1
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Wilson SJ, Song B, Anderson IC. Geochemical factors impacting nitrifying communities in sandy sediments. Environ Microbiol 2023; 25:3180-3191. [PMID: 37715648 DOI: 10.1111/1462-2920.16504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 09/18/2023]
Abstract
Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.
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Affiliation(s)
- Stephanie J Wilson
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, USA
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, USA
| | - Iris C Anderson
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, USA
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2
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Botchkova E, Vishnyakova A, Popova N, Sukhacheva M, Kolganova T, Litti Y, Safonov A. Characterization of Enrichment Cultures of Anammox, Nitrifying and Denitrifying Bacteria Obtained from a Cold, Heavily Nitrogen-Polluted Aquifer. BIOLOGY 2023; 12:biology12020221. [PMID: 36829499 PMCID: PMC9952944 DOI: 10.3390/biology12020221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 g/L, respectively) and a very low content of organic carbon (2.5 mg/L). To assess the potential for bioremediation of polluted groundwater in situ, enrichment cultures of anammox, nitrifying, and denitrifying bacteria were obtained and analyzed. Fed-batch enrichment of anammox bacteria was not successful. Stable removal of ammonium and nitrite (up to 100%) was achieved in a continuous-flow reactor packed with a nonwoven fabric at 15 °C, and enrichment in anammox bacteria was confirmed by FISH and qPCR assays. The relatively low total N removal efficiency (up to 55%) was due to nonstoichiometric nitrate buildup. This phenomenon can be explained by a shift in the metabolism of anammox bacteria towards the production of more nitrates and less N2 at low temperatures compared to the canonical stoichiometry. In addition, the too high an estimate of specific anammox activity suggests that N cycle microbial groups other than anammox bacteria may have contributed significantly to N removal. Stable nitrite production was observed in the denitrifying enrichment culture, while no "conventional" nitrifiers were found in the corresponding enrichment cultures. Xanthomonadaceae was a common taxon for all microbial communities, indicating its exclusive role in this ecosystem. This study opens up new knowledge about the metabolic capabilities of N cycle bacteria and potential approaches for sustainable bioremediation of heavily N-polluted cold ecosystems.
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Affiliation(s)
- Ekaterina Botchkova
- Winogradsky Institute of Microbiology, “Fundamentals of Biotechnology” Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Anastasia Vishnyakova
- Winogradsky Institute of Microbiology, “Fundamentals of Biotechnology” Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Nadezhda Popova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Marina Sukhacheva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Tatyana Kolganova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Yuriy Litti
- Winogradsky Institute of Microbiology, “Fundamentals of Biotechnology” Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
- Correspondence: ; Tel.: +7-9263699243
| | - Alexey Safonov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 117312 Moscow, Russia
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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.
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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.
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Watanabe K, Kohzu A, Suda W, Yamamura S, Takamatsu T, Takenaka A, Koshikawa MK, Hayashi S, Watanabe M. Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy. SPRINGERPLUS 2016; 5:1596. [PMID: 27652169 PMCID: PMC5026986 DOI: 10.1186/s40064-016-3286-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/11/2016] [Indexed: 12/29/2022]
Abstract
To investigate the nitrification potential of phyllospheric microbes, we incubated throughfall samples collected under the canopies of Japanese cedar (Cryptomeria japonica) and analyzed the transformation of inorganic nitrogen in the samples. Nitrate concentration increased in the unfiltered throughfall after 4 weeks of incubation, but remained nearly constant in the filtered samples (pore size: 0.2 and 0.4 µm). In the unfiltered samples, δ18O and δ15N values of nitrate decreased during incubation. In addition, archaeal ammonia monooxygenase subunit A (amoA) genes, which participate in the oxidation of ammonia, were found in the throughfall samples, although betaproteobacterial amoA genes were not detected. The amoA genes recovered from the leaf surface of C. japonica were also from archaea. Conversely, nitrate production, decreased isotope ratios of nitrate, and the presence of amoA genes was not observed in rainfall samples collected from an open area. Thus, the microbial nitrification that occurred in the incubated throughfall is likely due to ammonia-oxidizing archaea that were washed off the tree canopy by precipitation.
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Affiliation(s)
- Keiji Watanabe
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan ; Center for Environmental Science in Saitama, Kazo, Saitama 347-0115 Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Wataru Suda
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562 Japan
| | - Shigeki Yamamura
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Takejiro Takamatsu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Akio Takenaka
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Masami Kanao Koshikawa
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Seiji Hayashi
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Mirai Watanabe
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
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Gat D, Ronen Z, Tsesarsky M. Soil Bacteria Population Dynamics Following Stimulation for Ureolytic Microbial-Induced CaCO3 Precipitation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:616-624. [PMID: 26689904 DOI: 10.1021/acs.est.5b04033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Microbial-induced CaCO3 precipitation (MICP) via urea-hydrolysis (ureolysis) is an emerging soil improvement technique for various civil engineering and environmental applications. In-situ application of MICP in soils is performed either by augmenting the site with ureolytic bacteria or by stimulating indigenous ureolytic bacteria. Both of these approaches may lead to changes in the indigenous bacterial population composition and to the accumulation of large quantities of ammonium. In this batch study, effective ureolysis was stimulated in coastal sand from a semiarid environment, with low initial ureolytic bacteria abundance. Two different carbon sources were used: yeast-extract and molasses. No ureolysis was observed in their absence. Ureolysis was achieved using both carbon sources, with a higher rate in the yeast-extract enrichment resulting from increased bacterial growth. The changes to the indigenous bacterial population following biostimulation of ureolysis were significant: Bacilli class abundancy increased from 5% in the native sand up to 99% in the yeast-extract treatment. The sand was also enriched with ammonium-chloride, where ammonia-oxidation was observed after 27 days, but was not reflected in the bacterial population composition. These results suggest that biostimulation of ureolytic bacteria can be applied even in a semiarid and nutrient-poor environment using a simple carbon source, that is, molasses. The significant changes to bacterial population composition following ureolysis stimulation could result in a decrease in trophic activity and diversity in the treated site, thus they require further attention.
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Affiliation(s)
- Daniella Gat
- The Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev , Beer-Sheva 8410501, Israel
| | - Zeev Ronen
- The Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev , Sede-Boqer Campus 8499000, Israel
| | - Michael Tsesarsky
- The Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev , Beer-Sheva 8410501, Israel
- The Department of Structural Engineering, Ben-Gurion University of the Negev , Beer-Sheva 8410501, Israel
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6
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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.
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Affiliation(s)
- Jason M Smith
- Department of Environmental Earth System Science Stanford University, 473 Via Ortega, Room 140, Stanford, CA, USA
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Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol 2014; 90:39-53. [PMID: 24953994 DOI: 10.1111/1574-6941.12370] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/30/2014] [Accepted: 06/11/2014] [Indexed: 01/27/2023] Open
Abstract
We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics.
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Affiliation(s)
- Sebastian Opitz
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
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8
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Gerbl FW, Weidler GW, Wanek W, Erhardt A, Stan-Lotter H. Thaumarchaeal ammonium oxidation and evidence for a nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Front Microbiol 2014; 5:225. [PMID: 24904540 PMCID: PMC4032944 DOI: 10.3389/fmicb.2014.00225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/28/2014] [Indexed: 11/13/2022] Open
Abstract
Previous studies had suggested the presence of ammonium oxidizing Thaumarchaeota as well as nitrite oxidizing Bacteria in the subsurface spring called Franz Josef Quelle (FJQ), a slightly radioactive thermal mineral spring with a temperature of 43.6-47°C near the alpine village of Bad Gastein, Austria. The microbiological consortium of the FJQ was investigated for its utilization of nitrogen compounds and the putative presence of a subsurface nitrogen cycle. Microcosm experiments made with samples from the spring water, containing planktonic microorganisms, or from biofilms, were used in this study. Three slightly different media, enriched with vitamins and trace elements, and two incubation temperatures (30 and 40°C, respectively) were employed. Under aerobic conditions, high rates of conversion of ammonium to nitrite, as well as nitrite to nitrate were measured. Under oxygen-limited conditions nitrate was converted to gaseous compounds. Stable isotope probing with (15)NH4Cl or ((15)NH4)2SO4as sole energy sources revealed incorporation of (15)N into community DNA. Genomic DNA as well as RNA were extracted from all microcosms. The following genes or fragments of genes were successfully amplified, cloned and sequenced by standard PCR from DNA extracts: Ammonia monooxygenase subunit A (amoA), nitrite oxidoreductase subunits A and B (nxrA and nxrB), nitrate reductase (narG), nitrite reductase (nirS), nitric oxide reductases (cnorB and qnorB), nitrous oxide reductase (nosZ). Reverse transcription of extracted total RNA and real-time PCR suggested the expression of each of those genes. Nitrogen fixation (as probed with nifH and nifD) was not detected. However, a geological origin of NH(+) 4 in the water of the FJQ cannot be excluded, considering the silicate, granite and gneiss containing environment. The data suggested the operation of a nitrogen cycle in the subsurface environment of the FJQ.
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Affiliation(s)
| | - Gerhard W. Weidler
- Bioanalyticum, Institut für Mikrobiologie und Hygiene, Dr. Reisinger e. U.Perg, Austria
| | - Wolfgang Wanek
- Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Angelika Erhardt
- Analytec, Labor für Lebensmitteluntersuchung und UmweltanalytikSalzburg, Austria
| | - Helga Stan-Lotter
- Division of Molecular Biology, University of SalzburgSalzburg, Austria
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Bollmann A, Bullerjahn GS, McKay RM. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior. PLoS One 2014; 9:e97068. [PMID: 24819357 PMCID: PMC4018257 DOI: 10.1371/journal.pone.0097068] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/15/2014] [Indexed: 11/29/2022] Open
Abstract
Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.
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Affiliation(s)
- Annette Bollmann
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
- * E-mail: *
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Robert Michael McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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Abell GCJ, Robert SS, Frampton DMF, Volkman JK, Rizwi F, Csontos J, Bodrossy L. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array. PLoS One 2012; 7:e51542. [PMID: 23284709 PMCID: PMC3526613 DOI: 10.1371/journal.pone.0051542] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/08/2012] [Indexed: 11/17/2022] Open
Abstract
Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.
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Affiliation(s)
- Guy C J Abell
- CSIRO Marine and Atmospheric Research and Wealth from Oceans National Research Flagship, Hobart, Tasmania, Australia
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11
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Vissers EW, Blaga CI, Bodelier PL, Muyzer G, Schleper C, Sinninghe Damsté JS, Tourna M, Laanbroek HJ. Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake. FEMS Microbiol Ecol 2012; 83:515-26. [DOI: 10.1111/1574-6941.12013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 08/15/2012] [Accepted: 09/09/2012] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elisabeth W. Vissers
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen; the Netherlands
| | - Cornelia I. Blaga
- Faculty of Earth Sciences; Utrecht University; Utrecht; the Netherlands
| | - Paul L.E. Bodelier
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen; the Netherlands
| | | | - Christa Schleper
- Department of Genetics in Ecology; University of Vienna; Vienna; Austria
| | | | - Maria Tourna
- Ruakura centre; AgResearch Ltd; Hamilton; New Zealand
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12
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Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake. ISME JOURNAL 2012; 6:1786-97. [PMID: 22495069 DOI: 10.1038/ismej.2012.33] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter-spring (that is, the 0 (o)C slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer-autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC-1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC-1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC-1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments.
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Wu Y, Guo Y, Lin X, Zhong W, Jia Z. Inhibition of bacterial ammonia oxidation by organohydrazines in soil microcosms. Front Microbiol 2012; 3:10. [PMID: 22319517 PMCID: PMC3262162 DOI: 10.3389/fmicb.2012.00010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 01/05/2012] [Indexed: 11/25/2022] Open
Abstract
Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO) is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB). Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homolog in known ammonia-oxidizing archaea (AOA). In this study, the effects of three organohydrazines on activity, abundance, and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 μmol g−1 dry weight soil completely suppressed the activity of soil nitrification. Denaturing gradient gel electrophoresis fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA) clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear.
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Affiliation(s)
- Yucheng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, PR China
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Bouskill NJ, Eveillard D, Chien D, Jayakumar A, Ward BB. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments. Environ Microbiol 2011; 14:714-29. [PMID: 22050634 DOI: 10.1111/j.1462-2920.2011.02623.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution.
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Affiliation(s)
- Nicholas J Bouskill
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA.
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Mao Y, Yannarell AC, Mackie RI. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One 2011; 6:e24750. [PMID: 21935454 PMCID: PMC3173469 DOI: 10.1371/journal.pone.0024750] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 08/16/2011] [Indexed: 11/18/2022] Open
Abstract
Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.
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Affiliation(s)
- Yuejian Mao
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Anthony C. Yannarell
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Auguet JC, Nomokonova N, Camarero L, Casamayor EO. Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes. Appl Environ Microbiol 2011; 77:1937-45. [PMID: 21239556 PMCID: PMC3067326 DOI: 10.1128/aem.01213-10] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/03/2011] [Indexed: 02/01/2023] Open
Abstract
The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ± 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.
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Affiliation(s)
- Jean-Christophe Auguet
- Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc 14, E-17300, Blanes, Spain.
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Ammonium availability affects the ratio of ammonia-oxidizing bacteria to ammonia-oxidizing archaea in simulated creek ecosystems. Appl Environ Microbiol 2011; 77:1896-9. [PMID: 21239545 DOI: 10.1128/aem.02879-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 μM NH(4)(+) than in those incubated at 50 or 20 μM NH(4)(+). Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaeal amoA gene copy numbers.
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