1
|
Feng JR, Ni HG. Effects of heavy metals and metalloids on the biodegradation of organic contaminants. ENVIRONMENTAL RESEARCH 2024; 246:118069. [PMID: 38160966 DOI: 10.1016/j.envres.2023.118069] [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: 09/03/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Heavy metals and metalloids (HMMs) inhibit the biodegradation of organic pollutants. The degree of inhibition depends not only on the concentration and bioavailability of HMMs but also on additional factors, such as environmental variables (e.g., inorganic components, organic matter, pH, and redox potential), the nature of the metals, and microbial species. Based on the degradation pattern and metal concentrations causing half biodegradation rate reductions (RC50s), the inhibition of biodegradation was: Hg2+, As2O3 > Cu2+, Cd2+, Pb2+, Cr3+ > Ni2+, Co2+ > Mn2+, Zn2+ > Fe3+. Four patterns were observed: inhibition increases with increasing metal concentration; low concentrations stimulate, while high concentrations inhibit; high concentrations inhibit less; and mild inhibition remains constant. In addition, metal ion mixtures have more complex inhibitory effects on the degradation of organic pollutants, which may be greater than, similar to, or less than that of individual HMMs. Finally, the inhibitory mechanism of HMMs on biodegradation is reviewed. HMMs generally have little impact on the biodegradation pathway of organic pollutants for bacterial strains. However, when pollutants are biodegraded by the community, HMMs may activate microbial populations harbouring different transformation pathways. HMMs can affect the biodegradation efficiency of organic pollutants by changing the surface properties of microbes, interfering with degradative enzymes, and interacting with general metabolism.
Collapse
Affiliation(s)
- Jin-Ru Feng
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Hong-Gang Ni
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
| |
Collapse
|
2
|
Li T, Wang X, Huang J, Wang Y, Song S. Distribution of ammonia oxidizers and their role in N 2 O emissions in the reservoir riparian zone. J Basic Microbiol 2022; 62:1179-1192. [PMID: 35730619 DOI: 10.1002/jobm.202200190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/09/2022]
Abstract
As a transitional boundary between terrestrial and aquatic ecosystems, the riparian zone is considered a hotspot for N2 O production because of the active nitrogen processes. Ammoxidation is an important microbial pathway for N2 O production, but the distribution of ammonia oxidizers under different land-use types in the reservoir riparian zone and what role they played in N2 O emissions are still not clear. We investigated spatiotemporal distributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their role in N2 O emissions in different land-use types along the riparian zone of Miyun Reservoir: grassland, sparse woods, and woodland. We found significant differences in both AOA abundance and AOB diversity indices among land-use types. AOA and AOB communities were significantly separated by different land-use types. The main drivers to determine the distribution of ammonia-oxidizing microbial community were soil water content, NH4 + , NO3 - , and total organic carbon (TOC). In situ N2 O flux was highest in woodland with a mean value of 12.28 μg/m2 ·h, and it was substantially decreased by 121% and 123% in sparse woods and grassland. TOC content was decreased by 20% and 40% in sparse woods and grassland compared with woodland, and it was significantly positively correlated with in situ N2 O flux. Meanwhile, AOB diversity indices were significantly correlated with in situ N2 O flux. These results showed that the heterogeneity of physicochemical properties among different land-use types affected the community of AOA and AOB in riparian zones. AOB not AOA, and community diversity rather than abundance, played a role in N2 O emissions.
Collapse
Affiliation(s)
- Tingting Li
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, China
| | - Xiaoyan Wang
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, China
| | - Jingyu Huang
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, China
| | - Yubing Wang
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, China
| | - Shuang Song
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, China
| |
Collapse
|
3
|
Massarelli C, Losacco D, Tumolo M, Campanale C, Uricchio VF. Protection of Water Resources from Agriculture Pollution: An Integrated Methodological Approach for the Nitrates Directive 91-676-EEC Implementation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182413323. [PMID: 34948931 PMCID: PMC8704299 DOI: 10.3390/ijerph182413323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 11/26/2022]
Abstract
Nitrogen is a vital nutrient helpful to plants and crop growth. However, among the leading causes of water resources pollution is the excess nitrogen from agricultural sources. In European Union countries, the Nitrates Directive has been approved to reduce this problem monitoring of water bodies with regard to nitrate concentrations, designation of Nitrate Vulnerable Zones (NVZs), and establishing codes of good agricultural practices and measures to prevent and reduce water pollution from nitrates. In light of this, we propose an integrated methodological approach to better manage a environmental issue as the perimeter of NVZs with the prospective that our approach could be used in the future by other member states representing a Best Practice in that direction. The methodology is based on data integration applied in a GIS environment. Different available data representing the knowledge of the territory were harmonised, systematised and georeferenced, in order to increase the environmental framework, preserve the contamination of the water resource and give indications on the measures to be implemented to apply in the best way possible the Nitrates Directive. Finally, it was also possible to overcome the infringement procedure in progress for Italy and the Puglia region and proceed to new designation of NVZs.
Collapse
Affiliation(s)
- Carmine Massarelli
- Water Research Institute, Italian National Research Council (CNR-IRSA), Via F. De Blasio 5, Zona Industriale, 70132 Bari, Italy; (D.L.); (M.T.); (C.C.); (V.F.U.)
- Correspondence:
| | - Daniela Losacco
- Water Research Institute, Italian National Research Council (CNR-IRSA), Via F. De Blasio 5, Zona Industriale, 70132 Bari, Italy; (D.L.); (M.T.); (C.C.); (V.F.U.)
- Department of Biology, University of Bari, 70126 Bari, Italy
| | - Marina Tumolo
- Water Research Institute, Italian National Research Council (CNR-IRSA), Via F. De Blasio 5, Zona Industriale, 70132 Bari, Italy; (D.L.); (M.T.); (C.C.); (V.F.U.)
- Department of Biology, University of Bari, 70126 Bari, Italy
| | - Claudia Campanale
- Water Research Institute, Italian National Research Council (CNR-IRSA), Via F. De Blasio 5, Zona Industriale, 70132 Bari, Italy; (D.L.); (M.T.); (C.C.); (V.F.U.)
| | - Vito Felice Uricchio
- Water Research Institute, Italian National Research Council (CNR-IRSA), Via F. De Blasio 5, Zona Industriale, 70132 Bari, Italy; (D.L.); (M.T.); (C.C.); (V.F.U.)
| |
Collapse
|
4
|
MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes. mSystems 2021; 6:e0020121. [PMID: 34546069 PMCID: PMC8547451 DOI: 10.1128/msystems.00201-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably. IMPORTANCE Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. There is often a large diversity of genes represented for functional gene groups, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high-throughput primer design for various genes of interest and also allows for ranking gene targets by their presence and abundance in environmental data sets. Primers designed by this tool improve the characterization and quantification of functional genes in broad gene amplification platforms and can be powerful with high-throughput qPCR approaches.
Collapse
|
5
|
Jin Y, Miao Y, Geng Y, Huang M, Zhang Y, Song X, Li S, Zou J. Calcium Superphosphate-Mediated Reshaping of Denitrifying Bacteria Community Contributed to N 2O Mitigation in Pig Manure Windrow Composting. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 18:E171. [PMID: 33383657 PMCID: PMC7795020 DOI: 10.3390/ijerph18010171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022]
Abstract
Composting is recognized as an effective strategy for the sustainable use of organic wastes, but also as an important emission source of nitrous oxide (N2O) contributing to global warming. The effects of calcium superphosphate (CaSSP) on N2O production during composting are reported to be controversial, and the intrinsic microbial mechanism remains unclear. Here, a pig manure windrow composting experiment lasting for ~60 days was performed to evaluate the effects of CaSSP amendment (5%, w/w) on N2O fluxes in situ, and to determine the denitrifiers' response, and their driving factors. Results indicated that CaSSP amendment significantly reduced N2O emissions as compared to the control pile (maximum N2O emission rate reduced by 64.5% and total emission decreased by 49.8%). CaSSP amendment reduced the abundance of nirK gene encoding for nitrite reductase, while the abundance of nosZ gene (N2O reductase) was enriched. Finally, we built a schematic model and indicated that the abundance of nirK gene was likely to play a key role in mediating N2O production, which were correlated with NH4+-N and NO3--N changing responsive to CaSSP. Our finding implicates that CaSSP application could be a potential strategy for N2O mitigation in manure windrow composting, and the revealed microbial mechanism is helpful for deepening the understanding of the interaction among N-cycle functional genes, physicochemical factors, and greenhouse gases (GHG) emissions.
Collapse
Affiliation(s)
- Yaguo Jin
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
| | - Yingcheng Miao
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
| | - Yajun Geng
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
| | - Mengyuan Huang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
| | - Yihe Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
| | - Xiuchao Song
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Shuqing Li
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianwen Zou
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.J.); (Y.M.); (Y.G.); (M.H.); (Y.Z.); (J.Z.)
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
6
|
Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
Collapse
Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
| |
Collapse
|
7
|
Jantarakasem C, Kasuga I, Kurisu F, Furumai H. Temperature-Dependent Ammonium Removal Capacity of Biological Activated Carbon Used in a Full-Scale Drinking Water Treatment Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13257-13263. [PMID: 32969636 DOI: 10.1021/acs.est.0c02502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nitrification is a key function of biological activated carbon (BAC) filters for drinking water treatment. It is empirically known that the nitrification activity of BAC filters depends on water temperature, potentially resulting in the leakage of ammonium from BAC filters when the water temperature decreases. However, the ammonium removal capacity of BAC filters and factors governing the capacity remain unknown. This study employed a bench-scale column assay to determine the volumetric ammonium removal rate (VARR) of BAC collected from a full-scale drinking water treatment plant. VARR was determined at a fixed loading rate under different conditions. Seasonal variations of the VARR as well as impacts of the water matrix and water temperature on ammonium removal were quantitatively analyzed. While the VARR in an inorganic medium at 25 °C was maintained even during low water temperature periods and during breakpoint chlorination periods, the water matrix factor reduced the VARR in ozonated water at 25 °C by 33% on average. The VARR in ozonated water was dependent on water temperature, indicating that the microbial activity of BAC did not adapt to low water temperature. The Arrhenius equation was applied to reveal the relationship between VARR and water temperature. The actual ammonium removal performance of a full-scale BAC filter was predicted. VARR is useful for water engineers to reexamine the loading and filter depth of BAC filters.
Collapse
Affiliation(s)
- Chotiwat Jantarakasem
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ikuro Kasuga
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
8
|
Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. Appl Environ Microbiol 2020; 86:AEM.00736-20. [PMID: 32631866 DOI: 10.1128/aem.00736-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
Collapse
|
9
|
Maurya S, Abraham JS, Somasundaram S, Toteja R, Gupta R, Makhija S. Indicators for assessment of soil quality: a mini-review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:604. [PMID: 32857216 DOI: 10.1007/s10661-020-08556-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/16/2020] [Indexed: 05/20/2023]
Abstract
Soil quality is the competence of soil to perform necessary functions that are able to maintain animal and plant productivity of the soil. Soil consists of various physical, chemical, and biological parameters, and all these parameters are involved in the critical functioning of soil. There is a need for continuous assessment of soil quality as soil is a complex and dynamic constituent of Earth's biosphere that is continuously changing by natural and anthropogenic disturbances. Any perturbations in the soil cause disturbances in the physical (soil texture, bulk density, etc.), chemical (pH, salinity, organic carbon, etc.), and biological (microbes and enzymes) parameters. These physical, chemical, and biological parameters can serve as indicators for soil quality assessment. However, soil quality assessment cannot be possible by evaluating only one parameter out of physical, chemical, or biological. So, there is an emergent need to establish a minimum dataset (MDS) which shall include physical, chemical, and biological parameters to assess the quality of the given soil. This review attempts to describe various physical, chemical, and biological parameters, combinations of which can be used in the establishment of MDS.
Collapse
Affiliation(s)
- Swati Maurya
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Jeeva Susan Abraham
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Sripoorna Somasundaram
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Ravi Toteja
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Renu Gupta
- Department of Zoology, Maitreyi College, University of Delhi, Bapu dham, Chanakyapuri, New Delhi, 110021, India
| | - Seema Makhija
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India.
| |
Collapse
|
10
|
Wang Q, Liu Y, Liu Q, Liu X, Yang F, Wang M, Shao H, Jiang Y. Isolation and Complete Genome of the Marine Pseudoalteromonas Phage C7 from Coastal Seawater of Yellow Sea, China. Curr Microbiol 2019; 77:279-285. [DOI: 10.1007/s00284-019-01815-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022]
|
11
|
|
12
|
Zhuang M, Sanganyado E, Li P, Liu W. Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:482-492. [PMID: 31026695 DOI: 10.1016/j.envpol.2019.04.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/22/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Nearshore environments are a critical transitional zone that connects the marine and terrestrial/freshwater ecosystems. The release of anthropogenic chemicals into nearshore ecosystems pose a human and environmental health risk. We investigated the microbial diversity, abundance and function in metal-contaminated sediments collected from the Rongjiang, Hanjiang and Lianjiang River estuaries and adjacent coastal areas using high throughput sequencing. The concentration of nutrients (NO3-N, NO2-N, NH4-N, PO4-P) and metal (Cu, Zn, Cd, Pb, As, Hg) contaminants were higher at the mouth of the rivers compared to the coastal lines, and this was confirmed using cluster analysis. Estimates obtained using geoaccumulation index showed that about 38.9% of the sites were contaminated with Pb and the pollution load index showed that sediment from the mouth of Hanjiang River Estuary was moderately polluted with metals. In the nearshore sediment samples collected, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria were the dominant phylum with relative abundances of 46.6%, 8.05%, 6.47%, 5.26%, and 4.59%, respectively. There was no significant correlation between environmental variables and microbial abundance and diversity except for total organic carbon (TOC) (diversity; r = 0.569, p < 0.05) and Cr (diversity; r = 0.581, p < 0.05). At phyla level, Nitrospirae had a significant negative correlation with all metals except Cr, while OD1 had a significant positive correlation with all the metals. Overall, changes in nearshore sediment microbial communities by environmental factors were observed, and these may affect biogeochemical cycling.
Collapse
Affiliation(s)
- Mei Zhuang
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Edmond Sanganyado
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Ping Li
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China.
| |
Collapse
|
13
|
Brown MR, Baptista JC, Lunn M, Swan DL, Smith SJ, Davenport RJ, Allen BD, Sloan WT, Curtis TP. Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system. WATER RESEARCH 2019; 152:264-273. [PMID: 30682570 DOI: 10.1016/j.watres.2019.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Viruses are thought to control bacterial abundance, affect community composition and influence ecosystem function in natural environments. Yet their dynamics have seldom been studied in engineered systems, or indeed in any system, for long periods of time. We measured virus abundance in a full-scale activated sludge plant every week for two years. Total bacteria and ammonia oxidising bacteria (AOB) abundances, bacterial community profiles, and a suite of environmental and operational parameters were also monitored. Mixed liquor virus abundance fluctuated over an order of magnitude (3.18 × 108-3.41 × 109 virus's mL-1) and that variation was statistically significantly associated with total bacterial and AOB abundance, community composition, and effluent concentrations of COD and NH4+- N and thus system function. This suggests viruses play a far more important role in the dynamics of activated sludge systems than previously realised and could be one of the key factors controlling bacterial abundance, community structure and functional stability and may cause reactors to fail. These findings are based on statistical associations, not mechanistic models. Nevertheless, viral associations with abiotic factors, such as pH, make physical sense, giving credence to these findings and highlighting the role that physical factors play in virus ecology. Further work is needed to identify and quantify specific bacteriophage and their hosts to enable us to develop mechanistic models of the ecology of viruses in wastewater treatment systems. However, since we have shown that viruses can be related to effluent quality and virus quantification is simple and cheap, practitioners would probably benefit from quantifying viruses now.
Collapse
Affiliation(s)
- M R Brown
- School of Engineering, Newcastle University, NE1 7RU, UK.
| | - J C Baptista
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - M Lunn
- Department of Statistics, University of Oxford, OX1 3TG, UK
| | - D L Swan
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - S J Smith
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - R J Davenport
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - B D Allen
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - W T Sloan
- Department of Civil Engineering, University of Glasgow, G12 8LT, UK
| | - T P Curtis
- School of Engineering, Newcastle University, NE1 7RU, UK
| |
Collapse
|
14
|
Annual nitrification dynamics in a seasonally ice-covered lake. PLoS One 2019; 14:e0213748. [PMID: 30893339 PMCID: PMC6426244 DOI: 10.1371/journal.pone.0213748] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/27/2019] [Indexed: 11/25/2022] Open
Abstract
We investigated the variability in ammonia oxidation (AO) rates and the presence of ammonia-oxidizing archaea and bacteria (AOB and AOA) over an annual cycle in the water column of a small, seasonnally ice covered, temperate shield lake. AO, the first step of nitrification, was measured in situ using 15N-labelled ammonium (NH4+) at 1% and 10% of photosynthetic active radiation during day and at the same depths during night. AO was active across seasons and light levels, ranging from undetectable to 333 nmol L-1 d-1 with peak activity in winter under ice cover. NH4+ concentration was the single most important positive predictor of AO rates. High NH4+ concentrations and reduced chlorophyll a concentrations under ice, which favoured AO, were coherent with high nitrate concentrations and super saturation in nitrous oxide. When targeting the ammonia monooxygenase (amoA) gene in samples from the photic zone, we found AOA to be omnipresent throughout the year while AOB were observed predominantly during winter. Our results demonstrate that AO is an ongoing process in sunlit surface waters of temperate lakes and at all seasons with pronounced nitrification activity observed during winter under ice. The combination of high NH4+ concentrations due to fall overturn, reduced light availability that limited phytoplankton competition, and the presence of AOB together with AOA apparently favoured these elevated rates under ice. We suggest that lake ice could be a control point for nitrification in oligotrophic temperate shield lakes, characterized as a moment and place that exerts disproportionate influence on the biogeochemical behaviour of ecosystems.
Collapse
|
15
|
Oka M, Uchida Y. Heavy metals in slag affect inorganic N dynamics and soil bacterial community structure and function. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:713-722. [PMID: 30228069 DOI: 10.1016/j.envpol.2018.09.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Heavy metal contamination of soil in the vicinity of mining sites is a serious environmental problem around the world when mining residue (slag) is dispersed as dust. We conducted an incubation experiment to investigate the effect of a slag containing high levels of Pb and Zn (62.2 and 33.6 g kg-1 slag as PbO and ZnO, respectively, sampled from a site formerly used as a lead and zinc mine) on the nitrogen cycle when mixed with soil (0-0.048 g slag g-1 soil). The nitrogen cycle provides many life supporting-functions. To assess the quality of the soil in terms of the nitrogen cycle we focused on the dynamics of nitrate and ammonium, and bacterial community structure and functions within the soil. After two weeks of pre-incubation, 15N-labeled urea (500 mg N kg-1) was added to the soil. Changes in soil pH, the concentration and 15N ratio of nitrate (NO3--N) and ammonium, and bacterial relative abundance and community structure were measured. Results indicated that increasing the ratio of slag to soil had a stronger negative effect on nitrification than ammonification, as suggested by slower nitrate accumulation rates as the slag:soil ratio increased. In the treatment with the highest amount of slag, the concentration of NO3--N was 50% of that in the controls at the end of the incubation. Regarding the bacterial community, Firmicutes had a positive and Planctomycetes a negative correlation with increasing slag concentration. Bacterial community functional analysis showed the proportion of bacterial DNA sequences related to nitrogen metabolism was depressed with increasing slag, from 0.68 to 0.65. We concluded that the slag impacted the soil bacterial community structure, and consequently influenced nitrogen dynamics. This study could form the basis of further investigation into the resistance of the nitrogen cycle to contamination in relation to soil bacterial community.
Collapse
Affiliation(s)
- Miyuki Oka
- School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| |
Collapse
|
16
|
Urakawa H, Rajan S, Feeney ME, Sobecky PA, Mortazavi B. Ecological response of nitrification to oil spills and its impact on the nitrogen cycle. Environ Microbiol 2018; 21:18-33. [DOI: 10.1111/1462-2920.14391] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/11/2018] [Accepted: 08/17/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Hidetoshi Urakawa
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Suja Rajan
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Megan E. Feeney
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Patricia A. Sobecky
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Behzad Mortazavi
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
- Dauphin Island Sea Lab Dauphin Island AL, 36528 USA
| |
Collapse
|
17
|
Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P, Koide O, Morono Y, Fukui T, Inagaki F, Miyazaki J, Takaki Y, Takai K. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ 2018; 33:186-194. [PMID: 29806625 PMCID: PMC6031389 DOI: 10.1264/jsme2.me17194] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca. Marinimicrobia" (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and "Ca. Woesearchaeota" (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.
Collapse
Affiliation(s)
- Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Osamu Koide
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| |
Collapse
|
18
|
Laanbroek HJ, Veenhuizen PTM, Keijzer RM, Hefting MM. Numerical Relationships Between Archaeal and Bacterial amoA Genes Vary by Icelandic Andosol Classes. MICROBIAL ECOLOGY 2018; 75:204-215. [PMID: 28707145 PMCID: PMC5742608 DOI: 10.1007/s00248-017-1032-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/30/2017] [Indexed: 05/26/2023]
Abstract
Bacterial amoA genes had not been detectable by qPCR in freshly sampled Icelandic Andosols thus far. Hence, a new primer set yielding shorter gene fragments has been designed to verify the absence of ammonia-oxidizing bacteria in different Icelandic Andosol classes. At the same time, a new primer set was also constructed for archaeal amoA genes that should improve the quality of PCR products. Although a large part of the soil samples were found to be amoA-negative, bacterial amoA genes were detectable with new as well as old primer sets. The same results were obtained for the archaeal amoA genes. The relative distribution of archaeal and bacterial amoA genes varied between Andosol classes. Archaeal amoA genes were significantly more abundant in Brown than in Histic Andosols, while the opposite was observed for bacterial amoA genes. The numbers of archaeal and bacterial amoA genes in Gleyic Andosols were not significantly different from those in Histic and Brown Andosols. The numbers of bacterial amoA genes, but not the numbers of archaeal amoA genes, correlated significantly and positively with potential ammonia oxidation activities. The presence of the bacterial nitrification inhibitor allylthiourea inhibited the potential ammonia oxidation activities during the first 12 h of incubation. Hence, it was concluded that ammonia-oxidizing bacteria profited most from the conditions during the measurements of potential ammonia oxidation activities.
Collapse
Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands.
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands.
| | - Peter T M Veenhuizen
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
19
|
Ramanathan B, Boddicker AM, Roane TM, Mosier AC. Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage. Front Microbiol 2017; 8:2136. [PMID: 29209281 PMCID: PMC5701628 DOI: 10.3389/fmicb.2017.02136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022] Open
Abstract
Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 104 – 4.9 × 107 archaeal amoA copies ∗ μg DNA-1, 1.5 × 103 – 5.3 × 105 AOB 16S rRNA copies ∗ μg DNA-1, and 1.3 × 106 – 7.7 × 107Nitrospira nxrB copies ∗ μg DNA-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but were correlated to the relative abundances of several individual OTUs. These findings extend our understanding of the distribution of nitrifying microbes in AMD-impacted systems and provide a platform for further research.
Collapse
Affiliation(s)
- Bhargavi Ramanathan
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Timberley M Roane
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| |
Collapse
|
20
|
Mundepi A, Norton J, Cabrera M, Franklin D, Habteselassie MY. Ammonia Oxidizers in a Grazing Land with a History of Poultry Litter Application. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:994-1002. [PMID: 28991982 DOI: 10.2134/jeq2017.04.0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Poultry litter (PL) is widely applied on grazing lands in Georgia. However, it is not clear how its long-term use affects soil microorganisms and their function. We examined changes in activity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a grazing land with a history of PL application and compared it to treatment with urea ammonium nitrate (UAN). Soil samples (0-15 cm) were collected in 2009 (after 15 yr of PL application) and in 2013 (after 2 yr of no application). The abundance and community composition of ammonia oxidizers (AO) were determined with molecular techniques that targeted Nitrification potential (NP) was used for measuring their activity. Abundance of AO was significantly higher in PL (7.41 and 7.10 log copies g soil for AOB and AOA, respectively) than in UAN plots (6.82 and 6.50 log copies g soil for AOB and AOA, respectively) in 2009. This is consistent with NP, which was higher in PL (0.78 mg NO -N kg h) than in UAN (0.50 mg NO-N kg h) plots in 2009. The abundance of AO and NP decreased in 2013. There was no treatment effect on the composition of AO. Correlation analysis suggested that AOB were functionally more important than AOA, indicating the need to target AOB for efficient management of N in PL-receiving soils. Overall, the difference in nitrification between PL and UAN was mainly caused by the change in AO abundance rather than composition, and AO were not negatively affected by an increase in PL-derived trace metal concentrations.
Collapse
|
21
|
Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H. AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment. Front Microbiol 2017; 8:1508. [PMID: 28824606 PMCID: PMC5543084 DOI: 10.3389/fmicb.2017.01508] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/27/2017] [Indexed: 12/03/2022] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.
Collapse
Affiliation(s)
- Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Clemens Schauberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Lianna Poghosyan
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Craig W. Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Michaela Steinberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| |
Collapse
|
22
|
Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H. AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment. Front Microbiol 2017. [PMID: 28824606 DOI: 10.1101/096891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.
Collapse
Affiliation(s)
- Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Clemens Schauberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Lianna Poghosyan
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Maartje A H J van Kessel
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Michaela Steinberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| |
Collapse
|
23
|
Wang P, Di HJ, Cameron KC, Tan Q, Podolyan A, Zhao X, McLaren RG, Hu C. The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:2476-2483. [PMID: 27817146 DOI: 10.1007/s11356-016-8030-1] [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: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg-1), Zn (20 and 50 mg kg-1), and Cd (2 and 10 mg kg-1) were incubated for 14 days and then treated with 500 mg kg-1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.
Collapse
Affiliation(s)
- Pengcheng Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand.
| | - Keith C Cameron
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Qiling Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Ron G McLaren
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.
| |
Collapse
|
24
|
Doolette CL, Gupta VVSR, Lu Y, Payne JL, Batstone DJ, Kirby JK, Navarro DA, McLaughlin MJ. Quantifying the Sensitivity of Soil Microbial Communities to Silver Sulfide Nanoparticles Using Metagenome Sequencing. PLoS One 2016; 11:e0161979. [PMID: 27575719 PMCID: PMC5004803 DOI: 10.1371/journal.pone.0161979] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
Soils are a sink for sulfidised-silver nanoparticles (Ag2S-NPs), yet there are limited ecotoxicity data for their effects on microbial communities. Conventional toxicity tests typically target a single test species or function, which does not reflect the broader community response. Using a combination of quantitative PCR, 16S rRNA amplicon sequencing and species sensitivity distribution (SSD) methods, we have developed a new approach to calculate silver-based NP toxicity thresholds (HCx, hazardous concentrations) that are protective of specific members (operational taxonomic units, OTUs) of the soil microbial community. At the HC20 (80% of species protected), soil OTUs were significantly less sensitive to Ag2S-NPs compared to AgNPs and Ag+ (5.9, 1.4 and 1.4 mg Ag kg-1, respectively). However at more conservative HC values, there were no significant differences. These trends in OTU responses matched with those seen in a specific microbial function (rate of nitrification) and amoA-bacteria gene abundance. This study provides a novel molecular-based framework for quantifying the effect of a toxicant on whole soil microbial communities while still determining sensitive genera/species. Methods and results described here provide a benchmark for microbial community ecotoxicological studies and we recommend that future revisions of Soil Quality Guidelines for AgNPs and other such toxicants consider this approach.
Collapse
Affiliation(s)
- Casey L. Doolette
- School of Agriculture Food and Wine, The University of Adelaide, Adelaide, Australia
- * E-mail:
| | | | - Yang Lu
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Australia
| | - Justin L. Payne
- School of Natural and Built Environments, University of South Australia, Adelaide, Australia
| | - Damien J. Batstone
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Australia
| | - Jason K. Kirby
- CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies Research Program, Adelaide, Australia
| | - Divina A. Navarro
- School of Agriculture Food and Wine, The University of Adelaide, Adelaide, Australia
- CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies Research Program, Adelaide, Australia
| | - Mike J. McLaughlin
- School of Agriculture Food and Wine, The University of Adelaide, Adelaide, Australia
- CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies Research Program, Adelaide, Australia
| |
Collapse
|
25
|
Nunoura T, Hirai M, Yoshida-Takashima Y, Nishizawa M, Kawagucci S, Yokokawa T, Miyazaki J, Koide O, Makita H, Takaki Y, Sunamura M, Takai K. Distribution and Niche Separation of Planktonic Microbial Communities in the Water Columns from the Surface to the Hadal Waters of the Japan Trench under the Eutrophic Ocean. Front Microbiol 2016; 7:1261. [PMID: 27559333 PMCID: PMC4978738 DOI: 10.3389/fmicb.2016.01261] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/29/2016] [Indexed: 01/01/2023] Open
Abstract
The Japan Trench is located under the eutrophic Northwestern Pacific while the Mariana Trench that harbors the unique hadal planktonic biosphere is located under the oligotrophic Pacific. Water samples from the sea surface to just above the seafloor at a total of 11 stations including a trench axis station, were investigated several months after the Tohoku Earthquake in March 2011. High turbidity zones in deep waters were observed at most of the sampling stations. The small subunit (SSU) rRNA gene community structures in the hadal waters (water depths below 6000 m) at the trench axis station were distinct from those in the overlying meso-, bathy and abyssopelagic waters (water depths between 200 and 1000 m, 1000 and 4000 m, and 4000 and 6000 m, respectively), although the SSU rRNA gene sequences suggested that potential heterotrophic bacteria dominated in all of the waters. Potential niche separation of nitrifiers, including ammonia-oxidizing archaea (AOA), was revealed by quantitative PCR analyses. It seems likely that Nitrosopumilus-like AOAs respond to a high flux of electron donors and dominate in several zones of water columns including shallow and very deep waters. This study highlights the effects of suspended organic matter, as induced by seafloor deformation, on microbial communities in deep waters and confirm the occurrence of the distinctive hadal biosphere in global trench environments hypothesized in the previous study.
Collapse
Affiliation(s)
- Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Miho Hirai
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Taichi Yokokawa
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Osamu Koide
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Hiroko Makita
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Yoshihiro Takaki
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan; Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
| | - Michinari Sunamura
- Department of Earth and Planetary Science, The University of Tokyo Tokyo, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| |
Collapse
|
26
|
Retention of titanium dioxide nanoparticles in biological activated carbon filters for drinking water and the impact on ammonia reduction. Biodegradation 2016; 27:95-106. [PMID: 26931341 DOI: 10.1007/s10532-016-9758-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/25/2016] [Indexed: 01/12/2023]
Abstract
Given the increasing discoveries related to the eco-toxicity of titanium dioxide (TiO2) nanoparticles (NPs) in different ecosystems and with respect to public health, it is important to understand their potential effects in drinking water treatment (DWT). The effects of TiO2 NPs on ammonia reduction, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in biological activated carbon (BAC) filters for drinking water were investigated in static and dynamic states. In the static state, both the nitrification potential and AOB were significantly inhibited by 100 μg L(-1) TiO2 NPs after 12 h (p < 0.05), and the threshold decreased to 10 μg L(-1) with prolonged exposure (36 h, p < 0.05). However, AOA were not considerably affected in any of the tested conditions (p > 0.05). In the dynamic state, different amounts of TiO2 NP pulses were injected into three pilot-scale BAC filters. The decay of TiO2 NPs in the BAC filters was very slow. Both titanium quantification and scanning electron microscope analysis confirmed the retention of TiO2 NPs in the BAC filters after 134 days of operation. Furthermore, the TiO2 NP pulses considerably reduced the performance of ammonia reduction. This study identified the retention of TiO2 NPs in BAC filters and the negative effect on the ammonia reduction, suggesting a potential threat to DWT by TiO2 NPs.
Collapse
|
27
|
Crouzet O, Poly F, Bonnemoy F, Bru D, Batisson I, Bohatier J, Philippot L, Mallet C. Functional and structural responses of soil N-cycling microbial communities to the herbicide mesotrione: a dose-effect microcosm approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4207-4217. [PMID: 26122568 DOI: 10.1007/s11356-015-4797-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/27/2015] [Indexed: 06/04/2023]
Abstract
Microbial communities driving the nitrogen cycle contribute to ecosystem services such as crop production and air, soil, and water quality. The responses to herbicide stress of ammonia-oxidizing and ammonia-denitrifying microbial communities were investigated by an analysis of changes in structure-function relationships. Their potential activities, abundances (quantitative PCR), and genetic structure (denaturing gradient gel electrophoresis) were assessed in a microcosm experiment. The application rate (1 × FR, 0.45 μg g(-1) soil) of the mesotrione herbicide did not strongly affect soil N-nutrient dynamics or microbial community structure and abundances. Doses of the commercial product Callisto® (10 × FR and 100 × FR) or pure mesotrione (100 × FR) exceeding field rates induced short-term inhibition of nitrification and a lasting stimulation of denitrification. These effects could play a part in the increase in soil ammonium content and decrease in nitrate contents observed in treated soils. These functional impacts were mainly correlated with abundance shifts of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) or denitrifying bacteria. The sustained restoration of nitrification activity, from day 42 in the 100 × FR-treated soils, was likely promoted by changes in the community size and composition of AOB, which suggests a leading role, rather than AOA, for soil nitrification restoration after herbicide stress. This ecotoxicological community approach provides a nonesuch multiparameter assessment of responses of N-cycling microbial guilds to pesticide stress.
Collapse
Affiliation(s)
- Olivier Crouzet
- INRA UR 251 PESSAC, Centre Versailles-Grignon, RD 10, 78026, Versailles cedex, France.
| | - Franck Poly
- Ecologie Microbienne, INRA USC 1193 - CNRS UMR 5557, 69622, Villeurbanne, France
- Ecologie Microbienne, Université de Lyon, Université Lyon 1, 69622, Villeurbanne, France
| | - Frédérique Bonnemoy
- CNRS UMR 6023 LMGE, Campus de Cézeaux, 63171, Aubière cedex, France
- Clermont Université, Université Blaise Pascal, 63000, Clermont-Ferrand, France
| | - David Bru
- Agroécologie, INRA, UMR 1347, 17 rue Sully, BP 86510, 21065, Dijon cedex, France
| | - Isabelle Batisson
- CNRS UMR 6023 LMGE, Campus de Cézeaux, 63171, Aubière cedex, France
- Clermont Université, Université Blaise Pascal, 63000, Clermont-Ferrand, France
| | - Jacques Bohatier
- CNRS UMR 6023 LMGE, Campus de Cézeaux, 63171, Aubière cedex, France
- Clermont Université, Université Blaise Pascal, 63000, Clermont-Ferrand, France
| | - Laurent Philippot
- Agroécologie, INRA, UMR 1347, 17 rue Sully, BP 86510, 21065, Dijon cedex, France
| | - Clarisse Mallet
- CNRS UMR 6023 LMGE, Campus de Cézeaux, 63171, Aubière cedex, France
- Clermont Université, Université Blaise Pascal, 63000, Clermont-Ferrand, France
| |
Collapse
|
28
|
Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process. Appl Microbiol Biotechnol 2015; 100:729-42. [DOI: 10.1007/s00253-015-6969-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/13/2015] [Accepted: 08/27/2015] [Indexed: 11/26/2022]
|
29
|
Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
Collapse
Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| |
Collapse
|
30
|
Damashek J, Smith JM, Mosier AC, Francis CA. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta. Front Microbiol 2015; 5:743. [PMID: 25620958 PMCID: PMC4287051 DOI: 10.3389/fmicb.2014.00743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/08/2014] [Indexed: 11/17/2022] Open
Abstract
Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.
Collapse
Affiliation(s)
- Julian Damashek
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Jason M Smith
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Annika C Mosier
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Christopher A Francis
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| |
Collapse
|
31
|
Nelson KN, Neilson JW, Root RA, Chorover J, Maier RM. Abundance and Activity of 16S rRNA, AmoA and NifH Bacterial Genes During Assisted Phytostabilization of Mine Tailings. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2015; 17:493-502. [PMID: 25495940 PMCID: PMC4269300 DOI: 10.1080/15226514.2014.935284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings.
Collapse
Affiliation(s)
| | - Julia W. Neilson
- Corresponding author Julia Neilson: ; 520-621-9759 (phone); 520-626-6782 (FAX)
| | | | | | | |
Collapse
|
32
|
Smith JM, Mosier AC, Francis CA. Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments. MICROBIAL ECOLOGY 2015; 69:13-24. [PMID: 25038845 DOI: 10.1007/s00248-014-0450-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough--a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.
Collapse
Affiliation(s)
- Jason M Smith
- Department of Environmental Earth System Science Stanford University, 473 Via Ortega, Room 140, Stanford, CA, USA
| | | | | |
Collapse
|
33
|
Marusenko Y, Garcia-Pichel F, Hall SJ. Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils. FEMS Microbiol Ecol 2014; 91:1-11. [PMID: 25764551 DOI: 10.1093/femsec/fiu023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.
Collapse
Affiliation(s)
| | | | - Sharon J Hall
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| |
Collapse
|
34
|
Ahn GH, Moon JS, Shin SY, Min WK, Han NS, Seo JH. A competitive quantitative polymerase chain reaction method for characterizing the population dynamics during kimchi fermentation. J Ind Microbiol Biotechnol 2014; 42:49-55. [PMID: 25475752 DOI: 10.1007/s10295-014-1553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/19/2014] [Indexed: 01/05/2023]
Abstract
The aim of this study was to develop a competitive quantitative-PCR (CQ-PCR) method for rapid analysis of the population dynamics of lactic acid bacteria (LAB) in kimchi. For this, whole chromosome sequences of Leuconostoc mesenteroides, Lactobacillus plantarum, and Lb. brevis were compared and species-specific PCR primers targeting dextransucrase, 16S rRNA, and surface layer protein D (SlpD) genes, respectively, were constructed. The tested strains were quantified both in medium and kimchi by CQ-PCR and the results were compared with the data obtained using a conventional plate-counting method. As a result, the three species were successfully detected and quantified by the indicated primer sets. Our results show that the CQ-PCR method targeting species-specific genes is suitable for rapid estimation of LAB population to be used in the food fermentation industry.
Collapse
Affiliation(s)
- Gee-Hyun Ahn
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921, South Korea
| | | | | | | | | | | |
Collapse
|
35
|
Liu Y, Liu Y, Ding Y, Zheng J, Zhou T, Pan G, Crowley D, Li L, Zheng J, Zhang X, Yu X, Wang J. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China. PLoS One 2014; 9:e102000. [PMID: 25058658 PMCID: PMC4109924 DOI: 10.1371/journal.pone.0102000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/13/2014] [Indexed: 11/25/2022] Open
Abstract
While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.
Collapse
Affiliation(s)
- Yuan Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yongzhuo Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yuanjun Ding
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jinwei Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Tong Zhou
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Center of Ecosystem Carbon Sink and Environment Remediation, Zhejiang Agricultural and Forestry University, Linan, Hangzhou, China
- * E-mail:
| | - David Crowley
- Department of Environment Sciences, University of California Riverside, Riverside, California, United States of America
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xinyan Yu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jiafang Wang
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
36
|
Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge. Appl Environ Microbiol 2014; 80:5901-10. [PMID: 25002435 DOI: 10.1128/aem.01383-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial abundance is central to most investigations in microbial ecology, and its accurate measurement is a challenging task that has been significantly facilitated by the advent of molecular techniques over the last 20 years. Fluorescence in situ hybridization (FISH) is considered the gold standard of quantification techniques; however, it is expensive and offers low sample throughput, both of which limit its wider application. Quantitative PCR (qPCR) is an alternative that offers significantly higher throughput, and it is used extensively in molecular biology. The accuracy of qPCR can be compromised by biases in the DNA extraction and amplification steps. In this study, we compared the accuracy of these two established quantification techniques to measure the abundance of a key functional group in biological wastewater treatment systems, the ammonia-oxidizing bacteria (AOB), in samples from a time-series experiment monitoring a set of laboratory-scale reactors and a full-scale plant. For the qPCR analysis, we tested two different sets of AOB-specific primers, one targeting the 16SrRNA gene and one targeting the ammonia monooxygenase (amoA) gene. We found that there was a positive linear logarithmic relationship between FISH and the amoA gene-specific qPCR, where the data obtained from both techniques was equivalent at the order of magnitude level. The 16S rRNA gene-specific qPCR assay consistently underestimated AOB numbers.
Collapse
|
37
|
Oszust K, Frąc M, Gryta A, Bilińska N. The influence of ecological and conventional plant production systems on soil microbial quality under hops (Humulus lupulus). Int J Mol Sci 2014; 15:9907-23. [PMID: 24897025 PMCID: PMC4100129 DOI: 10.3390/ijms15069907] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/07/2014] [Accepted: 05/09/2014] [Indexed: 11/23/2022] Open
Abstract
The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional—with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application.
Collapse
Affiliation(s)
- Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, P.O. BOX 201, Lublin 20-290, Poland.
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, P.O. BOX 201, Lublin 20-290, Poland.
| | - Agata Gryta
- Institute of Agrophysics, Polish Academy of Sciences, P.O. BOX 201, Lublin 20-290, Poland.
| | - Nina Bilińska
- Institute of Agrophysics, Polish Academy of Sciences, P.O. BOX 201, Lublin 20-290, Poland.
| |
Collapse
|
38
|
Chen Y, Zhen Y, He H, Lu X, Mi T, Yu Z. Diversity, abundance, and spatial distribution of ammonia-oxidizing β-proteobacteria in sediments from Changjiang Estuary and its adjacent area in East China Sea. MICROBIAL ECOLOGY 2014; 67:788-803. [PMID: 24362769 DOI: 10.1007/s00248-013-0341-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.
Collapse
Affiliation(s)
- Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, 238 Songling Road, Qingdao, 266100, People's Republic of China
| | | | | | | | | | | |
Collapse
|
39
|
Chen YL, Hu HW, Han HY, Du Y, Wan SQ, Xu ZW, Chen BD. Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia. FEMS Microbiol Ecol 2014; 89:67-79. [PMID: 24712910 DOI: 10.1111/1574-6941.12336] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/23/2014] [Accepted: 03/24/2014] [Indexed: 11/27/2022] Open
Abstract
Based on a 6-year field trial in a temperate steppe in Inner Mongolia, we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. The results showed that N fertilization changed AOB community composition and increased AOB abundance in both May and August, but significantly decreased AOA abundance in May. By contrast, P fertilization significantly influenced AOB abundance only in August. Mowing significantly decreased AOA abundance and had little effect on AOA community compositions in May, while significantly influencing AOB abundance in both May and August, Moreover, AOA and AOB community structures showed obvious seasonal variations between May and August. Phylogenetic analysis showed that all AOA sequences fell into the Nitrososphaera cluster, and the AOB community was dominated by Nitrosospira Cluster 3. The results suggest that fertilization and mowing play important roles in affecting the abundance and community compositions of AOA and AOB.
Collapse
Affiliation(s)
- Yong-Liang Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | | | | |
Collapse
|
40
|
Satchanska G, Pentcheva E, Atanasova R, Groudeva V, Trifonova R, Golovinsky E. Microbial Diversity in Heavy-Metal Polluted Waters. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2005.10817228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
41
|
Niu J, Kasuga I, Kurisu F, Furumai H, Shigeeda T. Evaluation of autotrophic growth of ammonia-oxidizers associated with granular activated carbon used for drinking water purification by DNA-stable isotope probing. WATER RESEARCH 2013; 47:7053-7065. [PMID: 24200001 DOI: 10.1016/j.watres.2013.07.056] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/25/2013] [Accepted: 07/04/2013] [Indexed: 06/02/2023]
Abstract
Nitrification is an important biological function of granular activated carbon (GAC) used in advanced drinking water purification processes. Newly discovered ammonia-oxidizing archaea (AOA) have challenged the traditional understanding of ammonia oxidation, which considered ammonia-oxidizing bacteria (AOB) as the sole ammonia-oxidizers. Previous studies demonstrated the predominance of AOA on GAC, but the contributions of AOA and AOB to ammonia oxidation remain unclear. In the present study, DNA-stable isotope probing (DNA-SIP) was used to investigate the autotrophic growth of AOA and AOB associated with GAC at two different ammonium concentrations (0.14 mg N/L and 1.4 mg N/L). GAC samples collected from three full-scale drinking water purification plants in Tokyo, Japan, had different abundance of AOA and AOB. These samples were fed continuously with ammonium and (13)C-bicarbonate for 14 days. The DNA-SIP analysis demonstrated that only AOA assimilated (13)C-bicarbonate at low ammonium concentration, whereas AOA and AOB exhibited autotrophic growth at high ammonium concentration. This indicates that a lower ammonium concentration is preferable for AOA growth. Since AOA could not grow without ammonium, their autotrophic growth was coupled with ammonia oxidation. Overall, our results point towards an important role of AOA in nitrification in GAC filters treating low concentration of ammonium.
Collapse
Affiliation(s)
- Jia Niu
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-8656, Japan.
| | | | | | | | | |
Collapse
|
42
|
Alves RJE, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C, Urich T. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. THE ISME JOURNAL 2013; 7:1620-31. [PMID: 23466705 PMCID: PMC3721107 DOI: 10.1038/ismej.2013.35] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/09/2022]
Abstract
The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.
Collapse
Affiliation(s)
| | - Wolfgang Wanek
- Department of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Department of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, University of Tromsø, Tromsø, Norway
| | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| |
Collapse
|
43
|
Zhu J, Zhang J, Li Q, Han T, Xie J, Hu Y, Chai L. Phylogenetic analysis of bacterial community composition in sediment contaminated with multiple heavy metals from the Xiangjiang River in China. MARINE POLLUTION BULLETIN 2013; 70:134-139. [PMID: 23507235 DOI: 10.1016/j.marpolbul.2013.02.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 01/26/2013] [Accepted: 02/11/2013] [Indexed: 06/01/2023]
Abstract
Understanding the ecology of sediments that are contaminated with heavy metals is critical for bioremediating these sediments, which has become a public concern over the course of the development of modern industry. To investigate the bacterial community composition of sediments that are contaminated with heavy metals in the Xiangjiang River, a total of four sediment samples contaminated with multiple heavy metals were obtained, and a culture-independent molecular analysis, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), was performed. The results revealed that heavy metal pollution affected the sediment microbial community diversity, and the greatest species diversity appeared in the moderately polluted sediment X sample. The dominant family in these sediments includes α-Proteobacteria, β-Proteobacteria and Firmicutes. Moreover, α-Proteobacteria was significantly increased with increases in heavy metal. A redundancy analysis (RDA) also confirmed this phenomenon.
Collapse
Affiliation(s)
- Jianyu Zhu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | | | | | | | | | | | | |
Collapse
|
44
|
Pett-Ridge J, Petersen DG, Nuccio E, Firestone MK. Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil. FEMS Microbiol Ecol 2013; 85:179-94. [PMID: 23556538 DOI: 10.1111/1574-6941.12111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 11/29/2022] Open
Abstract
Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α-subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.
Collapse
|
45
|
Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles? Appl Environ Microbiol 2013; 79:2137-47. [PMID: 23335759 DOI: 10.1128/aem.03204-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO4(3-) concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2(-) concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.
Collapse
|
46
|
Lu L, Jia Z. Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils. Environ Microbiol 2013; 15:1795-809. [PMID: 23298189 DOI: 10.1111/1462-2920.12071] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 11/27/2022]
Abstract
The metabolic traits of ammonia-oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale. Ureolytic metabolism has long been proposed as a mechanism for AOB to cope with substrate paucity in acid soil, but it remains unclear whether urea hydrolysis could afford AOA greater ecological advantages. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, here we show that autotrophic ammonia oxidation in two acid soils was predominately driven by AOA that contain ureC genes encoding the alpha subunit of a putative archaeal urease. In urea-amended SIP microcosms of forest soil (pH 5.40) and tea orchard soil (pH 3.75), nitrification activity was stimulated significantly by urea fertilization when compared with water-amended soils in which nitrification resulted solely from the oxidation of ammonia generated through mineralization of soil organic nitrogen. The stimulated activity was paralleled by changes in abundance and composition of archaeal amoA genes. Time-course incubations indicated that archaeal amoA genes were increasingly labelled by (13) CO2 in both microcosms amended with water and urea. Pyrosequencing revealed that archaeal populations were labelled to a much greater extent in soils amended with urea than water. Furthermore, archaeal ureC genes were successfully amplified in the (13) C-DNA, and acetylene inhibition suggests that autotrophic growth of urease-containing AOA depended on energy generation through ammonia oxidation. The sequences of AOB were not detected, and active AOA were affiliated with the marine Group 1.1a-associated lineage. The results suggest that ureolytic N metabolism could afford AOA greater advantages for autotrophic ammonia oxidation in acid soil, but the mechanism of how urea activates AOA cells remains unclear.
Collapse
Affiliation(s)
- Lu Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
| | | |
Collapse
|
47
|
Ollivier J, Wanat N, Austruy A, Hitmi A, Joussein E, Welzl G, Munch JC, Schloter M. Abundance and diversity of ammonia-oxidizing prokaryotes in the root-rhizosphere complex of Miscanthus × giganteus grown in heavy metal-contaminated soils. MICROBIAL ECOLOGY 2012; 64:1038-1046. [PMID: 22688859 DOI: 10.1007/s00248-012-0078-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 05/23/2012] [Indexed: 06/01/2023]
Abstract
Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.
Collapse
Affiliation(s)
- Julien Ollivier
- Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Helbling DE, Johnson DR, Honti M, Fenner K. Micropollutant biotransformation kinetics associate with WWTP process parameters and microbial community characteristics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:10579-10588. [PMID: 22938719 DOI: 10.1021/es3019012] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The objective of this work was to identify relevant wastewater treatment plant (WWTP) parameters and underlying microbial processes that influence the biotransformation of a diverse set of micropollutants. To do this, we determined biotransformation rate constants for ten organic micropollutants in batch reactors seeded with activated sludge from ten diverse WWTPs. The estimated biotransformation rate constants for each compound ranged between one and four orders of magnitude among the ten WWTPs. The biotransformation rate constants were tested for statistical associations with various WWTP process parameters, amoA transcript abundance, and acetylene-inhibited monooxygenase activity. We determined that (i) ammonia removal associates with oxidative micropollutant biotransformation reaction rates; (ii) archaeal but not bacterial amoA transcripts associate with both ammonia removal and oxidative micropollutant biotransformation reaction rates; and (iii) the activity of acetylene-inhibited monooxygenases (including ammonia monooxygenase) associates with ammonia removal and the biotransformation rate of isoproturon, but does not associate with all oxidative micropollutant biotransformations. In combination, these results lead to the conclusion that ammonia removal and amoA transcript abundance can potentially be predictors of oxidative micropollutant biotransformation reactions, but that the biochemical mechanism is not necessarily linked to ammonia monooxygenase activity.
Collapse
Affiliation(s)
- Damian E Helbling
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
| | | | | | | |
Collapse
|
49
|
Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 2012; 46:1-9. [PMID: 19719577 DOI: 10.1016/s0168-6496(03)00153-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Abstract The initial phase of composting is the most dynamic part of the process and is characterized by rapid increases in temperature, large swings in pH, and the degradation of simple organic compounds. DNA samples were taken from an active compost system to determine the microbial 16S rRNA gene sequences that were present during this phase. We observed two significant shifts in the composition of the microbial community, one between 12 and 24 h and the other between 60 and 72 h into the process using automated 16S-23S rRNA intergenic spacer amplification (ARISA). The 16S rRNA gene sequences adjoining the most common ARISA fragments at each time point were determined. We found that sequences related to lactic acid bacteria were most common during the first 60 h and Bacillus-type sequences were most common between 72 and 96 h. While the temperature increased steadily over the first 96 h, the pH dropped after 12 h and increased after 60 h correlating with the shift from Bacillus to lactic acid sequences and the later return to Bacillus-type sequences.
Collapse
|
50
|
Wertz S, Goyer C, Zebarth BJ, Burton DL, Tatti E, Chantigny MH, Filion M. Effects of temperatures near the freezing point on N2O emissions, denitrification and on the abundance and structure of nitrifying and denitrifying soil communities. FEMS Microbiol Ecol 2012; 83:242-54. [PMID: 22882277 DOI: 10.1111/j.1574-6941.2012.01468.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/25/2012] [Accepted: 08/03/2012] [Indexed: 12/01/2022] Open
Abstract
Climate warming in temperate regions may lead to decreased soil temperatures over winter as a result of reduced snow cover. We examined the effects of temperatures near the freezing point on N(2)O emissions, denitrification, and on the abundance and structure of soil nitrifiers and denitrifiers. Soil microcosms supplemented with NO3 - and/or NO3 - plus red clover residues were incubated for 120 days at -4 °C, -1 °C, +2 °C or +5 °C. Among microcosms amended with residues, N(2)O emission and/or denitrification increased with increasing temperature on Days 2 and 14. Interestingly, N(2)O emission and/or denitrification after Day 14 were the greatest at -1 °C. Substantial N(2) O emissions were only observed on Day 2 at +2 °C and +5 °C, while at -1 °C, N(2)O emissions were consistently detected over the duration of the experiment. Abundances of ammonia oxidizing bacteria (AOB) and archaea (AOA), Nitrospira-like bacteria and nirK denitrifiers were the lowest in soils at -4 °C, while abundances of Nitrobacter-like bacteria and nirS denitrifiers did not vary among temperatures. Community structures of nirK and nirS denitrifiers and Nitrobacter-like bacteria shifted between below-zero and above-zero temperatures. Structure of AOA and AOB communities also changed but not systematically among frozen and unfrozen temperatures. Results indicated shifts in some nitrifier and denitrifier communities with freezing and a surprising stimulation of N(2)O emissions at -1 °C when NO3 - and C are present.
Collapse
Affiliation(s)
- Sophie Wertz
- Agriculture and Agri-Food Canada, Potato Research Centre, Fredericton, NB, Canada
| | | | | | | | | | | | | |
Collapse
|