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Laanbroek HJ, Rains MC, Verhoeven JTA, Whigham DF. The effect of intentional summer flooding for mosquito control on the nitrogen dynamics of impounded Avicennia germinans mangrove forests. Sci Rep 2024; 14:2165. [PMID: 38272989 PMCID: PMC10811325 DOI: 10.1038/s41598-024-52248-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coastal wetlands such as mangrove forests are breeding grounds for nuisance-causing insects. Rotational Impoundment Management (RIM) for mosquito control involves annual summer inundation of impounded mangrove forests with estuarine water during the summer half year. However, in addition to controlling mosquitos, RIM may change biogeochemical pathways. This study set out to investigate how RIM quantitatively affects physicochemical soil characteristics and potential nitrifying and denitrifying activities (PNA and PDA), which are key in the global nitrogen cycle. Before and after the implementation of RIM, soil samples were collected annually in habitats differing in size and abundance of black mangroves (Avicennia germinans) in an impoundment with RIM and in an adjacent impoundment with a more open connection to the lagoon. Compared to the non-managed impoundment, soil moisture content, total nitrogen and PDA increased, while salinity decreased after the start of annual summer flooding, but only in the dwarf habitat. In the sparse and dense habitats, total nitrogen and PDA increased independently of summer flooding, whereas soil moisture content and salinity were not affected by RIM. Labile organic nitrogen increased only in the RIM impoundment, irrespective of the habitat type. PNA was generally not affected with time, except in the dwarf habitat in the absence of intentional summer flooding where it increased. Changes in the non-managed impoundment adjacent to the RIM impoundment demonstrate the importance of groundwater exchange in linked ecosystems. The consequences of interventions in the management of mangrove impoundments and adjacent forests for the nitrogen budget are discussed.
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Affiliation(s)
- H J Laanbroek
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
- Department of Microbial Ecology, NIOO-KNAW, Wageningen, The Netherlands.
- Smithsonian Environmental Research Station, Edgewater, MD, USA.
| | - M C Rains
- School of Geosciences, University of South Florida, Tampa, FL, USA
| | - J T A Verhoeven
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- Smithsonian Environmental Research Station, Edgewater, MD, USA
| | - D F Whigham
- Smithsonian Environmental Research Station, Edgewater, MD, USA
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2
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Huang W, Li S, Li S, Laanbroek HJ, Zhang Q. Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian. Front Microbiol 2023; 14:1151768. [PMID: 37180236 PMCID: PMC10169824 DOI: 10.3389/fmicb.2023.1151768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.
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Affiliation(s)
- Weihong Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Shuantong Li
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Saisai Li
- Zhejiang Wanli University, Ningbo, China
| | - Hendrikus J. Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Qiufang Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
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3
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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Zhang QF, Laanbroek HJ. Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil. FEMS Microbiol Ecol 2020; 96:5876345. [PMID: 32710789 DOI: 10.1093/femsec/fiaa148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.
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Affiliation(s)
- Qiu-Fang Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, 398 Donghai Street, Quanzhou 362000, China.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou 362100, China
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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5
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Sedlacek CJ, McGowan B, Suwa Y, Sayavedra-Soto L, Laanbroek HJ, Stein LY, Norton JM, Klotz MG, Bollmann A. A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria. Microb Ecol 2019; 78:985-994. [PMID: 30976841 DOI: 10.1007/s00248-019-01378-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.
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Affiliation(s)
- Christopher J Sedlacek
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Brian McGowan
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA
| | - Yuichi Suwa
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Luis Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Jeanette M Norton
- Department of Plants, Soil and Climate, Utah State University, Logan, UT, 84322-4820, USA
| | - Martin G Klotz
- School of Molecular Biosciences, Washington State University, Richland, WA, 99354, USA
| | - Annette Bollmann
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA.
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Marcos MS, Barboza AD, Keijzer RM, Laanbroek HJ. Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle. Microb Ecol 2018; 75:997-1008. [PMID: 29063148 PMCID: PMC5906487 DOI: 10.1007/s00248-017-1091-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/07/2017] [Indexed: 05/13/2023]
Abstract
Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations were tidal locations, while the other location was impounded. Differences in the community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA genes and by MiSeq 16S rRNA gene-sequencing. The abundances of AOA and AOB were established by quantitative PCR of amoA genes. In addition, we analyzed the total microbial community composition based on 16S rRNA genes and explored the influence of soil physicochemical properties underneath Avicennia germinans and Rhizophora mangle on microbial communities. AOA were always more abundant than AOB, but the effect of mangrove species on total numbers of ammonia oxidizers was location-specific. The microbial communities including the ammonia oxidizers in soils associated with A. germinans and R. mangle differed only at the tidal locations. In conclusion, potential site-specific effects of mangrove species on soil microbial communities including those of the AOA and AOB are apparently overruled by the absence or presence of tide.
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Affiliation(s)
- Magalí S Marcos
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CONICET), Puerto Madryn, Argentina
| | - Anthony D Barboza
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
| | - 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.
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7
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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. Microb Ecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Balk M, Keuskamp JA, Laanbroek HJ. Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas. Front Microbiol 2016; 7:1855. [PMID: 27917167 PMCID: PMC5114281 DOI: 10.3389/fmicb.2016.01855] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/03/2016] [Indexed: 12/05/2022] Open
Abstract
Avicennia and Rhizophora are globally occurring mangrove genera with different traits that place them in different parts of the intertidal zone. It is generally accepted that the oxidizing capacity of Avicennia roots is larger than that of Rhizophora roots, which initiates more reduced conditions in the soil below the latter genus. We hypothesize that the more reduced conditions beneath Rhizophora stands lead to more active sulfate-reducing microbial communities compared to Avicennia stands. To test this hypothesis, we measured sulfate reduction traits in soil samples collected from neighboring Avicennia germinans and Rhizophora mangle stands at three different locations in southern Florida. The traits measured were sulfate reduction rates (SRR) in flow-through reactors containing undisturbed soil layers in the absence and presence of easily degradable carbon compounds, copy numbers of the dsrB gene, which is specific for sulfate-reducing microorganisms, and numbers of sulfate-reducing cells that are able to grow in liquid medium on a mixture of acetate, propionate and lactate as electron donors. At the tidal locations Port of the Islands and South Hutchinson Islands, steady state SRR, dsrB gene copy numbers and numbers of culturable cells were higher at the A. germinans than at the R. mangle stands, although not significantly for the numbers at Port of the Islands. At the non-tidal location North Hutchinson Island, results are mixed with respect to these sulfate reduction traits. At all locations, the fraction of culturable cells were significantly higher at the R. mangle than at the A. germinans stands. The dynamics of the initial SRR implied a more in situ active sulfate-reducing community at the intertidal R. mangle stands. It was concluded that in agreement with our hypothesis R. mangle stands accommodate a more active sulfate-reducing community than A. germinans stands, but only at the tidal locations. The differences between R. mangle and A. germinans stands were absent at the non-tidal, impounded location.
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Affiliation(s)
- Melike Balk
- Department of Microbial Ecology, Netherlands Institute of Ecology-Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands; Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - Joost A Keuskamp
- Department of Microbial Ecology, Netherlands Institute of Ecology-Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht UniversityUtrecht, Netherlands
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology-Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht UniversityUtrecht, Netherlands
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9
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Rice MC, Norton JM, Valois F, Bollmann A, Bottomley PJ, Klotz MG, Laanbroek HJ, Suwa Y, Stein LY, Sayavedra-Soto L, Woyke T, Shapiro N, Goodwin LA, Huntemann M, Clum A, Pillay M, Kyrpides N, Varghese N, Mikhailova N, Markowitz V, Palaniappan K, Ivanova N, Stamatis D, Reddy TBK, Ngan CY, Daum C. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. Stand Genomic Sci 2016; 11:46. [PMID: 27471578 PMCID: PMC4964001 DOI: 10.1186/s40793-016-0168-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 07/18/2016] [Indexed: 12/02/2022] Open
Abstract
Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
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Affiliation(s)
| | | | | | | | | | - Martin G. Klotz
- Queens College in The City University of New York, Flushing, NY USA
- The Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Hendrikus J. Laanbroek
- Netherlands Institute of Ecology, Wageningen, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM USA
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | | | | | | | | | | | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA USA
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10
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Soares JR, Cassman NA, Kielak AM, Pijl A, Carmo JB, Lourenço KS, Laanbroek HJ, Cantarella H, Kuramae EE. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil. Sci Rep 2016; 6:30349. [PMID: 27460335 PMCID: PMC4962081 DOI: 10.1038/srep30349] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/04/2016] [Indexed: 01/08/2023] Open
Abstract
Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.
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Affiliation(s)
- Johnny R Soares
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands.,Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, 13012-970, Campinas, SP, Brazil
| | - Noriko A Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands
| | - Anna M Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands
| | - Janaína B Carmo
- Environmental Science Department, Federal University of São Carlos, 1852-780, Sorocaba, SP, Brazil
| | - Kesia S Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands.,Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, 13012-970, Campinas, SP, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands.,Institute of Environmental Biology, Utrecht University, Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, 13012-970, Campinas, SP, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, Netherlands
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11
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Balk M, Keuskamp JA, Laanbroek HJ. Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast. Front Microbiol 2016; 6:1478. [PMID: 26733999 PMCID: PMC4686736 DOI: 10.3389/fmicb.2015.01478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/08/2015] [Indexed: 12/02/2022] Open
Abstract
After oxygen, sulfate is the most important oxidant for the oxidation of organic matter in mangrove forest soils. As sulfate reducers are poor competitors for common electron donors, their relative success depends mostly on the surplus of carbon that is left by aerobic organisms due to oxygen depletion. We therefore hypothesized that sulfate-cycling in mangrove soils is influenced by the size of net primary production, and hence negatively affected by mangrove degradation and exploitation, as well as by carbon-exporting waves. To test this, we compared quantitative and qualitative traits of sulfate-reducing communities in two Saudi-Arabian mangrove stands near Jeddah, where co-occurring differences in camel-grazing pressure and tidal exposure led to a markedly different stand height and hence primary production. Potential sulfate reduction rates measured in anoxic flow-through reactors in the absence and presence of additional carbon sources were significantly higher in the samples from the non-grazed site. Near the surface (0–2 cm depth), numbers of dsrB gene copies and culturable cells also tended to be higher in the non-grazed sites, while these differences were not detected in the sub-surface (4–6 cm depth). It was concluded that sulfate-reducing microbes at the surface were indeed repressed at the low-productive site as could be expected from our hypothesis. At both sites, sulfate reduction rates as well as numbers of the dsrB gene copies and viable cells increased with depth suggesting repression of sulfate reduction near the surface in both irrespective of production level. Additionally, sequence analysis of DNA bands obtained from DGGE gels based on the dsrB gene, showed a clear difference in dominance of sulfate-reducing genera belonging to the Deltaproteobacteria and the Firmicutes between sampling sites and depths.
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Affiliation(s)
- Melike Balk
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - Joost A Keuskamp
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Ecology and Biodiversity, Department of Biology, Utrecht UniversityUtrecht, Netherlands
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Ecology and Biodiversity, Department of Biology, Utrecht UniversityUtrecht, Netherlands
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12
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Zhang Q, Tang F, Zhou Y, Xu J, Chen H, Wang M, Laanbroek HJ. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China. Front Microbiol 2015; 6:1180. [PMID: 26579089 PMCID: PMC4621301 DOI: 10.3389/fmicb.2015.01180] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/12/2015] [Indexed: 12/11/2022] Open
Abstract
Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.
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Affiliation(s)
- Qiufang Zhang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Fangyuan Tang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Yangjing Zhou
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Jirong Xu
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Heping Chen
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Mingkuang Wang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Hendrikus J Laanbroek
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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13
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Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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14
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Steenbergh AK, Bodelier PLE, Hoogveld HL, Slomp CP, Laanbroek HJ. Phylogenetic Characterization of Phosphatase-Expressing Bacterial Communities in Baltic Sea Sediments. Microbes Environ 2015; 30:192-5. [PMID: 25817584 PMCID: PMC4462931 DOI: 10.1264/jsme2.me14074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Phosphate release from sediments hampers the remediation of aquatic systems from a eutrophic state. Microbial phosphatases in sediments release phosphorus during organic matter degradation. Despite the important role of phosphatase-expressing bacteria, the identity of these bacteria in sediments is largely unknown. We herein presented a culture-independent method to phylogenetically characterize phosphatase-expressing bacteria in sediments. We labeled whole-cell extracts of Baltic Sea sediments with an artificial phosphatase substrate and sorted phosphatase-expressing cells with a flow cytometer. Their phylogenetic affiliation was determined by Denaturing Gradient Gel Electrophoresis. The phosphatase-expressing bacterial community coarsely reflected the whole-cell bacterial community, with a similar dominance of Alphaproteobacteria.
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15
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Balk M, Laverman AM, Keuskamp JA, Laanbroek HJ. Nitrate ammonification in mangrove soils: a hidden source of nitrite? Front Microbiol 2015; 6:166. [PMID: 25784903 PMCID: PMC4345912 DOI: 10.3389/fmicb.2015.00166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/12/2015] [Indexed: 11/13/2022] Open
Abstract
Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils.
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Affiliation(s)
- Melike Balk
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Netherlands ; Faculty of Geosciences, Utrecht University Utrecht, Netherlands
| | | | - Joost A Keuskamp
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Netherlands ; Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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16
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Daebeler A, Bodelier PLE, Hefting MM, Laanbroek HJ. Ammonia-limited conditions cause of Thaumarchaeal dominance in volcanic grassland soil. FEMS Microbiol Ecol 2015; 91:fiv014. [DOI: 10.1093/femsec/fiv014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 11/12/2022] Open
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17
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Reis MP, Avila MP, Costa PS, Barbosa FAR, Laanbroek HJ, Chartone-Souza E, Nascimento AMA. The influence of human settlement on the distribution and diversity of iron-oxidizing bacteria belonging to the Gallionellaceae in tropical streams. Front Microbiol 2014; 5:630. [PMID: 25505456 PMCID: PMC4241827 DOI: 10.3389/fmicb.2014.00630] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/04/2014] [Indexed: 01/20/2023] Open
Abstract
Among the neutrophilic iron-oxidizing bacteria (FeOB), Gallionella is one of the most abundant genera in freshwater environments. By applying qPCR and DGGE based on 16S rRNA gene-directed primers targeting Gallionellaceae, we delineated the composition and abundance of the Gallionellaceae-related FeOB community in streams differentially affected by metal mining, and explored the relationships between these community characteristics and environmental variables. The sampling design included streams historically impacted by mining activity and a non-impacted stream. The sediment and water samples harbored a distinct community represented by Gallionella, Sideroxydans, and Thiobacillus species. Sequences affiliated with Gallionella were exclusively observed in sediments impacted by mining activities, suggesting an adaptation of this genus to these environments. In contrast, Sideroxydans-related sequences were found in all sediments including the mining impacted locations. The highest and lowest relative frequencies of Gallionellaceae-related FeOB were associated with the lowest and highest concentrations of Fe, respectively. The data enclosed here clearly show distinct species-specific ecological niches, with Gallionella species dominating in sediments impacted by anthropogenic activities over Sideroxydans species.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Marcelo P Avila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO - KNAW) Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
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18
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Verhoeven JTA, Laanbroek HJ, Rains MC, Whigham DF. Effects of increased summer flooding on nitrogen dynamics in impounded mangroves. J Environ Manage 2014; 139:217-26. [PMID: 24751377 DOI: 10.1016/j.jenvman.2014.02.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 01/31/2014] [Accepted: 02/23/2014] [Indexed: 05/26/2023]
Abstract
Mangroves are important for coastal protection, carbon sequestration and habitat provision for plants and animals in the tropics and subtropics. Mangroves are threatened by habitat destruction and sea level rise, but management activities such as impounding for mosquito control can also have negative effects. We studied the effects of Rotational Impoundment Management (RIM) on nitrogen dynamics in impoundments dominated by three types of Black mangrove (Avicennia germinans) stands along the Indian River Lagoon (Florida). RIM, designed for noxious insect control, involves pumping estuarine water into impoundments in this area during spring and summer to raise water levels by 30 cm. We compared aspects of the nitrogen cycle before and after the start of the RIM and measured the same variables in an impoundment without RIM management. RIM led to the accumulation of ammonium in the substrate which coincided with a lowering of nitrification rates and decreased denitrification rates. Salt pan habitats dominated by dwarf mangroves became less saline following RIM initiation. Shoot growth of mangroves increased in response to higher nitrogen availability and lower pore water salinity. Mangrove responses were greatest in areas with dwarf and sparse mangrove cover. Overall, RIM resulted in lower nitrification and denitrification leading to lower nitrogen losses and increased Black mangrove growth, all benefits of RIM beyond those associated with noxious insect control.
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Affiliation(s)
- Jos T A Verhoeven
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Smithsonian Environmental Research Center, P.O. Box 23, Edgewater, MA 21037, USA.
| | - Hendrikus J Laanbroek
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Smithsonian Environmental Research Center, P.O. Box 23, Edgewater, MA 21037, USA; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands.
| | - Mark C Rains
- School of Geosciences, University of South Florida, 4202 East Fowler Ave, SCA528 Tampa, FL 33620, USA.
| | - Dennis F Whigham
- Smithsonian Environmental Research Center, P.O. Box 23, Edgewater, MA 21037, USA.
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19
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Steenbergh AK, Bodelier PLE, Slomp CP, Laanbroek HJ. Effect of redox conditions on bacterial community structure in Baltic Sea sediments with contrasting phosphorus fluxes. PLoS One 2014; 9:e92401. [PMID: 24667801 PMCID: PMC3965429 DOI: 10.1371/journal.pone.0092401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 02/22/2014] [Indexed: 11/18/2022] Open
Abstract
Phosphorus release from sediments can exacerbate the effect of eutrophication in coastal marine ecosystems. The flux of phosphorus from marine sediments to the overlying water is highly dependent on the redox conditions at the sediment-water interface. Bacteria are key players in the biological processes that release or retain phosphorus in marine sediments. To gain more insight in the role of bacteria in phosphorus release from sediments, we assessed the effect of redox conditions on the structure of bacterial communities. To do so, we incubated surface sediments from four sampling sites in the Baltic Sea under oxic and anoxic conditions and analyzed the fingerprints of the bacterial community structures in these incubations and the original sediments. This paper describes the effects of redox conditions, sampling station, and sample type (DNA, RNA, or whole-cell sample) on bacterial community structure in sediments. Redox conditions explained only 5% of the variance in community structure, and bacterial communities from contrasting redox conditions showed considerable overlap. We conclude that benthic bacterial communities cannot be classified as being typical for oxic or anoxic conditions based on community structure fingerprints. Our results suggest that the overall structure of the benthic bacterial community has only a limited impact on benthic phosphate fluxes in the Baltic Sea.
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Affiliation(s)
- Anne K. Steenbergh
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Caroline P. Slomp
- Department of Earth Sciences (Geochemistry), Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Hendrikus J. Laanbroek
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Environmental Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
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20
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Laanbroek HJ, Keijzer RM, Verhoeven JTA, Whigham DF. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions. Front Microbiol 2013; 4:343. [PMID: 24312088 PMCID: PMC3834342 DOI: 10.3389/fmicb.2013.00343] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/30/2013] [Indexed: 11/13/2022] Open
Abstract
In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands ; Smithsonian Environmental Research Center Edgewater, MD, USA
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21
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Bollmann A, Sedlacek CJ, Norton J, Laanbroek HJ, Suwa Y, Stein LY, Klotz MG, Arp D, Sayavedra-Soto L, Lu M, Bruce D, Detter C, Tapia R, Han J, Woyke T, Lucas SM, Pitluck S, Pennacchio L, Nolan M, Land ML, Huntemann M, Deshpande S, Han C, Chen A, Kyrpides N, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Mikhailova N, Pagani I, Pati A, Peters L, Ovchinnikova G, Goodwin LA. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations. Stand Genomic Sci 2013; 7:469-82. [PMID: 24019993 PMCID: PMC3764937 DOI: 10.4056/sigs.3517166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.
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22
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Steenbergh AK, Bodelier PLE, Heldal M, Slomp CP, Laanbroek HJ. Does microbial stoichiometry modulate eutrophication of aquatic ecosystems? Environ Microbiol 2012; 15:1572-9. [PMID: 23227825 DOI: 10.1111/1462-2920.12042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 10/31/2012] [Accepted: 11/01/2012] [Indexed: 11/27/2022]
Abstract
The stoichiometry of prokaryotes (Bacteria and Archaea) can control benthic phosphorus (P) fluxes relative to carbon (C) and nitrogen (N) during organic matter remineralization. This paper presents the first experimental data on benthic microbial stoichiometry. We used X-ray microanalysis to determine C : N : P ratios of individual prokaryotes from C-limited Baltic Sea sediments incubated under oxic or anoxic conditions. At approximately 400:1, C : P ratios of prokaryotes from both oxic and anoxic incubations were higher than the Redfield ratio for marine organic matter (106:1), whereas prokaryotic C : N ratios (6.4:1) were close to the Redfield ratio. We conclude that high microbial C : P ratios contribute to the enhanced remineralization of P from organic matter relative to C and N observed in many low oxygen marine settings.
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Affiliation(s)
- A K Steenbergh
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands.
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Laanbroek HJ, Keijzer RM, Verhoeven JTA, Whigham DF. The Distribution of Ammonia-Oxidizing Betaproteobacteria in Stands of Black Mangroves (Avicennia germinans). Front Microbiol 2012; 3:153. [PMID: 22536201 PMCID: PMC3333478 DOI: 10.3389/fmicb.2012.00153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 04/02/2012] [Indexed: 12/02/2022] Open
Abstract
The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially stands of Black mangrove (Avicennia germinans) that differ in the size and density of individual plants. In March 2009, the management of one impoundment was changed to a regime of pumping estuarine water into the impoundment at critical times of the year to eliminate breeding sites for noxious insects. We collected soil samples in three different Black mangrove habitats before and after the change in management to determine the impacts of the altered hydrologic regimes on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB). We also sampled soils in an adjacent impoundment in which there had not been any hydrologic alteration. At the level of 97% mutual similarity in the 16s rRNA gene, 13 different operational taxonomic units were identified; the majority related to the lineages of Nitrosomonas marina (45% of the total clones), Nitrosomonas sp. Nm143 (23%), and Nitrosospira cluster 1 (19%). Long-term summer flooding of the impoundment in 2009, after initiation of the pumping regime, reduced the percentage of N. marina by half between 2008 and 2010 in favor of the two other major lineages and the potential ammonia-oxidizing activity decreased by an average of 73%. Higher interstitial salinities, probably due to a prolonged winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008: Nitrosomonas sp. Nm143 was replaced by Nitrosospira cluster 1 as the second most important lineage. There were small, but significant differences in the bacterial communities between the flooded and non-flooded impoundments. There were also differences in the community composition of the bacteria in the three Black mangrove habitats. N. marina was most dominant in all three habitats, but was partly replaced by Nitrosospira cluster 1 in sites dominated by sparsely distributed trees and by Nitrosomonas sp. Nm143 in sites characterized by taller, more densely distributed Black mangrove trees.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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Wang J, Krause S, Muyzer G, Meima-Franke M, Laanbroek HJ, Bodelier PLE. Spatial patterns of iron- and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland. Front Microbiol 2012; 3:64. [PMID: 22375139 PMCID: PMC3284728 DOI: 10.3389/fmicb.2012.00064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/06/2012] [Indexed: 11/13/2022] Open
Abstract
Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circumneutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and qPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidizers (Ga-FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Ga-FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of Ga-FeOB was assessed using PCR-DGGE and the abundance of both Ga-FeOB and MOB by qPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of Ga-FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Ga-FeOB outnumbered the MOB subgroups suggesting their competitiveness or the prevalence of Fe(2+) over CH(4) oxidation in this floodplain.
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Affiliation(s)
- Juanjuan Wang
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Gerard Muyzer
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, AmsterdamNetherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Hendrikus J. Laanbroek
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
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Bollmann A, French E, Laanbroek HJ. Isolation, Cultivation, and Characterization of Ammonia-Oxidizing Bacteria and Archaea Adapted to Low Ammonium Concentrations. Methods Enzymol 2011; 486:55-88. [DOI: 10.1016/b978-0-12-381294-0.00003-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Verhagen FJ, Duyts H, Laanbroek HJ. Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns. Appl Environ Microbiol 2010; 58:3303-11. [PMID: 16348787 PMCID: PMC183095 DOI: 10.1128/aem.58.10.3303-3311.1992] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the absence of nitrate formation in grassland soils rich in organic matter has often been reported, low numbers of nitrifying bacteria are still found in these soils. To obtain more insight into these observations, we studied the competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi with soil columns containing calcareous sandy soil. The soil columns were percolated continuously at a dilution rate of 0.007 h, based on liquid volumes, with medium containing 5 mM ammonium and different amounts of glucose ranging from 0 to 12 mM.A. globiformis was the most competitive organism for limiting amounts of ammonium. The numbers of N. europaea and N. winogradskyi cells were lower at higher glucose concentrations, and the potential ammonium-oxidizing activities in the uppermost 3 cm of the soil columns were nonexistent when at least 10 mM glucose was present in the reservoir, although 10 nitrifying cells per g of dry soil were still present. This result demonstrated that there was no correlation between the numbers of nitrifying bacteria and their activities. The numbers and activities of N. winogradskyi cells decreased less than those of N. europaea cells in all layers of the soil columns, probably because of heterotrophic growth of the nitrite-oxidizing bacteria on organic substrates excreted by the heterotrophic bacteria or because of nitrate reduction at reduced oxygen concentrations by the nitrite-oxidizing bacteria. Our conclusion was that the nitrifying bacteria were less competitive than the heterotrophic bacteria for ammonium in soil columns but that they survived as viable inactive cells. Inactive nitrifying bacteria may also be found in the rhizosphere of grassland plants, which is rich in organic carbon. They are possibly reactivated during periods of net mineralization.
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Affiliation(s)
- F J Verhagen
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 40, 6666 ZG Heteren, The Netherlands
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Kester RA, De Boer W, Laanbroek HJ. Production of NO and N(inf2)O by Pure Cultures of Nitrifying and Denitrifying Bacteria during Changes in Aeration. Appl Environ Microbiol 2010; 63:3872-7. [PMID: 16535707 PMCID: PMC1389263 DOI: 10.1128/aem.63.10.3872-3877.1997] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peak emissions of NO and N(inf2)O are often observed after wetting of soil. The reactions to sudden changes in the aeration of cultures of nitrifying and denitrifying bacteria with respect to NO and N(inf2)O emissions were compared to obtain more information about the microbiological aspects of peak emissions. In continuous culture, the nitrifier Nitrosomonas europaea and the denitrifiers Alcaligenes eutrophus and Pseudomonas stutzeri were cultured at different levels of aeration (80 to 0% air saturation) and subjected to changes in aeration. The relative production of NO and N(inf2)O by N. europaea, as a percentage of the ammonium conversion, increased from 0.87 and 0.17%, respectively, at 80% air saturation to 2.32 and 0.78%, respectively, at 1% air saturation. At 0% air saturation, ammonium oxidation and N(inf2)O production ceased but NO production was enhanced. Coculturing of N. europaea with the nitrite oxidizer Nitrobacter winogradskyi strongly reduced the relative levels of NO and N(inf2)O production, probably as an effect of the lowered nitrite concentration. After lowering the aeration, N. europaea produced large short-lasting peaks of NO and N(inf2)O emissions in the presence but not in the absence of nitrite. A. eutrophus and P. stutzeri began to denitrify below 1% air saturation, with the former accumulating nitrite and N(inf2)O and the latter reducing nitrate almost completely to N(inf2). Transition of A. eutrophus and P. stutzeri from 80 to 0% air saturation resulted in transient maxima of denitrification intermediates. Such transient maxima were not observed after transition from 1 to 0%. Reduction of nitrate by A. eutrophus continued 48 h after the onset of the aeration, whereas N(inf2)O emission by P. stutzeri increased for only a short period. It was concluded that only in the presence of nitrite are nitrifiers able to dominate the NO and N(inf2)O emissions of soils shortly after a rainfall event.
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Bodelier P, Libochant JA, Blom C, Laanbroek HJ. Dynamics of nitrification and denitrification in root-oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats. Appl Environ Microbiol 2010; 62:4100-7. [PMID: 16535441 PMCID: PMC1388979 DOI: 10.1128/aem.62.11.4100-4107.1996] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria. The oxygen-releasing, aerenchymatous emergent macrophyte Glyceria maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and early summer. The stimulation of the aerobic nitrifying bacteria in the freshwater sediment, ascribed to oxygen release by the roots of G. maxima, disappeared in late summer. Numbers and activities of the nitrifying bacteria were positively correlated, and a positive relationship with denitrification activities also was found. To assess possible adaptations of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats, a comparison was made between the freshwater lake sediment and three soils differing in oxicity profiles. Oxygen kinetics and tolerance to anoxia of the ammonia-oxidizing communities from these habitats were determined. The apparent K(infm) values for oxygen of the ammonia-oxidizing community in the lake sediment were in the range of 5 to 15 (mu)M, which was substantially lower than the range of K(infm) values for oxygen of the ammonia-oxidizing community from a permanently oxic dune location. Upon anoxic incubation, the ammonia-oxidizing communities of dune, chalk grassland, and calcareous grassland soils lost 99, 95, and 92% of their initial nitrifying capacity, respectively. In contrast, the ammonia-oxidizing community in the lake sediment started to nitrify within 1 h upon exposure to oxygen at the level of the initial capacity. It is argued that the conservation of the nitrifying capacity during anoxic periods and the ability to react instantaneously to the presence of oxygen are important traits of nitrifiers in fluctuating oxic-anoxic environments such as the root zone of aerenchymatous plant species.
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Verhagen FJ, Laanbroek HJ. Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Chemostats. Appl Environ Microbiol 2010; 58:1962-9. [PMID: 16348722 PMCID: PMC195710 DOI: 10.1128/aem.58.6.1962-1969.1992] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enhanced mineralization of organic nitrogen by bacteriophagous protozoa is thought to favor the nitrification process in soils, in which nitrifying bacteria have to compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the bacteriovorous flagellate Adriamonas peritocrescens on the competition for limiting amounts of ammonium between the ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h. The ammonium concentration in the reservoir was maintained at 2 mM, whereas the glucose concentration was increased stepwise from 0 to 7 mM. A. globiformis won the competition for limiting amounts of ammonium when the glucose concentration in the reservoirs increased, in agreement with previously described experiments in which the flagellates were not included. The numbers of nitrifying bacteria decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations. Critical C/N ratios, i.e., ratios between glucose and ammonium in the reservoirs at which no nitrate was found in the culture vessels, of 12.5 and 10.5 were determined at dilution rates of 0.004 and 0.01 h, respectively. Below these critical values, coexistence of the competing species was found. The numbers of nitrifying bacteria decreased more in the presence of flagellates than in their absence, presumably by selective predation on the nitrifying bacteria, either in the liquid culture or on the glass wall of the culture vessels. Despite this, the rate of nitrate production did not decrease more in the presence of flagellates than in their absence. This demonstrates that no correlation has to be expected between numbers of nitrifying bacteria and their activity and that a constant nitrification rate per cell cannot be assumed for nitrifying bacteria. Above the critical C/N ratios, low numbers of nitrifying bacteria were still found in the culture vessels, probably because of attachment of the nitrifying bacteria to the glass wall of the culture vessels. Like the numbers of heterotrophic bacteria, the numbers of flagellates increased when the glucose concentrations in the reservoirs increased. Numbers of 2 x 10 and 12 x 10 flagellates ml were found at 7 mM glucose at dilution rates of 0.004 and 0.01 h, respectively. It was concluded that the critical C/N ratios were practically unaffected by the presence of protozoa. Although nitrate production rates were equal in the presence and absence of flagellates, the numbers of nitrifying bacteria decreased more strongly in their presence. This indicates a higher activity per nitrifying cell in the presence of flagellates.
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Affiliation(s)
- F J Verhagen
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 40, 6666 ZG Heteren, The Netherlands
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Van Der Nat F, De Brouwer J, Middelburg JJ, Laanbroek HJ. Spatial distribution and inhibition by ammonium of methane oxidation in intertidal freshwater marshes. Appl Environ Microbiol 2010; 63:4734-40. [PMID: 16535750 PMCID: PMC1389306 DOI: 10.1128/aem.63.12.4734-4740.1997] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In two intertidal marshes, the vertical distribution in the sediment and inhibition by ammonium of methane oxidation were investigated by slurry incubation experiments. The two sites differ in their dominant vegetation type, i.e., reed and bulrush, and in their heights above sea level. The reed site was elevated with respect to the bulrush site, resulting in a lower frequency and duration of flooding and, consequently, a higher potential for methane oxidation. Methane oxidation decreased with depth in the bulrush and reed slurries, although methane oxidation associated with root material from the bulrush plants increased with depth. Reed root material had a limited capacity for methane oxidation and showed no significant increase with depth. Inhibition of methane oxidation by ammonium was observed in all samples and depended on methane and ammonium concentrations. Increasing ammonium concentrations resulted in greater inhibition, and increasing methane concentrations resulted in less. Ammonium concentrations had to exceed methane concentrations by at least 30-fold to become effective for inhibition. This ratio was found only in the surface layer of the sediment. Hence, the ecological relevance for ammonium inhibition of methane oxidation in intertidal marshes is rather limited and is restricted to the surface layer. Nitrate production was restricted to the 0- to 5-cm-depth slurries.
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Abstract
A study was performed to gain insight into the mechanism of acid-tolerant, chemolithotrophic nitrification. Microorganisms that nitrified at pH 4 were enriched from two Dutch acid soils. Nitrate production in the enrichment cultures was indicated to be of a chemolithoautotrophic nature as it was (i) completely inhibited by acetylene at a concentration as low as 1 mumol/liter and (ii) strongly retarded under conditions of carbon dioxide limitation. Electron microscopy of the enrichment cultures showed the presence of bacteria that were morphologically similar to strains of known chemolithotrophic nitrifying genera. Many of the enriched bacteria, in particular those that were identified as ammonium oxidizers, were aggregated. Filtration experiments indicated that aggregated cells were able to nitrify at low pH, whereas single cells were not. It is hypothesized that cells inside the aggregates are protected against the toxicity of nitrous acid. Nitrification by aggregated chemolithoautotrophic bacteria may be the dominating process of nitrate formation in many acid soils as it does not appear to depend on the existence of microsites of high pH (acid-sensitive autotrophic nitrification) or on the availability of organic carbon (heterotrophic nitrification).
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Affiliation(s)
- W De Boer
- Institute for Ecological Research, P.O. Box 40, 6666 ZG Heteren, and Laboratory for Electron Microscopy, Biological Centre, University of Groningen, 9751 NN Haren, The Netherlands, and Abteilung für Mikrobiologie, Institut für Allgemeine Botanik der Universität Hamburg, D-2000 Hamburg 52, Germany
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Nijburg JW, Coolen M, Gerards S, Gunnewiek P, Laanbroek HJ. Effects of Nitrate Availability and the Presence of Glyceria maxima on the Composition and Activity of the Dissimilatory Nitrate-Reducing Bacterial Community. Appl Environ Microbiol 2010; 63:931-7. [PMID: 16535557 PMCID: PMC1389122 DOI: 10.1128/aem.63.3.931-937.1997] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of nitrate availability and the presence of Glyceria maxima on the composition and activity of the dissimilatory nitrate-reducing bacterial community were studied in the laboratory. Four different concentrations of NO(inf3)(sup-), 0, 533, 1434, and 2,905 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1), were added to pots containing freshwater sediment, and the pots were then incubated for a period of 69 days. Upon harvest, NH(inf4)(sup+) was not detectable in sediment that received 0 or 533 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1). Nitrate concentrations in these pots ranged from 0 to 8 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1) at harvest. In pots that received 1,434 or 2,905 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1), final concentrations varied between 10 and 48 (mu)g of NH(inf4)(sup+)-N g of dry sediment(sup-1) and between 200 and 1,600 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1), respectively. Higher input levels of NO(inf3)(sup-) resulted in increased numbers of potential nitrate-reducing bacteria and higher potential nitrate-reducing activity in the rhizosphere. In sediment samples from the rhizosphere, the contribution of denitrification to the potential nitrate-reducing capacity varied from 8% under NO(inf3)(sup-)-limiting conditions to 58% when NO(inf3)(sup-) was in ample supply. In bulk sediment with excess NO(inf3)(sup-), this percentage was 44%. The nitrate-reducing community consisted almost entirely of NO(inf2)(sup-)-accumulating or NH(inf4)(sup+)-producing gram-positive species when NO(inf3)(sup-) was not added to the sediment. The addition of NO(inf3)(sup-) resulted in an increase of denitrifying Pseudomonas and Moraxella strains. The factor controlling the composition of the nitrate-reducing community when NO(inf3)(sup-) is limited is the presence of G. maxima. In sediment with excess NO(inf3)(sup-), nitrate availability determines the composition of the nitrate-reducing community.
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Laanbroek HJ, Geerligs HJ, Sijtsma L, Veldkamp H. Competition for sulfate and ethanol among desulfobacter, desulfobulbus, and desulfovibrio species isolated from intertidal sediments. Appl Environ Microbiol 2010; 47:329-34. [PMID: 16346474 PMCID: PMC239669 DOI: 10.1128/aem.47.2.329-334.1984] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Competition for sulfate and ethanol among Desulfobacter, Desulfobulbus, and Desulfovibrio species isolated from estuarine sediments was studied in energy-limited chemostats. Desulfovibrio baculatus was the most successful competitor for limiting amounts of sulfate and ethanol, followed by Desulfobulbus propionicus. The success of Desulfovibrio baculatus was dependent on the availability of sufficient iron. Of the three species studied, Desulfobacter postgatei was the least successful competitor for limiting amounts of sulfate. Although stimulating the growth of Desulfobacter postgatei, addition of Ca-saturated illite particles to culture media did not affect the outcome of competition for sulfate. Thus, under sulfate limitation acetate accumulated. This phenomenon was briefly discussed in relation to the flow of electrons during anaerobic mineralization in marine and estuarine sulfate-limited sediments.
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Affiliation(s)
- H J Laanbroek
- Laboratory of Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
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Miletto M, Loeb R, Antheunisse AM, Bodelier PLE, Laanbroek HJ. Response of the sulfate-reducing community to the re-establishment of estuarine conditions in two contrasting soils: a mesocosm approach. Microb Ecol 2010; 59:109-120. [PMID: 19953240 DOI: 10.1007/s00248-009-9614-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 10/25/2009] [Indexed: 05/28/2023]
Abstract
We studied the response of the sulfate-reducing prokaryote (SRP) communities to the experimental variation of salinity and tide in an outdoor mesocosm setup. Intact soil monoliths were collected at two areas of the Haringvliet lagoon (The Netherlands): one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century; the other of a freshwater marshland with more recent sea influence. Two factors, i.e., "salinity" (freshwater/oligohaline) and "tide" (nontidal/tidal), were tested in a full-factorial design. Soil samples were collected after 5 months (June-October). Dissimilatory (bi)sulfite reductase beta subunit-based denaturing gradient gel electrophoresis (dsrB-DGGE) analysis revealed that the SRP community composition in the agricultural grassland and in the freshwater marshland was represented mainly by microorganisms related to the Desulfobulbaceae and the Desulfobacteraceae, respectively. Desulfovibrio-related dsrB were detected only in the tidal treatments; Desulfomonile-related dsrB occurrence was related to the presence of oligohaline conditions. Treatments did have an effect on the overall SRP community composition of both soils, but not on the sulfate depletion rates in sulfate-amended anoxic slurry incubations. However, initiation of sulfate reduction upon sulfate addition was clearly different between the two soils.
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Affiliation(s)
- Marzia Miletto
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), AC Nieuwesluis, The Netherlands.
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Laanbroek HJ. Methane emission from natural wetlands: interplay between emergent macrophytes and soil microbial processes. A mini-review. Ann Bot 2010; 105:141-53. [PMID: 19689973 PMCID: PMC2794055 DOI: 10.1093/aob/mcp201] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 06/02/2009] [Accepted: 07/13/2009] [Indexed: 05/04/2023]
Abstract
BACKGROUND According to the Intergovernmental Panel on Climate Change (IPCC) 2007, natural wetlands contribute 20-39 % to the global emission of methane. The range in the estimated percentage of the contribution of these systems to the total release of this greenhouse gas is large due to differences in the nature of the emitting vegetation including the soil microbiota that interfere with the production and consumption of methane. SCOPE Methane is a dominant end-product of anaerobic mineralization processes. When all electron acceptors except carbon dioxide are used by the microbial community, methanogenesis is the ultimate pathway to mineralize organic carbon compounds. Emergent wetland plants play an important role in the emission of methane to the atmosphere. They produce the carbon necessary for the production of methane, but also facilitate the release of methane by the possession of a system of interconnected internal gas lacunas. Aquatic macrophytes are commonly adapted to oxygen-limited conditions as they prevail in flooded or waterlogged soils. By this system, oxygen is transported to the underground parts of the plants. Part of the oxygen transported downwards is released in the root zone, where it sustains a number of beneficial oxidation processes. Through the pores from which oxygen escapes from the plant into the root zone, methane can enter the plant aerenchyma system and subsequently be emitted into the atmosphere. Part of the oxygen released into the root zone can be used to oxidize methane before it enters the atmosphere. However, the oxygen can also be used to regenerate alternative electron acceptors. The continuous supply of alternative electron acceptors will diminish the role of methanogenesis in the anaerobic mineralization processes in the root zone and therefore repress the production and emission of methane. The role of alternative element cycles in the inhibition of methanogenesis is discussed. CONCLUSIONS The role of the nitrogen cycle in repression of methane production is probably low. In contrast to wetlands particularly created for the purification of nitrogen-rich waste waters, concentrations of inorganic nitrogen compounds are low in the root zones in the growing season due to the nitrogen-consuming behaviour of the plant. Therefore, nitrate hardly competes with other electron acceptors for reduced organic compounds, and repression of methane oxidation by the presence of higher levels of ammonium will not be the case. The role of the iron cycle is likely to be important with respect to the repression of methane production and oxidation. Iron-reducing and iron-oxidizing bacteria are ubiquitous in the rhizosphere of wetland plants. The cycling of iron will be largely dependent on the size of the oxygen release in the root zone, which is likely to be different between different wetland plant species. The role of the sulfur cycle in repression of methane production is important in marine, sulfate-rich ecosystems, but might also play a role in freshwater systems where sufficient sulfate is available. Sulfate-reducing bacteria are omnipresent in freshwater ecosystems, but do not always react immediately to the supply of fresh sulfate. Hence, their role in the repression of methanogenesis is still to be proven in freshwater marshes.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Nieuwersluis, The Netherlands.
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Vissers EW, Bodelier PLE, Muyzer G, Laanbroek HJ. A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiol Lett 2009; 298:193-8. [PMID: 19656198 DOI: 10.1111/j.1574-6968.2009.01718.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel electrophoresis (DGGE) with primer sets 21F-958R and Parch519f-Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared with other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea.
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Affiliation(s)
- Elisabeth W Vissers
- Department of Microbial Wetland Ecology, Centre for Limnology, Netherlands Institute of Ecology (NIOO-KNAW), Nieuwersluis, The Netherlands.
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Wang J, Muyzer G, Bodelier PLE, Laanbroek HJ. Diversity of iron oxidizers in wetland soils revealed by novel 16S rRNA primers targeting Gallionella-related bacteria. ISME J 2009; 3:715-25. [DOI: 10.1038/ismej.2009.7] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Tijdens M, Hoogveld HL, Kamst-van Agterveld MP, Simis SGH, Baudoux AC, Laanbroek HJ, Gons HJ. Population dynamics and diversity of viruses, bacteria and phytoplankton in a shallow eutrophic lake. Microb Ecol 2008; 56:29-42. [PMID: 17924158 PMCID: PMC2440944 DOI: 10.1007/s00248-007-9321-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 07/17/2007] [Accepted: 09/04/2007] [Indexed: 05/25/2023]
Abstract
We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 x 10(7) and 1.3 x 10(8) virus-like particles ml(-1) and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to covary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus-host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht.
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Affiliation(s)
- Marjolijn Tijdens
- Department of Microbial Wetland Ecology, Centre for Limnology, Netherlands Institute of Ecology NIOO-KNAW, Rijksstraatweg 6, AC, Nieuwersluis, The Netherlands.
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Abstract
Like many functional groups or guilds of microorganisms, the group of ammonia-oxidizing bacteria (AOB) consists of a number of physiologically different species or lineages. These physiological differences suggest niche differentiation among these bacteria depending on the environmental conditions. Species of AOB might be adapted to different zones in the flooding gradient of a tidal marsh. This issue has been studied by sampling sediments from different sites and depths within a tidal freshwater marsh along the river Scheldt near the village of Appels in Belgium. Samples were taken in February, April, July and October 1998. Communities of AOB in the sediment were analysed on the basis of the 16S rRNA gene by application of polymerase chain reaction in combination with denaturing gradient gel electrophoresis (DGGE). In addition, moisture content and concentrations of ammonium and nitrate were determined as well as the potential ammonia-oxidizing activities. Six different DGGE bands belonging to the beta-subclass of the Proteobacteria were observed across the marsh. The community composition of AOB was determined by the elevation in the flooding gradient as well as by the sampling depth. The presence of plants was less important for the community composition of AOB. DGGE bands affiliated with the Nitrosospira lineage were mostly found in the upper part of the marsh and in the deeper layers of the sediment. Two of the three DGGE bands related to the Nitrosomonas oligotropha lineage were more broadly distributed over the marsh, but were predominantly found in the upper layers of the sediment. Members of the environmental Nitrosomonas lineage 5 were predominantly detected in the deeper layers in the lower parts of the marsh. Potential driving factors for niche differentiation are discussed.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Nieuwersluis, the Netherlands.
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Miletto M, Loy A, Antheunisse AM, Loeb R, Bodelier PL, Laanbroek HJ. Biogeography of sulfate-reducing prokaryotes in river floodplains. FEMS Microbiol Ecol 2008; 64:395-406. [DOI: 10.1111/j.1574-6941.2008.00490.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Sekido T, Bodelier PLE, Shoji T, Suwa Y, Laanbroek HJ. Limitations of the use of group-specific primers in real-time PCR as appear from quantitative analyses of closely related ammonia-oxidising species. Water Res 2008; 42:1093-101. [PMID: 17889247 DOI: 10.1016/j.watres.2007.08.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 08/21/2007] [Accepted: 08/24/2007] [Indexed: 05/17/2023]
Abstract
To study the ecology of ammonia-oxidising bacteria (AOB), quantitative techniques are essential. Real-time PCR assays based on the 16S rRNA or on the structural amoA gene are routinely used. The CTO primer set rooted on the 16S rRNA gene has a number of mismatches with some of the cultures of AOB. To examine if these mismatches have an effect on the outcome of real-time PCR assays, the assay was tested with DNA from a number of closely related isolates of AOB. Standard curves of known amounts of initial DNA were similar among most of the tested cultures of AOB, except for the standard curves of Nitrosomonas strain AL212 and Nitrosospira strain NpAV. Nitrosomonas strain AL212 had 3 mismatches with the CTO primer set. Adaptation of the CTO primer set in order to perfectly match the Nitrosomonas strain AL212 gave a standard curve similar to the majority of the AOB tested. As Nitrosospira strain NpAV has no mismatches with the original CTO primer set, there must be another reason for the less efficient amplification than the sequence itself. Application of an existing sigmoidal mathematical model gave no other results with respect to the standard curves of Nitrosomonas europaea and Nitrosomonas strain AL212, but also demonstrated that primer mismatches can seriously underestimate the initial target concentration. It was concluded that in general correct interpretation of real-time PCR results requires knowledge of the target community composition, in particular of the target sequences of the dominant community members.
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Affiliation(s)
- Takako Sekido
- National Institute of Advanced Industrial Science and Technology, Ecological Control and Microbiology Research Group, Tsukuba, Ibaraki, Japan
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Miletto M, Bodelier PLE, Laanbroek HJ. Improved PCR-DGGE for high resolution diversity screening of complex sulfate-reducing prokaryotic communities in soils and sediments. J Microbiol Methods 2007; 70:103-11. [PMID: 17481757 DOI: 10.1016/j.mimet.2007.03.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2006] [Revised: 03/22/2007] [Accepted: 03/28/2007] [Indexed: 11/20/2022]
Abstract
In this study we evaluated a high resolution PCR-DGGE strategy for the characterization of complex sulfate-reducing microbial communities inhabiting natural environments. dsrB fragments were amplified with a two-step nested PCR protocol using combinations of primers targeting the dissimilatory (bi)sulfite reductase genes. The PCR-DGGE conditions were initially optimized using a dsrAB clone library obtained from a vegetated intertidal riparian soil along the river Rhine (Rozenburg, the Netherlands). Partial dsrB were successfully amplified from the same environmental DNA extracts used to construct the library, DGGE-separated and directly sequenced. The two approaches were in good agreement: the phylogenetic distribution of clones and DGGE-separated dsrB was comparable, suggesting the presence of sulfate-reducing prokaryotes (SRP) belonging to the families 'Desulfobacteraceae,' 'Desulfobulbaceae' and 'Syntrophobacteraceae,' and to the Desulfomonile tiedjei- and Desulfobacterium anilini-groups. The nested PCR-DGGE was also used to analyze sediment samples (Appels, Belgium) from a series of microcosms subjected to a tidal flooding regime with water of different salinity, and proved to be a valid tool also to monitor the SRP community variation over time and space as a consequence of environmental changes.
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Affiliation(s)
- Marzia Miletto
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Wetland Ecology, Rijksstraatweg 6, 3631 AC Nieuwersluis, The Netherlands.
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Coci M, Riechmann D, Bodelier PLE, Stefani S, Zwart G, Laanbroek HJ. Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment. FEMS Microbiol Ecol 2006; 53:359-68. [PMID: 16329955 DOI: 10.1016/j.femsec.2005.01.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Revised: 01/13/2005] [Accepted: 01/18/2005] [Indexed: 10/25/2022] Open
Abstract
Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper 5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas marina lineage, but only in the top 1cm. Shift in community composition occurred earlier in the marine microcosms than in the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community of this functional group of bacteria may occur at different rates.
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Affiliation(s)
- Manuela Coci
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Limnology, Department of Microbial Ecology, Rijksstraatweg 6, 3631 AC Nieuwersluis, The Netherlands.
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Bodelier PLE, Stomp M, Santamaria L, Klaassen M, Laanbroek HJ. Animal–plant–microbe interactions: direct and indirect effects of swan foraging behaviour modulate methane cycling in temperate shallow wetlands. Oecologia 2006; 149:233-44. [PMID: 16736186 DOI: 10.1007/s00442-006-0445-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 04/26/2006] [Indexed: 11/26/2022]
Abstract
Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH(4). Microbial processes catalyzing nutrient recycling and CH(4) production are controlled by sediment physico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We performed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick's swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tubers as a model system. A controlled foraging experiment using field enclosures indicated that swan bioturbation decreases CH(4) production, through a decrease in the activity of methanogenic Archaea and an increased rate of CH(4) oxidation in the bioturbated sediment. We also found a positive correlation between tuber density (a surrogate of plant density during the previous growth season) and CH(4) production activity. A laboratory experiment showed that sediment sterilization enhances pondweed growth, probably due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH(4) cycling by means of both direct and indirect (i.e. plant-mediated) effects with potential consequences for CH(4) emission from wetland systems.
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Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Centre for Limnology, Rijksstraatweg 6, 3631AC, Nieuwersluis, The Netherlands.
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Verspagen JMH, Passarge J, Jöhnk KD, Visser PM, Peperzak L, Boers P, Laanbroek HJ, Huisman J. Water management strategies against toxic Microcystis blooms in the Dutch delta. Ecol Appl 2006; 16:313-27. [PMID: 16705982 DOI: 10.1890/04-1953] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
To prevent flooding of the Dutch delta, former estuaries have been impounded by the building of dams and sluices. Some of these water bodies, however, experience major ecological problems. One of the problem areas is the former Volkerak estuary that was turned into a freshwater lake in 1987. From the early 1990s onward, toxic Microcystis blooms dominate the phytoplankton of the lake every summer. Two management strategies have been suggested to suppress these harmful algal blooms: flushing the lake with fresh water or reintroducing saline water into the lake. This study aims at an advance assessment of these strategies through the development of a mechanistic model of the population dynamics of Microcystis. To calibrate the model, we monitored the benthic and pelagic Microcystis populations in the lake during two years. Field samples of Microcystis were incubated in the laboratory to estimate growth and mortality rates as functions of light, temperature, and salinity. Recruitment and sedimentation rates were measured in the lake, using traps, to quantify benthic-pelagic coupling of the Microcystis populations. The model predicts that flushing with fresh water will suppress Microcystis blooms when the current flushing rate is sufficiently increased. Furthermore, the inlet of saline water will suppress Microcystis blooms for salinities exceeding 14 g/L. Both management options are technically feasible. Our study illustrates that quantitative ecological knowledge can be a helpful tool guiding large-scale water management.
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Affiliation(s)
- Jolanda M H Verspagen
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Nieuwe Achtergracht 127, 1018 WS Amsterdam, The Netherlands.
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Nijburg JW, Laanbroek HJ. The influence of Glyceria maxima and nitrate input on the composition and nitrate metabolism of the dissimilatory nitrate-reducing bacterial community. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00356.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Cébron A, Coci M, Garnier J, Laanbroek HJ. Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: impact of Paris wastewater effluents. Appl Environ Microbiol 2005; 70:6726-37. [PMID: 15528539 PMCID: PMC525213 DOI: 10.1128/aem.70.11.6726-6737.2004] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Seine River is strongly affected by the effluents from the Acheres wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was to investigate the diversity of the ammonia-oxidizing bacterial population by identifying autochthonous bacteria from upstream and/or allochthonous ammonia-oxidizing bacteria from the WWTP effluents. Measurements of potential nitrifying activity, competitive PCR, and denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments specific to ammonia-oxidizing bacteria (AOB) were used to explore the succession and shifts of the ammonia-oxidizing community in the lower Seine River and to analyze the temporal and spatial functioning of the system at several different sampling dates. A major revelation was the stability of the patterns. The CTO primers used in this study (G. A. Kowalchuk, J. R. Stephen, W. D. Boer, J. I. Prosser, T. M. Embley, and J. W. Woldendorp, Appl. Environ. Microbiol. 63:1489-1497, 1997) were shown not to be completely specific to AOB of the beta subclass of Proteobacteria. We further demonstrated that when DGGE patterns are interpreted, all the different bands must be sequenced, as one major DGGE band proved to be affiliated with a group of non-AOB in the beta subclass of Proteobacteria. The majority of AOB (75 to 90%) present in the lower Seine river downstream of the effluent output belong to lineage 6a, represented by Nitrosomonas oligotropha- and Nitrosomonas ureae-like bacteria. This dominant lineage was represented by three bands on the DGGE gel. The major lineage-6a AOB species, introduced by the WWTP effluents, survived and might have grown in the receiving medium far downstream, in the estuary; it represented about 40% of the whole AOB population. The other two species belonging to lineage 6a seem to be autochthonous bacteria. One of them developed a few kilometers downstream of the WWTP effluent input in an ammonia-enriched environment, and the other appeared in the freshwater part of the estuary and was apparently more adapted to estuarine conditions, i.e., an increase in the amount of suspended matter, a low ammonia concentration, and high turnover of organic matter. The rest of the AOB population was represented in equal proportions by Nitrosospira- and Nitrosococcus mobilis-like species.
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Affiliation(s)
- Aurélie Cébron
- UMR Sisyphe 7619, Université Pierre et Marie Curie--Paris 6, Paris, France.
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Bodelier PLE, Meima-Franke M, Zwart G, Laanbroek HJ. New DGGE strategies for the analyses of methanotrophic microbial communities using different combinations of existing 16S rRNA-based primers. FEMS Microbiol Ecol 2004; 52:163-74. [PMID: 16329903 DOI: 10.1016/j.femsec.2004.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Revised: 11/02/2004] [Accepted: 11/02/2004] [Indexed: 11/26/2022] Open
Abstract
Methane-oxidising microbial communities are studied intensively because of their importance for global methane cycling. A suite of molecular microbial techniques has been applied to the study of these communities. Denaturing gradient gel electrophoresis (DGGE) is a diversity screening tool combining high sample throughput with phylogenetic information of high resolution. The existing 16S rRNA-based DGGE assays available for methane-oxidising bacteria suffer from low-specificity, low phylogentic information due to the length of the amplified fragments and/or from lack of resolving power. In the present study we developed new combinations of existing primers and applied these on methane-oxidising microbial communities in a freshwater wetland marsh. The designed strategies comprised nested as well as direct amplification of environmental DNA. Successful application of direct amplification using combinations of universal and specific primers circumvents the nested designs currently used. All developed assays resulted in identical community profiles in wetland soil cores with Methylobacter sp. and Methylocystis sp.-related sequences. Changes in the occurrence of Methylobacter-related sequences with depth in the soil profile may be related to the decrease in methane-oxidizing activity.
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Affiliation(s)
- Paul L E Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Limnology, Department of Microbial Ecology, Rijksstraatweg 6, NL3631 AC Nieuwersluis, The Netherlands.
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