooxygenase genes (amoC). These viruses exhibit depth and latitude partitioning and are distributed globally in various marine habitats including pelagic waters, estuarine habitats, and hydrothermal plume water and sediments. We found evidence of viral amoC expression and that viral amoC AMGs sometimes comprise up to half of total amoC DNA copies in cellular fraction metagenomes, highlighting the potential impact of these viruses on N cycling in the oceans. Phylogenetics suggest they are potentially tailed viruses and share a common ancestor with related marine Euryarchaeota viruses. This work significantly expands our view of viruses of globally important marine Thaumarchaeota.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. .,Clark University, Worcester, MA, USA.
| | - Clara A Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland, Cambridge, MD, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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"Candidatus Nitrosotenuis aquarius," an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter. Appl Environ Microbiol 2018; 84:AEM.01430-18. [PMID: 29959256 DOI: 10.1128/aem.01430-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia is a metabolic waste product excreted by aquatic organisms that causes toxicity when it accumulates. Aquaria and aquaculture systems therefore use biological filters that promote the growth of nitrifiers to convert ammonia to nitrate. Ammonia-oxidizing bacteria (AOB) have been isolated from aquarium biofilters and are available as commercial supplements, but recent evidence suggests that ammonia-oxidizing archaea (AOA) are abundant in aquarium biofilters. In this study, we report the cultivation and closed genome sequence of the novel AOA representative "Candidatus Nitrosotenuis aquarius," which was enriched from a freshwater aquarium biofilter. "Ca Nitrosotenuis aquarius" oxidizes ammonia stoichiometrically to nitrite with a concomitant increase in thaumarchaeotal cells and a generation time of 34.9 h. "Ca Nitrosotenuis aquarius" has an optimal growth temperature of 33°C, tolerates up to 3 mM NH4Cl, and grows optimally at 0.05% salinity. Transmission electron microscopy revealed that "Ca Nitrosotenuis aquarius" cells are rod shaped, with a diameter of ∼0.4 μm and length ranging from 0.6 to 3.6 μm. In addition, these cells possess surface layers (S-layers) and multiple proteinaceous appendages. Phylogenetically, "Ca Nitrosotenuis aquarius" belongs to the group I.1a Thaumarchaeota, clustering with environmental sequences from freshwater aquarium biofilters, aquaculture systems, and wastewater treatment plants. The complete 1.70-Mbp genome contains genes involved in ammonia oxidation, bicarbonate assimilation, flagellum synthesis, chemotaxis, S-layer production, defense, and protein glycosylation. Incubations with differential inhibitors indicate that "Ca Nitrosotenuis aquarius"-like AOA contribute to ammonia oxidation within the aquarium biofilter from which it originated.IMPORTANCE Nitrification is a critical process for preventing ammonia toxicity in engineered biofilter environments. This work describes the cultivation and complete genome sequence of a novel AOA representative enriched from a freshwater aquarium biofilter. In addition, despite the common belief in the aquarium industry that AOB mediate ammonia oxidation, the present study suggests an in situ role for "Ca Nitrosotenuis aquarius"-like AOA in freshwater aquarium biofilters.
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Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:8429145. [PMID: 30302054 PMCID: PMC6158934 DOI: 10.1155/2018/8429145] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.
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Kiran GS, Sekar S, Ramasamy P, Thinesh T, Hassan S, Lipton AN, Ninawe AS, Selvin J. Marine sponge microbial association: Towards disclosing unique symbiotic interactions. MARINE ENVIRONMENTAL RESEARCH 2018; 140:169-179. [PMID: 29935729 DOI: 10.1016/j.marenvres.2018.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/01/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.
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Affiliation(s)
- G Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Sivasankari Sekar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Pasiyappazham Ramasamy
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | | | - Saqib Hassan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - A S Ninawe
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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49
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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: 63] [Impact Index Per Article: 10.5] [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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Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME JOURNAL 2018; 12:2706-2722. [PMID: 29991764 DOI: 10.1038/s41396-018-0223-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.
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Affiliation(s)
- Sangita Ganesh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.,Radiant Genomics, Emeryville, 94608, CA, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Laura A Bristow
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Nigel Blackwood
- Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Montserrat Aldunate
- Graduate Program in Oceanography, Department of Oceanography, Faculty of Natural Sciences and Oceanography, University of Concepción, Casilla 160-C, Concepción, Chile.,Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | - Annie Bourbonnais
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Mark A Altabet
- School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | | | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.
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