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Chen J, Zhao S, Gan Y, Wu J, Dai J, Chao HJ, Yan D. Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122063. [PMID: 37330184 DOI: 10.1016/j.envpol.2023.122063] [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: 02/09/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0-6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3--N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3--N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3--N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.
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Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Shuo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yating Gan
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jing Wu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jingcheng Dai
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hong-Jun Chao
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Dazhong Yan
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
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Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions. NITROGEN 2022. [DOI: 10.3390/nitrogen3030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Permafrost-affected tundra soils are large carbon (C) and nitrogen (N) reservoirs. However, N is largely bound in soil organic matter (SOM), and ecosystems generally have low N availability. Therefore, microbial induced N-cycling processes and N losses were considered negligible. Recent studies show that microbial N processing rates, inorganic N availability, and lateral N losses from thawing permafrost increase when vegetation cover is disturbed, resulting in reduced N uptake or increased N input from thawing permafrost. In this review, we describe currently known N hotspots, particularly bare patches in permafrost peatland or permafrost soils affected by thermokarst, and their microbiogeochemical characteristics, and present evidence for previously unrecorded N hotspots in the tundra. We summarize the current understanding of microbial N cycling processes that promote the release of the potent greenhouse gas (GHG) nitrous oxide (N2O) and the translocation of inorganic N from terrestrial into aquatic ecosystems. We suggest that certain soil characteristics and microbial traits can be used as indicators of N availability and N losses. Identifying N hotspots in permafrost soils is key to assessing the potential for N release from permafrost-affected soils under global warming, as well as the impact of increased N availability on emissions of carbon-containing GHGs.
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Burnett MS, Schütte UM, Harms TK. WIDESPREAD CAPACITY FOR DENITRIFICATION ACROSS A BOREAL FOREST LANDSCAPE. BIOGEOCHEMISTRY 2022; 158:215-232. [PMID: 36186670 PMCID: PMC9518932 DOI: 10.1007/s10533-022-00895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/18/2022] [Indexed: 06/16/2023]
Abstract
A warming climate combined with frequent and severe fires cause permafrost to thaw, especially in the region of discontinuous permafrost, where soil temperatures may only be a few degrees below 0 °C. Soil thaw releases carbon (C) and nitrogen (N) into the actively cycling pools, and whereas C emissions following permafrost thaw are well documented, the fates of N remain unclear. Denitrification could release N from ecosystems as nitrous oxide (N2O) or nitrogen gas (N2), but the contributions of these processes to the high-latitude N cycle remain uncertain. We quantified microbial capacity for denitrification and N2O production in boreal soils, lakes, and streams using anoxic C- and N-amended assays, and assessed correlates of denitrifying enzyme activity (DEA) in Interior Alaska. Riparian soils and stream sediments supported the highest potential rates of denitrification, upland soils were intermediate, and lakes supported lower rates, whereas deep permafrost soils supported little denitrification. Time since fire had no effect on denitrification potential in upland soils. Across all landscape positions, DEA was negatively correlated with ammonium pools. Within each landscape position, potential rate of denitrification increased with soil or sediment organic matter content. Widespread N loss to denitrification in boreal forests could constrain the capacity for N-limited primary producers to maintain C stocks in soils following permafrost thaw.
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Affiliation(s)
- Melanie S. Burnett
- Institute of Arctic Biology and Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
- Department of Earth and Planetary Science, McGill University, Montréal, Quebec H3A 2A7, Canada
| | - Ursel M.E. Schütte
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Tamara K. Harms
- Institute of Arctic Biology and Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
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4
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Nutrient fluxes from an Arctic seabird colony to the adjacent coastal marine ecosystem. Polar Biol 2022. [DOI: 10.1007/s00300-022-03024-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractSeabirds are important vectors for nutrient transfer across ecosystem boundaries. In this seasonal study, we evaluate the impact of an Arctic colony (Alkhornet, Svalbard) of Black-legged Kittiwakes (Rissa tridactyla) and Brünnich’s Guillemots (Uria lomvia) on stream nutrient concentrations and fluxes, as well as utilization by coastal biota. Water samples from seabird-impacted and control streams were collected regularly throughout the melt season (June–September) for nutrient and organic carbon analysis. Stable carbon and nitrogen isotope analysis (δ13C and δ15N) was used to assess whether seabird-derived nitrogen (N) could be traced into filamentous stream algae and marine algae as well as consumers (amphipods). Concentrations of nitrate (NO3−) and nitrite (NO2−) peaked in July at 9200 µg N L−1 in seabird-impacted streams, 70 times higher than for control streams. Mean concentrations of phosphate (PO43−) in seabird-impacted streams were 21.9 µg P L−1, tenfold higher than in controls. Areal fluxes from seabird-impacted study catchments of NO3− + NO2− and PO43− had estimated ranges of 400–2100 kg N km−2 and 15–70 kg P km−2, respectively. Higher δ15N was found in all biota collected from seabird-impacted sites, indicating utilization of seabird-derived nitrogen. Acrosiphonia sp. from seabird-impacted sites had higher δ15N values (20–23‰ vs. 3–6‰) and lower C:N ratios (10.9 vs. 14.3) than specimens collected from control sites, indicating reliance on seabird-derived nitrogen sources and potentially higher N-availability at seabird-impacted nearshore sites. Our study demonstrates how marine nutrients brought onshore by seabirds also can return to the ocean and be utilized by nearshore primary producers and consumers.
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Zhang Y, Zhang N, Yin J, Yang F, Zhao Y, Jiang Z, Tao J, Yan X, Qiu Y, Guo H, Hu S. Combination of warming and N inputs increases the temperature sensitivity of soil N 2O emission in a Tibetan alpine meadow. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135450. [PMID: 31896220 DOI: 10.1016/j.scitotenv.2019.135450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Many high-elevation alpine ecosystems have been experiencing significant increases in air temperature and, to a lesser extent, nitrogen (N) deposition. These changes may affect N-cycling microbes and enhance emissions of nitrous oxide (N2O, a potent greenhouse gas) from soil. However, few studies have investigated whether and how the resulting changes in N-cycling microbes may affect the temperature sensitivity (Q10) of N2O emission and in turn feed back to N2O emissions. We conducted two incubation experiments to examine N2O emissions and their temperature sensitivities in soils that had experienced 3-yr field treatments of warming, N inputs and their combination in a Tibetan alpine meadow. Our results showed that neither N inputs nor warming alone affected the rate or Q10 of soil N2O emission, but combining the two significantly increased both parameters. Also, combined N and warming significantly increased the abundance of ammonia-oxidizing bacteria (AOB), corresponding with high soil N2O emission. In addition, N2O emission from nitrification accounted for 60-80% of total emissions in all soils, indicating that nitrifying microbes dominated the N2O production and its temperature sensitivity. Using random forest (RF) and structural equation model (SEM) analyses, we further evaluated the effects of various soil characteristics on soil N2O emissions and Q10. We identified soil moisture, pH, N mineralization and AOB abundance as the main predictors of the Q10 of N2O emissions. Together, these findings suggest that alterations in soil moisture, pH and ammonia-oxidizing bacteria induced by long-term N inputs and warming may increase temperature sensitivity of soil N2O emissions, leading to a positive climate feedback in this high-altitude alpine ecosystem.
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Affiliation(s)
- Yi Zhang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Nan Zhang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingjing Yin
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Yang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yexin Zhao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongquan Jiang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinjin Tao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuebin Yan
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunpeng Qiu
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Guo
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuijin Hu
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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6
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Sanders T, Fiencke C, Hüpeden J, Pfeiffer EM, Spieck E. Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia. Microorganisms 2019; 7:E699. [PMID: 31847402 PMCID: PMC6955795 DOI: 10.3390/microorganisms7120699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 01/01/2023] Open
Abstract
Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.
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Affiliation(s)
- Tina Sanders
- Helmholtz Zentrum Geesthacht, Institut für Küstenforschung, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Claudia Fiencke
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Jennifer Hüpeden
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
| | - Eva Maria Pfeiffer
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Eva Spieck
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
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7
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Mori JF, Chen LX, Jessen GL, Rudderham SB, McBeth JM, Lindsay MBJ, Slater GF, Banfield JF, Warren LA. Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake. Front Microbiol 2019; 10:2435. [PMID: 31708903 PMCID: PMC6824324 DOI: 10.3389/fmicb.2019.02435] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/09/2019] [Indexed: 11/24/2022] Open
Abstract
Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO2-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.
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Affiliation(s)
- Jiro F Mori
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, United States
| | - Gerdhard L Jessen
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Sarah B Rudderham
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joyce M McBeth
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew B J Lindsay
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Gregory F Slater
- School of Geography and Earth Science, McMaster University, Hamilton, ON, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, United States
| | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada.,School of Geography and Earth Science, McMaster University, Hamilton, ON, Canada
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8
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Alves RJE, Kerou M, Zappe A, Bittner R, Abby SS, Schmidt HA, Pfeifer K, Schleper C. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front Microbiol 2019; 10:1571. [PMID: 31379764 PMCID: PMC6657660 DOI: 10.3389/fmicb.2019.01571] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (-13-4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20-45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4-8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.
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Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Romana Bittner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Sophie S Abby
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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9
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Martínez-Olivas MA, Jiménez-Bueno NG, Hernández-García JA, Fusaro C, Luna-Guido M, Navarro-Noya YE, Dendooven L. Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale. PeerJ 2019; 7:e6127. [PMID: 31249729 PMCID: PMC6587938 DOI: 10.7717/peerj.6127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/17/2018] [Indexed: 11/20/2022] Open
Abstract
Background A great number of studies have shown that the distribution of microorganisms in the soil is not random, but that their abundance changes along environmental gradients (spatial patterns). The present study examined the spatial variability of the physicochemical characteristics of an extreme alkaline saline soil and how they controlled the archaeal and bacterial communities so as to determine the main spatial community drivers. Methods The archaeal and bacterial community structure, and soil characteristics were determined at 13 points along a 211 m transect in the former lake Texcoco. Geostatistical techniques were used to describe spatial patterns of the microbial community and soil characteristics and determine soil properties that defined the prokaryotic community structure. Results A high variability in electrolytic conductivity (EC) and water content (WC) was found. Euryarchaeota dominated Archaea, except when the EC was low. Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacterial phyla independent of large variations in certain soil characteristics. Multivariate analysis showed that soil WC affected the archaeal community structure and a geostatistical analysis found that variation in the relative abundance of Euryarchaeota was controlled by EC. The bacterial alpha diversity was less controlled by soil characteristics at the scale of this study than the archaeal alpha diversity. Discussion Results indicated that WC and EC played a major role in driving the microbial communities distribution and scale and sampling strategies were important to define spatial patterns.
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Affiliation(s)
| | | | - Juan Alfredo Hernández-García
- Laboratory of Biological Variation and Evolution, Department of Zoology, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Carmine Fusaro
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Tlaxcala, Mexico
| | | | | | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico
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10
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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11
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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.
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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
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12
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McNickle GG, Lamb EG, Lavender M, Cahill JF, Schamp BS, Siciliano SD, Condit R, Hubbell SP, Baltzer JL. Checkerboard score-area relationships reveal spatial scales of plant community structure. OIKOS 2017. [DOI: 10.1111/oik.04620] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gordon G. McNickle
- Dept of Botany and Plant Pathology and Center for Plant Biology; Purdue Univ.; West Lafayette IN USA
| | - Eric G. Lamb
- Dept of Plant Sciences; Univ. of Saskatchewan; Saskatoon SK Canada
| | - Mike Lavender
- Dept of Biological Sciences; Queen's Univ.; Kingston ON Canada
| | - James F Cahill
- Dept of Biological Sciences; Univ. of Alberta; Edmonton AB Canada
| | | | | | | | - Stephen P. Hubbell
- Dept of Ecology and Evolutionary Biology; Univ. of California Los Angeles; Los Angeles CA USA
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13
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Peixoto J, Silva LP, Krüger RH. Brazilian Cerrado soil reveals an untapped microbial potential for unpretreated polyethylene biodegradation. JOURNAL OF HAZARDOUS MATERIALS 2017; 324:634-644. [PMID: 27889181 DOI: 10.1016/j.jhazmat.2016.11.037] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/07/2016] [Accepted: 11/13/2016] [Indexed: 05/16/2023]
Abstract
Discarded PE-based products pose a social and environmental threat because of their recalcitrance to degradation, a consequence of the unique set of PE's physicochemical properties. In this study we isolated nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado. These bacterial strains from the genera Comamonas, Delftia, and Stenotrophomonas showed metabolic activity and cellular viability after a 90-day incubation with PE as the sole carbon source. ATR/FTIR indicated that biodegraded PE undergone oxidation, vinylene formation, chain scission, among other chemical changes. Considerable nanoroughness shifts and vast damages to the micrometric surface were confirmed by AFM and SEM. Further, phase imaging revealed a 46.7% decrease in the viscous area of biodegraded PE whereas Raman spectroscopy confirmed a loss in its crystalline content, suggesting the assimilation of smaller fragments. Intriguingly, biodegraded PE chemical fingerprint suggests that these strains use novel biochemical strategies in the biodegradation process. Our results indicate that these microbes are capable of degrading unpretreated PE of very high molecular weight (191,000gmol-1) and survive for long periods under this condition, suggesting not only practical applications in waste management and environmental decontamination, but also future directions to understand the unraveled metabolism of synthetic polymers.
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Affiliation(s)
- Julianna Peixoto
- Laboratory of Enzymology, Cellular Biology Department, Biological Sciences Institute, University of Brasilia, Brasilia, 70910-900, DF, Brazil.
| | - Luciano P Silva
- Laboratory of Nanobiotechnology, Embrapa Genetic Resources and Biotechnology, Brasilia, 70770-917, DF, Brazil.
| | - Ricardo H Krüger
- Laboratory of Enzymology, Cellular Biology Department, Biological Sciences Institute, University of Brasilia, Brasilia, 70910-900, DF, Brazil.
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14
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Banerjee S, Kennedy N, Richardson AE, Egger KN, Siciliano SD. Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis. Can J Microbiol 2016; 62:485-91. [PMID: 27045904 DOI: 10.1139/cjm-2015-0669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2-5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.
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Affiliation(s)
- Samiran Banerjee
- a Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.,b CSIRO Agriculture, Crace, ACT 2911, Australia
| | - Nabla Kennedy
- c Ecosystem Science & Management Program, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | | | - Keith N Egger
- c Ecosystem Science & Management Program, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Steven D Siciliano
- a Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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15
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Hayashi K, Shimomura Y, Morimoto S, Uchida M, Nakatsubo T, Hayatsu M. Characteristics of ammonia oxidation potentials and ammonia oxidizers in mineral soil under Salix polaris–moss vegetation in Ny-Ålesund, Svalbard. Polar Biol 2015. [DOI: 10.1007/s00300-015-1829-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Lamb EG, Mengersen KL, Stewart KJ, Attanayake U, Siciliano SD. Spatially explicit structural equation modeling. Ecology 2014. [DOI: 10.1890/13-1997.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Tsiknia M, Paranychianakis NV, Varouchakis EA, Moraetis D, Nikolaidis NP. Environmental drivers of soil microbial community distribution at the Koiliaris Critical Zone Observatory. FEMS Microbiol Ecol 2014; 90:139-52. [DOI: 10.1111/1574-6941.12379] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Myrto Tsiknia
- School of Environmental Engineering; Technical University of Crete; Chania Greece
| | | | | | - Daniel Moraetis
- School of Environmental Engineering; Technical University of Crete; Chania Greece
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18
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van Dorst J, Bissett A, Palmer AS, Brown M, Snape I, Stark JS, Raymond B, McKinlay J, Ji M, Winsley T, Ferrari BC. Community fingerprinting in a sequencing world. FEMS Microbiol Ecol 2014; 89:316-30. [DOI: 10.1111/1574-6941.12308] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 01/25/2023] Open
Affiliation(s)
- Josie van Dorst
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | | | - Anne S. Palmer
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mark Brown
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Ian Snape
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Jonathan S. Stark
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Ben Raymond
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - John McKinlay
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Tristrom Winsley
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
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19
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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.
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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
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20
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Zeng Y, De Guardia A, Ziebal C, De Macedo FJ, Dabert P. Impact of biodegradation of organic matters on ammonia oxidation in compost. BIORESOURCE TECHNOLOGY 2013; 136:49-57. [PMID: 23563438 DOI: 10.1016/j.biortech.2013.02.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 06/02/2023]
Abstract
Nitrification plays an important role in nitrogen turnover in composting process. It has been believed that nitrification occurs mainly during the maturation phase due to the elevated temperature during the active phase of composting. In this work, the intense biodegradation of organic matters is demonstrated to be another negative impact on the ammonia oxidation, the first step of nitrification. We investigated the ammonia oxidation in compost following organic matters addition at intermediate temperature. Different indicators of ammonia oxidation were studied, respectively. The accumulation of nitrite and nitrate was 10(2)-10(3) lower in composts with organic matters addition. The nitrous oxide emissions were absent or 40-fold inferior in these composts. The nitrogen mass balance indicated a less amount of oxidized ammonia after the addition. The ammonia-oxidizing bacteria declined following the organic matters addition. In contrast, the ammonia-oxidizing archaea were supported by the organic matters. Possible mechanisms of this impact were also discussed.
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Affiliation(s)
- Yang Zeng
- Irstea, UR GERE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes Cedex, France.
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21
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Daebeler A, Abell GCJ, Bodelier PLE, Bodrossy L, Frampton DMF, Hefting MM, Laanbroek HJ. Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating. Front Microbiol 2012; 3:352. [PMID: 23060870 PMCID: PMC3463987 DOI: 10.3389/fmicb.2012.00352] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 09/14/2012] [Indexed: 11/13/2022] Open
Abstract
The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.
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Affiliation(s)
- Anne Daebeler
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Institute of Environmental Biology, University of Utrecht Utrecht, Netherlands
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22
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Banerjee S, Siciliano SD. Spatially tripartite interactions of denitrifiers in arctic ecosystems: activities, functional groups and soil resources. Environ Microbiol 2012; 14:2601-13. [DOI: 10.1111/j.1462-2920.2012.02814.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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