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Tong Y, Zhang Q, Li Z, Meng G, Liu B, Jiang Y, Li S. Autotrophic denitrification by sulfur-based immobilized electron donor for enhanced nitrogen removal: Denitrification performance, microbial interspecific interaction and functional traits. BIORESOURCE TECHNOLOGY 2024; 401:130747. [PMID: 38677382 DOI: 10.1016/j.biortech.2024.130747] [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: 12/29/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
Sulfur-driven autotrophic denitrification (SdAD) is a promising nitrogen removing process, but its applications were generally constrained by conventional electron donors (i.e., thiosulfate (Na2S2O3)) with high valence and limited bioavailability. Herein, an immobilized electron donor by loading elemental sulfur on the surface of polyurethane foam (PFSF) was developed, and its feasibility for SdAD was investigated. The denitrification efficiency of PFSF was 97.3%, higher than that of Na2S2O3 (91.1%). Functional microorganisms (i.e., Thiobacillus and Sulfurimonas) and their metabolic activities (i.e., nir and nor) were substantially enhanced by PFSF. PFSF resulted in the enrichment of sulfate-reducing bacteria, which can reduce sulfate (SO42-). It attenuated the inhibitory effect of SO42-, whereas the generated product (hydrogen sulfide) also served as an electron donor for SdAD. According to the economic evaluation, PFSF exhibited strong market potential. This study proposes an efficient and low-cost immobilized electron donor for SdAD and provides theoretical support to its practical applications.
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Affiliation(s)
- Yangyang Tong
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China
| | - Qin Zhang
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China; Engineering Research Center of Biofilm Water Purification and Utilization Technology of Ministry of Education, Anhui University of Technology, Ma'anshan 243032, China
| | - Zhenghui Li
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China
| | - Guanhua Meng
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China; Engineering Research Center of Biofilm Water Purification and Utilization Technology of Ministry of Education, Anhui University of Technology, Ma'anshan 243032, China.
| | - Baohe Liu
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China; Engineering Research Center of Biofilm Water Purification and Utilization Technology of Ministry of Education, Anhui University of Technology, Ma'anshan 243032, China
| | - Yongbin Jiang
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China; Engineering Research Center of Biofilm Water Purification and Utilization Technology of Ministry of Education, Anhui University of Technology, Ma'anshan 243032, China
| | - Susu Li
- School of Energy and Environment, Anhui University of Technology, Ma'anshan 243002, China
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2
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Visser AN, Martin JD, Osenbrück K, Rügner H, Grathwohl P, Kappler A. In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172062. [PMID: 38554974 DOI: 10.1016/j.scitotenv.2024.172062] [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: 12/04/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.
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Affiliation(s)
- Anna-Neva Visser
- GeoZentrum Nordbayern, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Germany; Department of Geosciences, University of Tübingen, Germany.
| | - Joseph D Martin
- Department of Biology, Terrestrial Ecology, University of Copenhagen, Denmark
| | - Karsten Osenbrück
- Department of Geosciences, University of Tübingen, Germany; Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Hermann Rügner
- Department of Geosciences, University of Tübingen, Germany
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3
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Sharma A, Taubert M, Pérez-Carrascal OM, Lehmann R, Ritschel T, Totsche KU, Lazar CS, Küsel K. Iron coatings on carbonate rocks shape the attached bacterial aquifer community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170384. [PMID: 38281639 DOI: 10.1016/j.scitotenv.2024.170384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 105 cells/mm2 after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 106: 1 and 103: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.
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Affiliation(s)
- Alisha Sharma
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743 Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Grüne Aue, 07745 Jena, Germany
| | - Olga M Pérez-Carrascal
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743 Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Grüne Aue, 07745 Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749 Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749 Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Grüne Aue, 07745 Jena, Germany; Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749 Jena, Germany
| | - Cassandre S Lazar
- Department of Biological Sciences, University of Quebec at Montreal, C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743 Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Grüne Aue, 07745 Jena, Germany; German Center for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany.
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4
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Hermawan OR, Hosono T, Yasumoto J, Yasumoto K, Song KH, Maruyama R, Iijima M, Yasumoto-Hirose M, Takada R, Hijikawa K, Shinjo R. Mechanism of denitrification in subsurface-dammed Ryukyu limestone aquifer, southern Okinawa Island, Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169457. [PMID: 38135078 DOI: 10.1016/j.scitotenv.2023.169457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Denitrification crucially regulates the attenuation of groundwater nitrate and is unlikely to occur in a fast-flowing aquifer such as the Ryukyu limestone aquifer in southern Okinawa Island, Japan. However, evidences of denitrification have been observed in several wells within this region. This study analyzed environmental isotopes (δ15NNO3 and ẟ18ONO3) to derive the rationale for denitrification at this site. Additionally, the presence of two subsurface dams in the study area may influence the processes involved in nitrate attenuation. Herein, we analyzed 150 groundwater samples collected spatially and seasonally to characterize the variations in the groundwater chemistry and stable isotopes during denitrification. The values of δ15NNO3 and δ18ONO3 displayed a progressive trend up to +59.7 ‰ and + 21 ‰, respectively, whereas the concentrations of NO3--N decreased to 0.1 mg L-1. In several wells, the enrichment factors of δ15NNO3 ranged from -6.6 to -2.1, indicating rapid denitrification, and the δ15NNO3 to δ18ONO3 ratios varied from 1.3:1 to 2:1, confirming the occurrence of denitrification. Denitrification intensively proceeds under conditions of depleted dissolved oxygen concentrations (<2 mg L-1), sluggish groundwater flow with longer residence times, high concentrations of dissolved organic carbon (>1.2 mg L-1), and low groundwater levels during the dry season with precipitation rates of <100 mm per month (Jun-Sep). SF6 analysis indicated the exclusive occurrence of denitrification in specific wells with groundwater residence times exceeding 30 years. These wells are located in close proximity to the major NE-SW fault system in the Komesu area, where the hydraulic gradient was below 0.005. Detailed geological and lithological investigations based on borehole data revealed that subsurface dams did not cause denitrification while the major NE-SW fault system uplifted the impermeable basement rock of the Shimajiri Group, creating a lithological gap at an equivalent depth that ultimately formed a sluggish groundwater area, promoting denitrification.
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Affiliation(s)
- Oktanius Richard Hermawan
- Department of Earth and Environmental Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.
| | - Takahiro Hosono
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan; International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan; Research Institute for Humanity and Nature, 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047, Japan
| | - Jun Yasumoto
- Department of Regional Agriculture Engineering, University of the Ryukyus, 1-Senbaru, Nakagami District, Nishihara, Okinawa 903-0213, Japan
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0373, Japan
| | - Ke-Han Song
- Graduate School of Engineering and Science, University of the Ryukyus, 1-Senbaru, Nakagami District, Nishihara, Okinawa 903-0213, Japan
| | - Rio Maruyama
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0373, Japan
| | - Mariko Iijima
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | | | - Ryogo Takada
- Center for Strategic Research Projects, University of the Ryukyus, 1-Senbaru, Nakagami District, Nishihara, Okinawa 903-0213, Japan
| | - Kento Hijikawa
- Department of Regional Agriculture Engineering, University of the Ryukyus, 1-Senbaru, Nakagami District, Nishihara, Okinawa 903-0213, Japan; Overseas Land Improvement Cooperation Office, Rural Development Bureau, Ministry of Agriculture, Forestry, and Fisheries of Japan, 1-2-1 Kasumigaseki, Chiyoda, Tokyo 100-8950, Japan
| | - Ryuichi Shinjo
- Research Institute for Humanity and Nature, 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047, Japan; Graduate School of Engineering and Science, University of the Ryukyus, 1-Senbaru, Nakagami District, Nishihara, Okinawa 903-0213, Japan
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5
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Qin Y, Wu L, Zhang Q, Wen C, Van Nostrand JD, Ning D, Raskin L, Pinto A, Zhou J. Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing. mSystems 2023; 8:e0102523. [PMID: 38038441 PMCID: PMC10734440 DOI: 10.1128/msystems.01025-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.
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Affiliation(s)
- Yujia Qin
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Qiuting Zhang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Chongqin Wen
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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6
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Lazar CS, Schwab VF, Ueberschaar N, Pohnert G, Trumbore S, Küsel K. Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters. Front Microbiol 2023; 14:1252498. [PMID: 37901809 PMCID: PMC10602745 DOI: 10.3389/fmicb.2023.1252498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, University of Quebec at Montreal (UQAM), Montreal, QC, Canada
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Valérie F. Schwab
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Susan Trumbore
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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7
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Langlois K, Collier JL. Matrix-associated microbial communities in a nitrogen-removing on-site wastewater treatment system are largely structured by niche processes. JOURNAL OF ENVIRONMENTAL QUALITY 2023; 52:35-48. [PMID: 36305592 DOI: 10.1002/jeq2.20422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
On-site wastewater treatment systems (OWTSs) can be designed to promote microbial communities with naturally occurring metabolic functions desirable to wastewater treatment. Among such OWTSs are nitrogen-removing biofilters (NRBs), comprising a sand layer overlying a sand-lignocellulose (sand-lc) layer and intended to promote sequential nitrification and denitrification. The design of NRBs is based on the hypothesis that niche processes like environmental selection strongly structure the microbial communities, which predicts that immigrating wastewater communities and matrix-associated communities will be distinct and that the matrix communities in the two layers will be distinct. We characterized NRB microbial communities by 16S ribosomal RNA amplicon sequencing. Selection of the matrix-associated communities was indicated by clear differences from the immigrating community. For matrix-associated communities, alpha and beta diversity differed between the matrix layers, as did the relative abundances of many functional groups and genera. Functional groups with strict metabolisms were nearly exclusively detected in either the sand (ammonia and nitrite oxidizers) or sand-lc layer (methanogens), consistent with the niche hypothesis. Contrary to expectations, denitrifiers as a functional group were not present at greater relative abundance in the sand-lc than sand matrix because of a portfolio effect: some denitrifying genera were more abundant in the sand layer, whereas others were more abundant in the sand-lc layer. This study reveals niche processes acting at different levels of community organization for different biogeochemical functions, a crucial consideration in designing effective and reliable OWTSs to mitigate nitrogen pollution.
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Affiliation(s)
- Kylie Langlois
- School of Marine and Atmospheric Sciences, Stony Brook Univ., Stony Brook, NY, 11794, USA
- Center for Clean Water Technology, Stony Brook Univ., Stony Brook, NY, 11794, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook Univ., Stony Brook, NY, 11794, USA
- Center for Clean Water Technology, Stony Brook Univ., Stony Brook, NY, 11794, USA
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8
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Shu W, Wang P, Zhao J, Ding M, Zhang H, Nie M, Huang G. Sources and migration similarly determine nitrate concentrations: Integrating isotopic, landscape, and biological approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158216. [PMID: 36028031 DOI: 10.1016/j.scitotenv.2022.158216] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Rapid land use change has significantly increased nitrate (NO3-) loading to rivers, leading to eutrophication, and posing water security problems. Determining the sources of NO3- to waters and the underlying influential factors is critical for effectively reducing pollution and better managing water resources. Here, we identified the sources and influencing mechanisms of NO3- in a mixed land-use watershed by integrating stable isotopes (δ15N-NO3- and δ18O-NO3-), molecular biology, water chemistry, and landscape metrics measurements. Weak transformation processes of NO3- were identified in the river, as evinced by water chemistry, isotopes, species compositions, and predicted microbial genes related to nitrogen metabolism. NO3- concentrations were primarily influenced by exogenous inputs (i.e., from soil nitrogen (NS), nitrogen fertilizer (NF), and manure & sewage (MS)). The proportions of NO3- sources seasonally varied. In the wet season, the source contributions followed the order of NS (38.6 %) > NF (31.4 %) > atmospheric deposition (ND, 16.2 %) > MS (13.8 %). In the dry season, the contributions were in the order of MS (39.2 %) > NS (29.2 %) > NF (29 %) > ND (2.6 %). Farmland and construction land were the original factors influencing the spatial distribution of NO3- in the wet and dry seasons, respectively, while slope, basin relief (HD), hypsometric integral (HI), and COHESION, HD were the primary indicators associated with NO3- transport in the wet and dry seasons, respectively. Additionally, spatial scale differences were observed for the effects of landscape structure on NO3- concentrations, with the greatest effect at the 1000-m buffer zone scale in the wet season and at the sub-basin scale in the dry season. This study overcomes the limitation of isotopes in identifying nitrate sources by combining multiple approaches and provides new research perspectives for the determination of nitrate sources and migration in other watersheds.
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Affiliation(s)
- Wang Shu
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, Jiangxi, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research, Beijing 101408, China
| | - Peng Wang
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Jun Zhao
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Minjun Ding
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Hua Zhang
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Minghua Nie
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Gaoxiang Huang
- School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
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9
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Zhou N, Kupper RJ, Catalano JG, Thompson A, Chan CS. Biological Oxidation of Fe(II)-Bearing Smectite by Microaerophilic Iron Oxidizer Sideroxydans lithotrophicus Using Dual Mto and Cyc2 Iron Oxidation Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17443-17453. [PMID: 36417801 PMCID: PMC9731265 DOI: 10.1021/acs.est.2c05142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Fe(II) clays are common across many environments, making them a potentially significant microbial substrate, yet clays are not well established as an electron donor. Therefore, we explored whether Fe(II)-smectite supports the growth of Sideroxydans lithotrophicus ES-1, a microaerophilic Fe(II)-oxidizing bacterium (FeOB), using synthesized trioctahedral Fe(II)-smectite and 2% oxygen. S. lithotrophicus grew substantially and can oxidize Fe(II)-smectite to a higher extent than abiotic oxidation, based on X-ray near-edge spectroscopy (XANES). Sequential extraction showed that edge-Fe(II) is oxidized before interior-Fe(II) in both biotic and abiotic experiments. The resulting Fe(III) remains in smectite, as secondary minerals were not detected in biotic and abiotic oxidation products by XANES and Mössbauer spectroscopy. To determine the genes involved, we compared S. lithotrophicus grown on smectite versus Fe(II)-citrate using reverse-transcription quantitative PCR and found that cyc2 genes were highly expressed on both substrates, while mtoA was upregulated on smectite. Proteomics confirmed that Mto proteins were only expressed on smectite, indicating that ES-1 uses the Mto pathway to access solid Fe(II). We integrate our results into a biochemical and mineralogical model of microbial smectite oxidation. This work increases the known substrates for FeOB growth and expands the mechanisms of Fe(II)-smectite alteration in the environment.
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Affiliation(s)
- Nanqing Zhou
- School
of Marine Science and Policy, University
of Delaware, Newark, Delaware 19716, United
States
| | - Robert J. Kupper
- Department
of Earth and Planetary Sciences, Washington
University in St. Louis, Saint
Louis, Missouri 63130, United States
| | - Jeffrey G. Catalano
- Department
of Earth and Planetary Sciences, Washington
University in St. Louis, Saint
Louis, Missouri 63130, United States
| | - Aaron Thompson
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
| | - Clara S. Chan
- School
of Marine Science and Policy, University
of Delaware, Newark, Delaware 19716, United
States
- Department
of Earth Sciences, University of Delaware, Newark, Delaware 19716, United States
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10
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Guan Y, Hou T, Li X, Feng L, Wang Z. Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments. ENVIRONMENTAL RESEARCH 2022; 212:113592. [PMID: 35654160 DOI: 10.1016/j.envres.2022.113592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/17/2022] [Accepted: 05/29/2022] [Indexed: 05/27/2023]
Abstract
As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO3--N and NO2--N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH4+-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH4+-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO3-, NO2--N and an increase in NH4+-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO3--N to N2. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.
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Affiliation(s)
- Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Leilei Feng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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11
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A Plea for Considering Processes That Take Place on the Micrometer Scale in Modelling the Groundwater Ecosystems’ Functions. WATER 2022. [DOI: 10.3390/w14121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The largest freshwater ecosystem on earth is in the subsurface: the groundwater. It is populated by animals of almost all phyla and by bacteria, archaea, and fungi. Processes on the macro-, meso-, and micro-scale shape this ecosystem. Bioremediation, i.e., the degradation of contaminants, is steered on the scale of micrometers. However, processes that take place on the micrometer scale are still poorly understood and have not been studied extensively. They are usually lacking from models. In this communication, the plea for studying and making models for the processes that take place on the micrometer scale is based on the conceptual model of bottom-up effects of the pore scale environment. Such conceptual models may influence how quantitative models are built by structuring them.
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Chakraborty A, Suchy M, Hubert CRJ, Ryan MC. Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153092. [PMID: 35038526 DOI: 10.1016/j.scitotenv.2022.153092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/29/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Nitrate pollution is a major threat to groundwater quality in agricultural areas. Natural attenuation of nitrate in contaminated aquifers is mediated by denitrifying microbial populations in anoxic environments. Vertical distribution of denitrifying microbial communities in aquifers is greatly influenced by groundwater redox conditions, local hydrogeological parameters, and seasonal variability in groundwater flow and recharge. In this study, we investigated groundwater geochemistry and the composition of bacterial and archaeal communities with increasing depth in a shallow nitrate-contaminated aquifer in British Columbia, Canada. High-resolution passive diffusion sampling was conducted to collect groundwater at 10-cm intervals from 4 to 20 m below ground surface (mbgs) in the aquifer. Geochemical analyses of major ions indicated a general shift in the groundwater chemistry below 16 mbgs including decreasing chloride concentrations that suggest two-end member mixing of shallow and deep groundwater with different chemistries. A redoxcline was further observed within a 2 m transition zone at 18-20 mbgs characterized by sharp declines in nitrate concentrations and increases in sulfate and total inorganic carbon. Excursions in δ15N-NO3- and δ18O-NO3- in the same depth interval are consistent with denitrification, and a concomitant decrease in δ34S-SO42- suggested that denitrification was coupled to sulfide or sulfur oxidation. Microbial communities within this depth interval were significantly dissimilar to those above and below, featuring putative lithotrophic denitrifying bacteria belonging to the genera Sulfurifustis, Sulfuritalea and Sulfuricella. These lineages were detected in greatest abundance at 19 mbgs while the abundances of putative heterotrophic sulfate-reducing bacteria belonging to the genus Desulfosporosinus were greatest at 20 mbgs. In addition to help distinguish denitrification from mixing-induced changes in groundwater chemistry, the above observed vertical stratification of the microbial key players connects nitrate removal to the locations of the aquifer sampled.
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Affiliation(s)
- Anirban Chakraborty
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Martin Suchy
- Environment and Climate Change Canada, Vancouver, British Columbia, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - M Cathryn Ryan
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
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Zhou N, Keffer JL, Polson SW, Chan CS. Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR. Appl Environ Microbiol 2022; 88:e0159521. [PMID: 34788064 PMCID: PMC8788666 DOI: 10.1128/aem.01595-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/11/2021] [Indexed: 11/20/2022] Open
Abstract
Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.
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Affiliation(s)
- Nanqing Zhou
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
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14
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Nicholls HCG, Rolfe SA, Mallinson HEH, Hjort M, Spence MJ, Bonte M, Thornton SF. Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1223-1238. [PMID: 34350568 PMCID: PMC8724112 DOI: 10.1007/s11356-021-15606-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Microbes in aquifers are present suspended in groundwater or attached to the aquifer sediment. Groundwater is often sampled at gasoline ether oxygenate (GEO)-impacted sites to assess the potential biodegradation of organic constituents. However, the distribution of GEO-degrading microorganisms between the groundwater and aquifer sediment must be understood to interpret this potential. In this study, the distribution of ethyl tert-butyl ether (ETBE)-degrading organisms and ETBE biodegradation potential was investigated in laboratory microcosm studies and mixed groundwater-aquifer sediment samples obtained from pumped monitoring wells at ETBE-impacted sites. ETBE biodegradation potential (as determined by quantification of the ethB gene) was detected predominantly in the attached microbial communities and was below detection limit in the groundwater communities. The copy number of ethB genes varied with borehole purge volume at the field sites. Members of the Comamonadaceae and Gammaproteobacteria families were identified as responders for ETBE biodegradation. However, the detection of the ethB gene is a more appropriate function-based indicator of ETBE biodegradation potential than taxonomic analysis of the microbial community. The study shows that a mixed groundwater-aquifer sediment (slurry) sample collected from monitoring wells after minimal purging can be used to assess the aquifer ETBE biodegradation potential at ETBE-release sites using this function-based concept.
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Affiliation(s)
- Henry C G Nicholls
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK
| | - Stephen A Rolfe
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, S10 2TN, Sheffield, UK
| | - Helen E H Mallinson
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK
| | - Markus Hjort
- Concawe, Boulevard du Souverain 165, 1160, Brussels, Belgium
| | - Michael J Spence
- Concawe, Boulevard du Souverain 165, 1160, Brussels, Belgium
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham, NG12 5GG, UK
| | - Matthijs Bonte
- Concawe, Boulevard du Souverain 165, 1160, Brussels, Belgium
- Shell Global Solutions International B.V., Rijswijk, 2288GK, The Netherlands
- Ministry of Infrastructure and Water Management, The Hague, The Netherlands
| | - Steven F Thornton
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK.
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15
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Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer. Appl Environ Microbiol 2021; 87:e0046021. [PMID: 34085863 DOI: 10.1128/aem.00460-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer, and as such, there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic cosubstrates for growth, within 7 to 11 days, 0.3 to 0.5 mM nitrate was reduced and 1.3 to 2 mM iron(II) was oxidized, leading to a stoichiometric NO3-/Fe(II) ratio of 0.2, with N2 and N2O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals, but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, and microaerophilic iron(II) oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically affected aquifers. IMPORTANCE Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment, and as such, there are no model cultures available to study the rate-limiting factors of this potentially important process. Here, we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II) oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N2O and N2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.
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16
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Ruiz-González C, Rodellas V, Garcia-Orellana J. The microbial dimension of submarine groundwater discharge: current challenges and future directions. FEMS Microbiol Rev 2021; 45:6128669. [PMID: 33538813 PMCID: PMC8498565 DOI: 10.1093/femsre/fuab010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC). Passeig Marítim de la Barceloneta 37-49, E08003 Barcelona, Spain
| | - Valentí Rodellas
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
| | - Jordi Garcia-Orellana
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain.,Departament de Física, Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
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17
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Xia Z, Liu G, She Z, Gao M, Zhao Y, Guo L, Jin C. Performance and bacterial communities in unsaturated and saturated zones of a vertical-flow constructed wetland with continuous-feed. BIORESOURCE TECHNOLOGY 2020; 315:123859. [PMID: 32707509 DOI: 10.1016/j.biortech.2020.123859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/12/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
In this study, a partially-saturated vertical-flow constructed wetland (VFCW) with continuous-feed was operated to investigate nutrients transformation and possible pathways in unsaturated and saturated zones. Effect of temperature on nutrients removal and microbial community was also evaluated. The variation of temperature barely affected removal of NH4+-N and COD, achieving removal efficiencies of 99.5-100.0% and 96.8-100.0% at effluent temperature of 14.9-27.7 °C. The removal of COD, NH4+-N, total inorganic nitrogen (TIN) and total phosphorus mainly occurred in unsaturated zone, achieving much higher removal rates than saturated zone. Nitrification process in the VFCW was associated with autotrophic/heterotrophic ammonia oxidizing bacteria and nitrite oxidizing bacteria. Denitrification process relied on both autotrophic and heterotrophic denitrifiers. Anaerobic ammonium oxidizing bacteria was also detected, contributing to TIN removal. All of the groups for nutrients removal exhibited higher abundance in unsaturated zone. Diverse pathways co-existed for nitrogen removal, while the main metabolic pathways were different along the depth.
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Affiliation(s)
- Zhengang Xia
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China
| | - Guochen Liu
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China. 266100 Qingdao, China.
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China. 266100 Qingdao, China
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China. 266100 Qingdao, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China. 266100 Qingdao, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China. 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China. 266100 Qingdao, China
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18
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Kirs M, Kisand V, Nelson CE, Dudoit T, Moravcik PS. Distinct bacterial communities in tropical island aquifers. PLoS One 2020; 15:e0232265. [PMID: 32353009 PMCID: PMC7192444 DOI: 10.1371/journal.pone.0232265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/10/2020] [Indexed: 11/23/2022] Open
Abstract
The groundwater biome is a poorly characterized habitat hypothesized to harbor uniquely diverse bacterial communities; the degree to which these communities differ from associated soils is a central question in environmental microbiology. We characterized the Bacterial community composition in 37 aquifer and 32 surface soil samples across the island of O‘ahu, Hawaiʻi. Several bacterial phyla (Acetothermia, Omnitrophica, Parcubacteria, Peregrinibacteria) relatively abundant in the aquifer samples were rare to absent in the soils. Immense bacterial diversity detected in the deep aquifers indicates that these environments are not as homogenous as expected, but provide various niches and energy sources for wide variety of bacteria. A small proportion of OTUs were widespread in all the basal (0.63%) and all the dike aquifer (0.31%) samples. However, these core bacteria comprised an average of 31.8% (ranging 16.2%-62.0%) and 15.4% (0.1%-31.5%) of all sequences isolated from the basal and dike aquifers respectively. Bacterial community composition correlated significantly with the sodium, sulfate, potassium, total dissolved solids, nitrate, conductivity, and pH in the basal aquifers, while phosphate and bicarbonate levels were also highly important when dike water samples were included in the analyses. This was consistent with high relative abundance of putative chemolithoautoroph taxa in the aquifer communities relative to soils. Targeted molecular and culture-based fecal indicator microbial analyses indicated good water quality of aquifers. The dominance of unique, deeply branching lineages in tropical aquifers emphasizes a large adaptive potential in O‘ahu’s aquifers; variability among groundwater samples suggests that aquifer habitats are surprisingly variable potentially harboring a variety of chemolithotrophic energy sources. Although parallel analyses of conventional and alternative indicators indicated good groundwater quality, this study calls for groundwater monitoring programs which would consider public as well as ecosystem health.
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Affiliation(s)
- Marek Kirs
- Water Resources Research Center, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
- * E-mail:
| | - Veljo Kisand
- Institute of Technology, Tartu University, Tartu, Estonia
| | - Craig E. Nelson
- Department of Oceanography and UH Sea Grant, Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
| | - Tineill Dudoit
- Water Resources Research Center, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
| | - Philip S. Moravcik
- Water Resources Research Center, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
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Yang Z, Guan Y, Bello A, Wu Y, Ding J, Wang L, Ren Y, Chen G, Yang W. Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China. PeerJ 2020; 8:e8844. [PMID: 32341890 PMCID: PMC7182023 DOI: 10.7717/peerj.8844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China.
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Affiliation(s)
- Zhongzan Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yupeng Guan
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yanxiang Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jiayi Ding
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Leiqi Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yuqing Ren
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Guangxin Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
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20
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Abstract
Groundwater is the environmental matrix that is most frequently affected by anthropogenic hexavalent chromium contamination. Due to its carcinogenicity, Cr(VI) has to be removed, using environmental-friendly and economically sustainable remediation technologies. BioElectrochemical Systems (BESs), applied to bioremediation, thereby offering a promising alternative to traditional bioremediation techniques, without affecting the natural groundwater conditions. Some bacterial families are capable of oxidizing and/or reducing a solid electrode obtaining an energetic advantage for their own growth. In the present study, we assessed the possibility of stimulating bioelectrochemical reduction of Cr(VI) in a dual-chamber polarized system using an electrode as the sole energy source. To develop an electroactive microbial community three electrodes were, at first, inserted into the anodic compartment of a dual-chamber microbial fuel cell, and inoculated with sludge from an anaerobic digester. After a period of acclimation, one electrode was transferred into a polarized system and it was fixed at −0.3 V (versus standard hydrogen electrode, SHE), to promote the reduction of 1000 µg Cr(VI) L−1. A second electrode, served for the set-up of an open circuit control, operated in parallel. Cr(VI) dissolved concentration was analysed at the initial, during the experiment and final time by spectrophotometric method. Initial and final microbial characterization of the communities enriched in polarized system and open circuit control was performed by 16S rRNA gene sequencing. The bioelectrode set at −0.3 V showed high Cr(VI) removal efficiency (up to 93%) and about 150 µg L−1 day−1 removal rate. Similar efficiency was observed in the open circuit (OC) even at about half rate. Whereas, purely electrochemical reduction, limited to 35%, due to neutral operating conditions. These results suggest that bioelectrochemical Cr(VI) removal by polarized electrode offers a promising new and sustainable approach to the treatment of groundwater Cr(VI) plumes, deserving further research.
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21
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Xia Z, Wang Q, She Z, Gao M, Zhao Y, Guo L, Jin C. Nitrogen removal pathway and dynamics of microbial community with the increase of salinity in simultaneous nitrification and denitrification process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134047. [PMID: 31491641 DOI: 10.1016/j.scitotenv.2019.134047] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
In this study, simultaneous nitrification and denitrification (SND) process was successfully established in a hybrid sequencing batch biofilm reactor (HSBBR). High removal efficiency of NH4+-N (98.0±2.4% to 99.8±0.4%) and COD (86.6±4.0% to 91.6±1.8%) was observed in the salinity range of 0.0 to 2.4%. SND via nitrite, replacing SND via nitrate, became the main nitrogen removal pathway at 1.6% and 2.4% salinity. Suspended sludge and biofilm shared similar microbial composition. Dominant genera were substituted by salt-adaptable microbes as salinity increasing. Abundance of autotrophic ammonia-oxidizing bacteria (Nitrosomonas) increased with elevated salinity, while autotrophic nitrite-oxidizing bacteria (Nitrospira) exhibited extreme sensitivity to salinity. The presence of Gemmata demonstrated that heterotrophic nitrification co-existed with autotrophic nitrification in the SND process. Aerobic denitrifiers (Denitratisoma and Thauera) were also identified. Thiothrix, Sedimenticola, Sulfuritalea, Arcobacter (sulfide-based autotrophic denitrifier) and Hydrogenophaga (hydrogen-based autotrophic denitrifier) were detected in both S-sludge and biofilm. The occurrence of ANAMMOX bacteria Pirellula and Planctomyces indicated that ANAMMOX process was another pathway for nitrogen removal. Nitrogen removal in the HSBBR was accomplished via diverse pathways, including traditional autotrophic nitrification/heterotrophic denitrification, heterotrophic nitrification, aerobic and autotrophic denitrification, and ANAMMOX.
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Affiliation(s)
- Zhengang Xia
- College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China
| | - Qun Wang
- College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China.
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, 266100 Qingdao, China; College of Environmental Science and Engineering, Ocean University of China, 266100 Qingdao, China
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22
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Watanabe T, Kojima H, Umezawa K, Hori C, Takasuka TE, Kato Y, Fukui M. Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera. Front Microbiol 2019; 10:316. [PMID: 30858836 PMCID: PMC6397845 DOI: 10.3389/fmicb.2019.00316] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/06/2019] [Indexed: 01/08/2023] Open
Abstract
Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘Sulfuricellaceae’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.
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Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Umezawa
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Chiaki Hori
- Research Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yukako Kato
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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23
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Savio D, Stadler P, Reischer GH, Demeter K, Linke RB, Blaschke AP, Mach RL, Kirschner AKT, Stadler H, Farnleitner AH. Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community. Front Microbiol 2019; 10:28. [PMID: 30828319 PMCID: PMC6385617 DOI: 10.3389/fmicb.2019.00028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/09/2019] [Indexed: 11/13/2022] Open
Abstract
Alpine karst aquifers are important groundwater resources for the provision of drinking water all around the world. Yet, due to difficult accessibility and long-standing methodological limitations, the microbiology of these systems has long been understudied. The aim of the present study was to investigate the structure and dynamics of bacterial communities in spring water of an alpine limestone karst aquifer (LKAS2) under different hydrological conditions (base vs. event flow). The study was based on high-throughput 16S rRNA gene amplicon sequencing, study design and sample selection were guided by hydrology and pollution microbiology data. Spanning more than 27 months, our analyses revealed a taxonomically highly stable bacterial community, comprising high proportions of yet uncultivated bacteria in the suspended bacterial community fraction. Only the three candidate phyla Parcubacteria (OD1), Gracilibacteria (GN02), Doudnabacteria (SM2F11) together with Proteobacteria and Bacteroidetes contributed between 70.0 and 88.4% of total reads throughout the investigation period. A core-community of 300 OTUs consistently contributed between 37.6 and 56.3% of total reads, further supporting the hypothesis of a high temporal stability in the bacterial community in the spring water. Nonetheless, a detectable response in the bacterial community structure of the spring water was discernible during a high-discharge event. Sequence reads affiliated to the class Flavobacteriia clearly increased from a mean proportion of 2.3% during baseflow to a maximum of 12.7% during the early phase of the studied high-discharge event, suggesting direct impacts from changing hydrological conditions on the bacterial community structure in the spring water. This was further supported by an increase in species richness (Chao1) at higher discharge. The combination of these observations allowed the identification and characterization of three different discharge classes (Q1-Q3). In conclusion, we found a taxonomically stable bacterial community prevailing in spring waters from an alpine karst aquifer over the entire study period of more than 2 years. Clear response to changing discharge conditions could be detected for particular bacterial groups, whereas the most responsive group - bacteria affiliated to the class of Flavobacteriia - might harbor potential as a valuable natural indicator of "system disturbances" in karst aquifers.
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Affiliation(s)
- Domenico Savio
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
| | - Philipp Stadler
- Centre for Water Resource Systems, TU Wien, Vienna, Austria.,Research Unit for Water Quality Management, Institute for Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Georg H Reischer
- Molecular Diagnostics Group, Institute of Chemical, Environmental and Bioscience Engineering, Department of Agrobiotechnology, IFA-Tulln, TU Wien, Tulln an der Donau, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katalin Demeter
- Centre for Water Resource Systems, TU Wien, Vienna, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Rita B Linke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alfred P Blaschke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Vienna, Austria
| | - Robert L Mach
- Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alexander K T Kirschner
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Hermann Stadler
- Department for Water Resources Management and Environmental Analytics, Institute for Water, Energy and Sustainability, Joanneum Research, Graz, Austria
| | - Andreas H Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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24
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Li M, Ren L, Zhang J, Luo L, Qin P, Zhou Y, Huang C, Tang J, Huang H, Chen A. Population characteristics and influential factors of nitrogen cycling functional genes in heavy metal contaminated soil remediated by biochar and compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:2166-2174. [PMID: 30326449 DOI: 10.1016/j.scitotenv.2018.10.152] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Sixteen treatments of soil contaminated by Cu, Pb, and Zn by the addition of a different percentage of biochar and compost were incubated for 120 days. The abundance of denitrifying genes such as narG, nirK, nirS and nosZ and the ammonia-oxidizing amoA genes of ammonia-oxidizing archaea/bacteria (AOA/AOB), soil nitrite reductase activity (S-NiR) and their shaping factors were also determined. The relationships between functional genes, S-NiR, and physico-chemical parameters were analyzed using the Pearson correlation method. The study found that the changes in physico-chemical parameters, including water-soluble organic carbon (WSC), nitrate (NO3-) and ammonium (NH4+), were predominant in different treatments. The abundance of nirK and narG genes is most sensitive to the changes in the properties of the soil sample. Bacterial 16S rDNA gene abundance was significantly affected by NO3- and S-NiR (P < 0.05). Nitrifying genes were mainly correlated to WSC and S-NiR, while denitrifying genes were associated with pH, electrical conductivity, NO3- and S-NiR. The systematic study for the relationship between the genes and the environmental parameters will help us to deep understand the biological mechanisms of nitrogen cycle in heavy metal contaminated soils remediated by biochar and compost.
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Affiliation(s)
- Mingyue Li
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Liheng Ren
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Pufeng Qin
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.
| | - Chao Huang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jiayi Tang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
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25
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Effects of the natural restoration time of abandoned farmland in a semiarid region on the soil denitrification rates and abundance and community structure of denitrifying bacteria. Appl Microbiol Biotechnol 2019; 103:1939-1951. [DOI: 10.1007/s00253-018-09575-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/11/2022]
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26
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Hershey OS, Kallmeyer J, Wallace A, Barton MD, Barton HA. High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer. Front Microbiol 2018; 9:2823. [PMID: 30534116 PMCID: PMC6275181 DOI: 10.3389/fmicb.2018.02823] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56-9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.
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Affiliation(s)
- Olivia S Hershey
- Department of Biology, University of Akron, Akron, OH, United States
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Andrew Wallace
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, United States
| | | | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, United States.,Department of Geosciences, University of Akron, Akron, OH, United States
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27
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Bryce C, Blackwell N, Schmidt C, Otte J, Huang YM, Kleindienst S, Tomaszewski E, Schad M, Warter V, Peng C, Byrne JM, Kappler A. Microbial anaerobic Fe(II) oxidation - Ecology, mechanisms and environmental implications. Environ Microbiol 2018; 20:3462-3483. [DOI: 10.1111/1462-2920.14328] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/15/2018] [Accepted: 06/16/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Casey Bryce
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Nia Blackwell
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | | | - Julia Otte
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Yu-Ming Huang
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | | | | | - Manuel Schad
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Viola Warter
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Chao Peng
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - James M. Byrne
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Andreas Kappler
- Geomicrobiology; University of Tübingen; Tübingen Germany
- Center for Geomicrobiology, Department of Bioscience; Aarhus University; Aarhus Denmark
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28
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Kumar S, Herrmann M, Blohm A, Hilke I, Frosch T, Trumbore SE, Küsel K. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol Ecol 2018; 94:5056153. [DOI: 10.1093/femsec/fiy141] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/18/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Swatantar Kumar
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Annika Blohm
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, D-07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Torsten Frosch
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, D-07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Albert-Einstein-Strasse 6, D-07745, Jena, Germany
| | - Susan E Trumbore
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
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29
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Wu Y, Xu L, Wang S, Wang Z, Shang J, Li X, Zheng C. Nitrate attenuation in low-permeability sediments based on isotopic and microbial analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:15-25. [PMID: 29126024 DOI: 10.1016/j.scitotenv.2017.11.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/03/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
This study investigated nitrate attenuation in low-permeability sediments (LPS) in a multi-layer aquifer by integrating hydrochemical, isotopic and microbiological molecular techniques in a field site. In the meantime, the overlying high-permeability sediment (HPS) was also examined on the nitrate attenuation for the sake of comparison. Additionally, laboratory flow-through experiments were conducted to assess the overall nitrate reduction rate in the two types of sediment. The δ15N-NO3- and δ34S-SO42- values were more enriched by approximately 37‰ and 15‰ in the LPS than the overlying HPS associated with substantial reductions of the NO3- and SO42- concentration, indicating the occurrence of strong bio-reductions in nitrate and sulfate. The microbial community diversity analyses showed a higher diversity of the denitrifiers encoding nirS- (Shannon Index SI=6.3) and nrf-type gene (SI=2.7), and the sulfate reduction bacteria (SRB) encoding the dsr gene (SI=6.4) in the LPS than in the HPS. The bacterial community structure was influenced by the groundwater hydrochemistry and the redox conditions. Due to the presence of anoxic groundwater with low levels of nutrients, the LPS featured higher abundances of nitrate reducers belonging to Alphaproteobacteria and SRB belonging to the strictly anaerobic class Clostridia relative to the HPS. Notably, chemolithotrophs were abundant in the LPS and likely coupled the reduction of nitrate with the oxidation of iron. Furthermore, the LPS was demonstrated to attenuate nitrate at a rate two times of the HPS in flow-through experiments, and denitrification accounted for approximately 93% of the nitrate reduction. The high nitrate reduction rate of the LPS was likely attributable to its high functional genes diversity. This study confirmed the occurrence of strong nitrate attenuation in the LPS. The LPS was found to play a significant role in protecting aquifers from anthropogenic contamination.
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Affiliation(s)
- Yuexia Wu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, 73 East Beijing Road, 210008 Nanjing, PR China; Institute of Water Sciences, College of Engineering, Peking University, No. 5 Yiheyuan Road, 100871 Beijing, PR China
| | - Ligang Xu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, 73 East Beijing Road, 210008 Nanjing, PR China.
| | - Sai Wang
- Center for Hydrogeology and Environmental Geology, China Geological Survey, No. 1305 Qiyi Road, North District, Baoding, Hebei Province, PR China
| | - Zhenglu Wang
- College of Urban and Environmental Science, Peking University, 100871 Beijing, PR China
| | - Jianying Shang
- College of Resources & Environmental Science, China Agricultural University, 100193 Beijing, PR China
| | - Xiqing Li
- College of Urban and Environmental Science, Peking University, 100871 Beijing, PR China
| | - Chunmiao Zheng
- School of Environmental Science and Engineering, South University of Science and Technology, 518025 Shenzhen, PR China
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30
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Hernández-Del Amo E, Menció A, Gich F, Mas-Pla J, Bañeras L. Isotope and microbiome data provide complementary information to identify natural nitrate attenuation processes in groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:579-591. [PMID: 28926812 DOI: 10.1016/j.scitotenv.2017.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
Natural attenuation processes alleviate the impact of fertilization practices on groundwater resources. Therefore, identifying the occurrence of denitrification has become a requirement for water quality management. Several approaches are useful for this purpose, such as isotopic and microbiological methods, each of them providing distinct but complementary information about denitrification reactions, attenuation rates and their occurrence in the aquifer. In this paper, we investigate the contribution of both approaches to describe denitrification in a consolidated rock aquifer (limestone and marls), with a porosity related to fracture networks located in the northeastern sector of the Osona basin (NE Spain). Isotopic methods indicated the origin of nitrate (fertilization using manure) and that denitrification occurred, reaching a reduction of near 25% of the nitrate mass in groundwater. The studied area could be divided in two zones with distinct agricultural pressures and, consequently, nitrate concentrations in groundwater. Denitrification occurred in both zones and at different levels, indicating that attenuation processes took place all along the whole hydrogeological unit, and that the observed levels could be attributed to a larger flow path or, in a minor extent, to mixing processes that mask the actual denitrification rates. Microbiological data showed a correlation between denitrifier genes and the isotopic composition. However, the groundwater microbiome and the distribution of denitrifying bacteria did not reveal a major influence on the denitrification level observed by isotopic methods. This focuses the interest of microbiological analysis to identify functional genes within the bacteria present in the aquifer. Results indicated that isotopic methods provide information of the overall denitrification ability of the hydrogeological unit, and that genomic data represent the processes actually acting nearby the well. A combination of both approaches is advised to support induced in situ attenuation actions in polluted sites.
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Affiliation(s)
- Elena Hernández-Del Amo
- Grup d'Ecologia Microbiana Molecular (gEMM), Institut d'Ecologia Aquàtica, Facultat de Ciències, Universitat de Girona, 17003 Girona, Spain
| | - Anna Menció
- Grup de Geologia Aplicada i Ambiental (GAiA), Departament de Ciències Ambientals, Universitat de Girona, 17003 Girona, Spain.
| | - Frederic Gich
- Grup d'Ecologia Microbiana Molecular (gEMM), Institut d'Ecologia Aquàtica, Facultat de Ciències, Universitat de Girona, 17003 Girona, Spain
| | - Josep Mas-Pla
- Grup de Geologia Aplicada i Ambiental (GAiA), Departament de Ciències Ambientals, Universitat de Girona, 17003 Girona, Spain; Institut Català de Recerca de l'Aigua, 17003 Girona, Spain.
| | - Lluís Bañeras
- Grup d'Ecologia Microbiana Molecular (gEMM), Institut d'Ecologia Aquàtica, Facultat de Ciències, Universitat de Girona, 17003 Girona, Spain.
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31
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Kumar S, Herrmann M, Thamdrup B, Schwab VF, Geesink P, Trumbore SE, Totsche KU, Küsel K. Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes. Front Microbiol 2017; 8:1951. [PMID: 29067012 PMCID: PMC5641322 DOI: 10.3389/fmicb.2017.01951] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/22/2017] [Indexed: 11/22/2022] Open
Abstract
Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5–4.7 nmol L−1 d−1, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L−1 oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.
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Affiliation(s)
- Swatantar Kumar
- Aquatic Geomicrobiology Group, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology Group, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bo Thamdrup
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
| | - Valérie F Schwab
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Patricia Geesink
- Aquatic Geomicrobiology Group, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Susan E Trumbore
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Kai-Uwe Totsche
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology Group, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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32
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Chen W, Gu Y, Xu H, Liu Z, Lu C, Lin C. Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:15347-15359. [PMID: 28502052 DOI: 10.1007/s11356-017-9125-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to investigate the variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems without prechlorination and associated effects on the transformation of nitrogen pollutants by using a designed model pipe system. The results showed the transformation of nitrogen pollutants was obvious during the biofilm formation. The richness and diversity of the microbial communities changed significantly. The higher abundance of Nitrospirae in biofilm samples significantly contributed to biological nitrification. In particular, the stable content of Bacteroidetes in the biofilm and soluble microbial products released by the biomass might have enhanced the increase in dissolved organic nitrogen. In addition, the variation tendency of nitrogen functional gene abundances and their strong effects on NH4+-N, NO2--N, and NO3--N transformation were clearly observed. These findings provide new insights into the evolution of microbial communities and functional genes during the initial operation period of real-world raw water distribution pipes and highlight management and possible safety issues in the subsequent water treatment process.
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Affiliation(s)
- Wei Chen
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Yanmei Gu
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Hang Xu
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China.
- College of Environment, Hohai University, Nanjing, 210098, China.
| | - Zhigang Liu
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Chunhui Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Chenshuo Lin
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
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