1
|
Virgin TL, Sonthiphand P, Coyotzi S, Hall MW, Venkiteswaran JJ, Elgood RJ, Schiff SL, Neufeld JD. Microbial communities change along the 300 km length of the Grand River for extreme high- and low-flow regimes. Can J Microbiol 2024; 70:289-302. [PMID: 38747604 DOI: 10.1139/cjm-2023-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The Grand River watershed is the largest catchment in southern Ontario. The river's northern and southern sections are influenced by agriculture, whereas central regions receive wastewater effluent and urban runoff. To characterize in-river microbial communities, as they relate to spatial and environmental factors, we conducted two same-day sampling events along the entire 300 km length of the river, representing contrasting flow seasons (high flow spring melt and low flow end of summer). Through high-throughput sequencing of 16S rRNA genes, we assessed the relationship between river microbiota and spatial and physicochemical variables. Flow season had a greater impact on communities than spatial or diel effects and profiles diverged with distance between sites under both flow conditions, but low-flow profiles exhibited higher beta diversity. High-flow profiles showed greater species richness and increased presence of soil and sediment taxa, which may relate to increased input from terrestrial sources. Total suspended solids, dissolved inorganic carbon, and distance from headwaters significantly explained microbial community variation during the low-flow event, whereas conductivity, sulfate, and nitrite were significant explanatory factors for spring melt. This study establishes a baseline for the Grand River's microbial community, serving as a foundation for modeling the microbiology of anthropogenically impacted freshwater systems affected by lotic processes.
Collapse
Affiliation(s)
- Taylor L Virgin
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Prinpida Sonthiphand
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Michael W Hall
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
- Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS B3H 1W5, Canada
| | - Jason J Venkiteswaran
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
- Department of Geography and Environmental Studies, Wilfrid Laurier University, 75 University Ave West, Waterloo, ON N2L 3C5, Canada
| | - Richard J Elgood
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Sherry L Schiff
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| |
Collapse
|
2
|
Kallistova A, Nikolaev Y, Grachev V, Beletsky A, Gruzdev E, Kadnikov V, Dorofeev A, Berestovskaya J, Pelevina A, Zekker I, Ravin N, Pimenov N, Mardanov A. New Insight Into the Interspecies Shift of Anammox Bacteria Ca. "Brocadia" and Ca. "Jettenia" in Reactors Fed With Formate and Folate. Front Microbiol 2022; 12:802201. [PMID: 35185828 PMCID: PMC8851195 DOI: 10.3389/fmicb.2021.802201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
The sensitivity of anaerobic ammonium-oxidizing (anammox) bacteria to environmental fluctuations is a frequent cause of reactor malfunctions. It was hypothesized that the addition of formate and folate would have a stimulating effect on anammox bacteria, which in turn would lead to the stability of the anammox process under conditions of a sharp increase in ammonium load, i.e., it helps overcome a stress factor. The effect of formate and folate was investigated using a setup consisting of three parallel sequencing batch reactors equipped with a carrier. Two runs of the reactors were performed. The composition of the microbial community was studied by the 16S rRNA gene profiling and metagenomic analysis. Among anammox bacteria, Ca. "Brocadia" spp. dominated during the first run. A stimulatory effect of folate on the daily nitrogen removal rate (dN) was identified. The addition of formate led to progress in dissimilatory nitrate reduction and stimulated the growth of Ca. "Jettenia" spp. The spatial separation of two anammox species was observed in the formate reactor: Ca. "Brocadia" occupied the carrier and Ca. "Jettenia"-the walls of the reactors. Biomass storage at low temperature without feeding led to an interspecies shift in anammox bacteria in favor of Ca. "Jettenia." During the second run, a domination of Ca. "Jettenia" spp. was recorded along with a stimulating effect of formate, and there was no effect of folate on dN. A comparative genome analysis revealed the patterns suggesting different strategies used by Ca. "Brocadia" and Ca. "Jettenia" spp. to cope with environmental changes.
Collapse
Affiliation(s)
- Anna Kallistova
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yury Nikolaev
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Grachev
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Beletsky
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny Gruzdev
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly Kadnikov
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Dorofeev
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Julia Berestovskaya
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Pelevina
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivar Zekker
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Nikolai Ravin
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Pimenov
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mardanov
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
3
|
Anaerobic Ammonium Oxidation Bacteria in a Freshwater Recirculating Pond Aquaculture System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094941. [PMID: 34066435 PMCID: PMC8124726 DOI: 10.3390/ijerph18094941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/26/2022]
Abstract
Anaerobic ammonium oxidation (anammox) is a key biochemical process to reduce nitrogen pollution in aquaculture, especially in water recirculating pond aquaculture system (RPAS). We used 16S RNA and quantified PCR to study the distribution and environmental impacts of anammox bacteria in RPAS. The results show that the anammox bacterial community distributions and diversities that are apparently unit-specific and seasonal have significant (p < 0.05) difference variation in the RPAS. Most of the anaerobic ammonium oxidation bacteria sequences (77.72%) retrieved from the RPAS belong to the Brocadia cluster. The abundance of anammox bacterial in the RPAS ranged from 3.33 × 101 to 41.84 × 101 copies per ng of DNA. The environmental parameter of temperature and nitrogen composition in water could have impacted the anammox bacterial abundance. This study provides more information on our understanding of the anammox bacteria in the RPAS, and provides an important basis for RPAS improvement and regulation.
Collapse
|
4
|
Agrawal S, Weissbrodt DG, Annavajhala M, Jensen MM, Arroyo JMC, Wells G, Chandran K, Vlaeminck SE, Terada A, Smets BF, Lackner S. Time to act-assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems. WATER RESEARCH 2021; 190:116604. [PMID: 33279744 DOI: 10.1016/j.watres.2020.116604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg-1 wet biomass. The variability among the qPCR abundance data of different labs was very high (1-7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3-7 log fold), followed by the primers (1-3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.
Collapse
Affiliation(s)
- Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany.
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Medini Annavajhala
- Department of Earth and Environmental Engineering, Columbia University, New York, USA
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Microbial Ecology & Technology Laboratory, Technical University of Denmark, Bygningtorvet, Bldg 115, DK-2800, Lyngby, Denmark
| | | | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, USA
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, New York, USA
| | - Siegfried E Vlaeminck
- Department of Bioscience Engineering, Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Akihiko Terada
- Institute of Global Innovation Research and Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo 184-8588, Japan
| | - Barth F Smets
- Department of Environmental Engineering, Microbial Ecology & Technology Laboratory, Technical University of Denmark, Bygningtorvet, Bldg 115, DK-2800, Lyngby, Denmark
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| |
Collapse
|
5
|
Kallistova AY, Nikolaev YA, Mardanov AV, Berestovskaya YY, Grachev VA, Kostrikina NA, Pelevina AV, Ravin NV, Pimenov NV. Investigation of Formation and Development of Anammox Biofilms by Light, Epifluorescence, and Electron Microscopy. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
6
|
Ding C, Adrian L, Peng Y, He J. 16S rRNA gene-based primer pair showed high specificity and quantification accuracy in detecting freshwater Brocadiales anammox bacteria. FEMS Microbiol Ecol 2020; 96:5714083. [PMID: 31967636 DOI: 10.1093/femsec/fiaa013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/21/2020] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria are widely distributed and contribute significantly to the global nitrogen cycle. Traditionally, identification and quantification based on the 16S rRNA gene were considered not reliable because of low 16S rRNA gene sequence identity within Brocadiales. Here we hypothesize that by using appropriate primers and methodology, 16S-based detection and quantification of anammox bacteria can be accurate. We modified an existing 16S rRNA gene-based primer pair (Amx694F-Amx960R) by changing one nucleotide (Amx694F position 18, G→C) (Amx694PF-Amx960R) so that they match the sequences of most Brocadiales anammox bacteria, and evaluated the modified primer pair with 29 freshwater samples from microcosms, anammox reactors and wastewater treatment plants of various geographical origins. The primer pair showed high specificity in detection and quantification of anammox populations in samples that contained >0.1% anammox bacteria. Quantification of anammox abundance by quantitative real-time PCR and delineation of anammox species by denaturing gradient gel electrophoresis agreed well with amplicon sequencing results. A clear shift of anammox population towards 'Candidatus Kuenenia' was observed under laboratory cultivation conditions. With the help of amplicon sequencing, we demonstrated that 16S rRNA gene-based anammox-specific primers are able to achieve qualitative and quantitative monitoring of anammox communities in wastewater treatment plants and natural freshwater environments.2007;73:5261-7.
Collapse
Affiliation(s)
- Chang Ding
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Leipzig, Germany.,Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, China
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| |
Collapse
|
7
|
Bias of marker genes in PCR of anammox bacteria in natural habitats. PLoS One 2020; 15:e0239736. [PMID: 33002008 PMCID: PMC7529225 DOI: 10.1371/journal.pone.0239736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/13/2020] [Indexed: 12/30/2022] Open
Abstract
The identification of anammox bacteria is mostly relied on PCR with various marker genes. However, the community composition revealed by different marker genes and whether the marker genes influence the resulted community composition remain unclear. We compared the community structure of anammox bacteria in enriched and natural environments revealed by 16S rRNA and functional genes (hzo, hzsA and hzsB) from public database and published papers. The genus of Ca. Scalindua showed the lowest similarities with other genera, especially for the hzsA gene (66.9%-68.6%). The 16S rRNA gene is the most commonly used marker gene in natural habitats with 151 out 221 papers in total. The anammox bacterial community composition is distributed according to the source of habitat regardless the use of various marker genes. The role of marker gene is limited with explanatory of 5.4% for variance of community composition, versus 20.5% of habitat. The effect of marker gene is mainly acted on freshwater habitat, which shows significant different community composition revealed by 16S rRNA and hzo, with Ca. Brocadia and Ca. Jettenia as dominant genus, respectively.
Collapse
|
8
|
Yang Y, Li M, Li H, Li XY, Lin JG, Denecke M, Gu JD. Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139387. [PMID: 32460079 DOI: 10.1016/j.scitotenv.2020.139387] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N2). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.
Collapse
Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.
| | - Hui Li
- School of Resource and Environmental Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
| | - Xiao-Yan Li
- Department of Civil and Environmental Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City 30010, Taiwan
| | - Martin Denecke
- Department of Urban Water- and Waste Management, University of Duisburg-Essen, Universitätsstraße 15, 45141 Essen, Germany
| | - Ji-Dong Gu
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, Guangdong 510300, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China.
| |
Collapse
|
9
|
Wang Q, He J. Newly designed high-coverage degenerate primers for nitrogen removal mechanism analysis in a partial nitrification-anammox (PN/A) process. FEMS Microbiol Ecol 2020; 96:5679889. [PMID: 31845981 DOI: 10.1093/femsec/fiz202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/13/2019] [Indexed: 11/14/2022] Open
Abstract
Reliable tools for quantification of different functional populations are required to achieve stable, effective nutrients removal in partial nitrification and anammox (PN/A) processes. Here we report the design and validation of degenerate PCR primer pairs targeting anammox bacteria, aerobic ammonium-oxidizing bacteria (AeAOB) and nitrite-oxidizing bacteria (NOB) with high coverage but without sacrificing specificity. The new primer pairs are able to cover a broader range of the targeted populations (58.4 vs 21.7%, 49.5 vs 47.6%, 80.7 vs 57.2% and 70.5 vs 42.3% of anammox bacteria, AeAOB, Nitrobacter and Nitrospina, respectively) than previously published primers. Particularly, the Amx719F/875R primer can retrieve a larger number of 16S rRNA genes from different types of samples with amplicons covering all known anammox bacteria genera (100% coverage) including the recently found novel genus, Asahi BRW. These newly desinged primers will provide a more reliable molecular tool to investigate the mechanisms of nitrogen removal in PN/A processes, which can provide clearer links between reactor performance, the metabolic activities and abundances of functional populations, shedding light on conditions that are favorable to the establishment of stable PN/A.
Collapse
Affiliation(s)
- Qingkun Wang
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| |
Collapse
|
10
|
Zhao MM, Chen YP, Xue LG, Fan TT. Three kinds of ammonia oxidizing microorganisms play an important role in ammonia nitrogen self-purification in the Yellow River. CHEMOSPHERE 2020; 243:125405. [PMID: 31995872 DOI: 10.1016/j.chemosphere.2019.125405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
To develop the microbial resources of the Yellow River, seven water samples were collected along the Lanzhou region of the river from upstream to downstream for testing. Analysis of various physico-chemical indexes was conducted, and key parameters influencing the water quality were selected through principal component analysis, after which the decisive factors impacting water quality were determined by correlation and regression analysis. The results indicated that (1) DO, NH3-N, NO2--N, TN, TC, As, Cr6+ and Pb were the main physico-chemical factors influencing water quality in the Lanzhou region, with NH3-N having the greatest effect. (2) Ammonia-oxidizing microorganisms [ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonia-oxidizing bacteria (AMX)] were found to mediate the transformation of NH3-N in the studied section. AOA was the primary microbe community among the two aerobic ammonia-oxidizing microorganisms (AOA and AOB) in the Yellow River. (3) Phylogenetic analysis showed that there were some known groups, and there were still many unknown species in the water of the studied section, especially within the AMX population. (4) Correlation analysis revealed that AOA has strong adaptability to unhealthy environments, and that some environmental factors (higher concentrations of carbon, nitrogen and some heavy metals) could increase the AOA gene abundance. Overall, these results suggested there are rich ammonia-oxidizing microbial resources, especially AOA, in the Lanzhou section of the Yellow River, which have the potential for application in nitrogen sewage treatment.
Collapse
Affiliation(s)
- Meng M Zhao
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Yi-Ping Chen
- SKLLQG, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China.
| | - Lin-Gui Xue
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Tao T Fan
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| |
Collapse
|
11
|
Bagnoud A, Guye-Humbert S, Schloter-Hai B, Schloter M, Zopfi J. Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils. FEMS Microbiol Ecol 2020; 96:5647352. [PMID: 31782780 DOI: 10.1093/femsec/fiz191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/26/2019] [Indexed: 11/13/2022] Open
Abstract
In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using 15N-labeled substrates revealed that anammox processes contributed about <2% to total N2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs.
Collapse
Affiliation(s)
- Alexandre Bagnoud
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland.,Institut de Génie Thermique, Haute École d'Ingénierie et de Gestion du Canton de Vaud, Avenue des Sports 20, CH-1400 Yverdon-les-Bains, Switzerland
| | - Sylvia Guye-Humbert
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland
| | - Brigitte Schloter-Hai
- Research Unit for Comparative Microbiome Analysis; Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis; Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Jakob Zopfi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland.,Aquatic and Stable Isotope Biogeochemistry, University of Basel, Bernoullistrasse 30, CH-4056 Basel, Switzerland
| |
Collapse
|
12
|
Sonthiphand P, Ruangroengkulrith S, Mhuantong W, Charoensawan V, Chotpantarat S, Boonkaewwan S. Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:26765-26781. [PMID: 31300992 DOI: 10.1007/s11356-019-05905-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.
Collapse
Affiliation(s)
- Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand.
| | - Siwat Ruangroengkulrith
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, Thailand
- Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, Thailand
| | - Srilert Chotpantarat
- Department of Geology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand
- Research Unit of Green Mining (GMM), Chulalongkorn University, Bangkok, Thailand
| | - Satika Boonkaewwan
- Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand
- International Postgraduate Program in Hazardous Substance and Environmental Management, Chulalongkorn University, 9th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand
| |
Collapse
|
13
|
Islam GM, Gilbride KA. The effect of tetracycline on the structure of the bacterial community in a wastewater treatment system and its effects on nitrogen removal. JOURNAL OF HAZARDOUS MATERIALS 2019; 371:130-137. [PMID: 30849567 DOI: 10.1016/j.jhazmat.2019.02.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 06/09/2023]
Abstract
This study examined the impact of tetracycline at two environmentally relevant concentrations (1 μg/L and 10 μg/L) and one synthetically high concentration (500 μg/L) on the structure and function of the microbial community from the secondary treatment process of a municipal wastewater treatment plant (WWTP). Specifically, this study examined whether the introduction of tetracycline into bench scale reactors at two different replacement volume rates would cause a shift in the composition profile of the bacterial community. Furthermore concentrations of ammonia, nitrate/nitrite and total Kjeldahl nitrogen were monitored to examine the effect of the antibiotic on ammonia and nitrogen removal. At the low volume replacement rate, tetracycline was observed to have a positive impact on nitrogen removal. Total Kjeldahl nitrogen concentrations were also observed to decrease suggesting a role for tetracycline as a carbon source. However, at the higher volume replacement rate, the removal of ammonia and nitrogen were not significantly different from reactors that did not contain tetracycline. Over time, the bacterial composition profiles changed under all the conditions studied, however, the bacterial composition profiles appeared to be more influenced by the replacement volume rate than the presence of tetracycline even at concentrations many times higher than environmentally relevant amounts.
Collapse
Affiliation(s)
- G M Islam
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3, Canada
| | - K A Gilbride
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3, Canada.
| |
Collapse
|
14
|
On resolving ambiguities in microbial community analysis of partial nitritation anammox reactors. Sci Rep 2019; 9:6954. [PMID: 31061389 PMCID: PMC6502876 DOI: 10.1038/s41598-019-42882-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 04/11/2019] [Indexed: 11/08/2022] Open
Abstract
PCR-based methods have caused a surge for integration of eco-physiological approaches into research on partial nitritation anammox (PNA). However, a lack of rigorous standards for molecular analyses resulted in widespread data misinterpretation and consequently lack of consensus. Data consistency and accuracy strongly depend on the primer selection and data interpretation. An in-silico evaluation of 16S rRNA gene eubacterial primers used in PNA studies from the last ten years unraveled the difficulty of comparing ecological data from different studies due to a variation in the coverage of these primers. Our 16S amplicon sequencing approach, which includes parallel sequencing of six 16S rRNA hypervariable regions, showed that there is no perfect hypervariable region for PNA microbial communities. Using qPCR analysis, we emphasize the significance of primer choice for quantification and caution with data interpretation. We also provide a framework for PCR based analyses that will improve and assist to objectively interpret and compare such results.
Collapse
|
15
|
Ding Y, Xiong J, Zhou B, Wei J, Qian A, Zhang H, Zhu W, Zhu J. Odor removal by and microbial community in the enhanced landfill cover materials containing biochar-added sludge compost under different operating parameters. WASTE MANAGEMENT (NEW YORK, N.Y.) 2019; 87:679-690. [PMID: 31109570 DOI: 10.1016/j.wasman.2019.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/29/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Odor problem has become a growing concern for municipal solid waste (MSW) operators and communities located close to landfill sites. In this study, nine laboratory-scale landfill reactors were used to simulate in-situ odor control by a novel landfill cover material consisting of biochar-added sludge compost under various operating parameters. Characterization of odor removal and microbial community in the cover layer under various operating parameters was conducted using gas chromatograph-mass spectrometry and 454 high-throughput pyrosequencing, respectively. Results showed that H2S (76.9-86.0%) and volatile organic sulfur compounds (VOSCs) (12.3-21.7%) were dominant according to their theoretical generated odor concentrations. The total odor REs calculated using the theoretical odor concentrations in the landfill reactors were different than using the measured odor values, which were ranked from high to low as: R6 > R5 > R7 > R4 > R8 > R9 > R3 > R2 > R1, showing the largest discrepancy of 25.3%. The optimum combination of operating parameters based on the theoretical odor concentration was different with that based on the measured odor concentrations. Moreover, although Firmicutes (12.21-91.48%), Proteobacteria (3.55-51.03%), and Actinobacteria (4.01-47.39%) were in general the three major bacterial phyla found in the landfill covers, the detailed bacterial communities in the cover materials of the simulated reactors varied with various operating parameters. Alicyclobacillus and Tuberibacillus showed positive correlations with the removal efficiencies (REs) of chlorinated compounds, H2S, aromatic compounds, volatile organic sulfur compounds (VOSCs), and organic acids. The correlations of Rhodanobacter, Gemmatimonas, Flavisolibacter and Sphingomonas were strongly positive with ammonia RE and relatively positive with REs of organic acids, VOSCs, and aromatic compounds. These findings are instrumental in understanding the relationship between the structure of microbial communities and odor removal performances, and in developing techniques for in-situ odor control at landfills.
Collapse
Affiliation(s)
- Ying Ding
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China.
| | - Junsheng Xiong
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China; Hubei Academy of Environmental Sciences, Wuhan 430070, PR China
| | - Bowei Zhou
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China
| | - Jiaojiao Wei
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China
| | - Aiai Qian
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China
| | - Hangjun Zhang
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China
| | - Weiqin Zhu
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou 310016, PR China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310016, PR China
| | - Jun Zhu
- Department of Biological & Agricultural Engineering, University of Arkansas, AR 72701, USA.
| |
Collapse
|
16
|
Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes. Appl Microbiol Biotechnol 2017; 101:7689-7702. [PMID: 28932888 DOI: 10.1007/s00253-017-8502-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 08/26/2017] [Indexed: 10/18/2022]
Abstract
Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd 1-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.
Collapse
|
17
|
Black EM, Chimenti MS, Just CL. Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment. PeerJ 2017; 5:e3536. [PMID: 28717594 PMCID: PMC5510576 DOI: 10.7717/peerj.3536] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/13/2017] [Indexed: 01/03/2023] Open
Abstract
Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.
Collapse
Affiliation(s)
- Ellen M Black
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States of America
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, United States of America
| | - Craig L Just
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States of America
| |
Collapse
|
18
|
Dudefoi W, Moniz K, Allen-Vercoe E, Ropers MH, Walker VK. Impact of food grade and nano-TiO 2 particles on a human intestinal community. Food Chem Toxicol 2017; 106:242-249. [PMID: 28564612 DOI: 10.1016/j.fct.2017.05.050] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/01/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022]
Abstract
Titanium dioxide (TiO2) nanoparticles (NPs) are used as an additive (E171 or INS171) in foods such as gum, candy and puddings. To address concerns about the potential hazardous effects of ingested NPs, the toxicity of these food-grade NPs was investigated with a defined model intestinal bacterial community. Each titania preparation (food-grade TiO2 formulations, E171-1 and E171-6a) was tested at concentrations equivalent to those found in the human intestine after sampling 1-2 pieces of gum or candy (100-250 ppm). At the low concentrations used, neither the TiO2 food additives nor control TiO2 NPs had an impact on gas production and only a minor effect on fatty acids profiles (C16:00, C18:00, 15:1 w5c, 18:1 w9c and 18:1 w9c, p < 0.05). DNA profiles and phylogenetic distributions confirmed limited effects on the bacterial community, with a modest decrease in the relative abundance of the dominant Bacteroides ovatus in favor of Clostridium cocleatum (-13% and +14% respectively, p < 0.05). Such minor shifts in the treated consortia suggest that food grade and nano-TiO2 particles do not have a major effect on human gut microbiota when tested in vitro at relevant low concentrations. However, the cumulative effects of chronic TiO2 NP ingestion remain to be tested.
Collapse
Affiliation(s)
- William Dudefoi
- INRA, UR1268 Biopolymères Interactions Assemblages, 44300 Nantes, France
| | - Kristy Moniz
- Department of Biology, Queen's University, Kingston ON K7L 3N6, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Virginia K Walker
- Department of Biology, Queen's University, Kingston ON K7L 3N6, Canada; Department of Biomedical and Molecular Sciences, School of Environmental Studies, Queen's University, Kingston, ON K7L 3N6, Canada.
| |
Collapse
|
19
|
Yang Y, Dai Y, Li N, Li B, Xie S, Liu Y. Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes. MICROBIAL ECOLOGY 2017; 73:285-295. [PMID: 27726034 DOI: 10.1007/s00248-016-0872-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/29/2016] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.
Collapse
Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| |
Collapse
|
20
|
Sun F, Su X, Kang T, Wu S, Yuan M, Zhu J, Zhang X, Xu F, Wu W. Integrating landfill bioreactors, partial nitritation and anammox process for methane recovery and nitrogen removal from leachate. Sci Rep 2016; 6:27744. [PMID: 27279481 PMCID: PMC4899737 DOI: 10.1038/srep27744] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/24/2016] [Indexed: 11/30/2022] Open
Abstract
A new process consisting of a landfill bioreactor, partial-nitritation (PN) and the anammox process has been developed for landfill leachate treatment. In this study, the landfill bioreactor exhibited excellent performance in methane-rich biogas recovery, with a specific biogas yield of 0.47 L gas g−1 COD and methane percentages of 53–76%. PN was achieved in the aerobic reactor by high free ammonia (101 ± 83 mg NH3 L−1) inhibition for nitrite-oxidizing bacteria, and the desired PN effluent composition (effluent nitrite: ammonium ratio of 1.1 ± 0.3) was controlled by adjusting the alkalinity concentration per unit of ammonium oxidized to approximately 14.3 mg CaCO3 mg−1 N in the influent. The startup of anammox process was successfully achieved with a membrane bioreactor in 160 d, and a maximum nitrogen removal rate of 216 mg N L−1 d−1 was attained for real landfill leachate treatment. The quantitative polymerase chain reaction results confirmed that the cell-specific anammox activity was approximately 68–95 fmol N cell−1 d−1, which finally led to the stable operation of the system.
Collapse
Affiliation(s)
- Faqian Sun
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Xiaomei Su
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Tingting Kang
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Songwei Wu
- Quzhou Environmental Sanitation Department, Quzhou 324000, China
| | - Mengdong Yuan
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Jing Zhu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Xiayun Zhang
- Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Fang Xu
- Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
21
|
Sonthiphand P, Hall MW, Neufeld JD. Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. Front Microbiol 2014; 5:399. [PMID: 25147546 PMCID: PMC4123730 DOI: 10.3389/fmicb.2014.00399] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/15/2014] [Indexed: 02/01/2023] Open
Abstract
Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.
Collapse
Affiliation(s)
| | - Michael W Hall
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| |
Collapse
|
22
|
Sun W, Xia C, Xu M, Guo J, Wang A, Sun G. Diversity and distribution of planktonic anaerobic ammonium-oxidizing bacteria in the Dongjiang River, China. Microbiol Res 2014; 169:897-906. [PMID: 24932882 DOI: 10.1016/j.micres.2014.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 02/16/2014] [Accepted: 05/14/2014] [Indexed: 01/21/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) process has recently been recognized as an important pathway for removing fixed nitrogen (N) from aquatic ecosystems. Anammox organisms are widely distributed in freshwater environments. However, little is known about their presence in the water column of riverine ecosystems. Here, the existence of a diverse anammox community was revealed in the water column of the Dongjiang River by analyzing 16S rRNA and hydrazine oxidation (hzo) genes of anammox bacteria. Phylogenetic analyses of hzo genes showed that Candidatus Jettenia related clades of anammox bacteria were dominant in the river, suggesting the ecological microniche distinction from freshwater/estuary and marine anammox bacteria with Ca. Brocadia and Kuenenia genera mainly detected in freshwater/estuary ecosystems, and Ca. Scalindua genus mainly detected in marine ecosystems. The abundance and diversity of anammox bacteria along the river were both significantly correlated with concentrations of NH4(+)-N based on Pearson and partial correlation analyses. Redundancy analyses showed the contents of NH4(+)-N, NO3(-)-N and the ratio of NH4(+)-N to NO2(-)-N significantly influenced the spatial distributions of anammox bacteria in the water column of the Dongjiang River. These results expanded our understanding of the distribution and potential roles of anammox bacteria in the water column of the river ecosystem.
Collapse
Affiliation(s)
- Wei Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Chunyu Xia
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Aijie Wang
- Harbin Institute of Technology, Harbin 150090, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
| |
Collapse
|
23
|
Laverock B, Tait K, Gilbert JA, Osborn AM, Widdicombe S. Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:113-21. [PMID: 24596269 PMCID: PMC4208606 DOI: 10.1111/1758-2229.12115] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/11/2013] [Indexed: 05/13/2023]
Abstract
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.
Collapse
Affiliation(s)
- B Laverock
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
- Department of Animal and Plant Sciences, University of SheffieldSheffield, S10 2TN, UK
- School of Plant Biology and the UWA Oceans Institute, University of Western AustraliaCrawley, WA, 6009, Australia
| | - K Tait
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
| | - J A Gilbert
- Argonne National Laboratory, Institute of Genomic and Systems Biology9700 South Cass Avenue, Argonne, IL, 60439, USA
- Department of Ecology and Evolution, University of Chicago5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - A M Osborn
- Department of Animal and Plant Sciences, University of SheffieldSheffield, S10 2TN, UK
- Department of Biological Sciences, University of HullHull, HU6 7RX, UK
- School of Life Sciences, University of Lincoln, Brayford PoolLincoln, LN6 7TS, UK
| | - S Widdicombe
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
| |
Collapse
|
24
|
Han P, Huang YT, Lin JG, Gu JD. A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples. Appl Microbiol Biotechnol 2013; 97:10521-9. [PMID: 24177731 DOI: 10.1007/s00253-013-5305-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.
Collapse
Affiliation(s)
- Ping Han
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | | | | | | |
Collapse
|
25
|
Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada. Appl Environ Microbiol 2013; 79:7454-65. [PMID: 24056472 DOI: 10.1128/aem.02202-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3- or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.
Collapse
|