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      Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

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      Author(s): 1 , * , 2
      Publication date (Electronic):
      Journal: BioMed Research International
      Publisher: Hindawi Publishing Corporation

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          Abstract

          The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness ( S) and the Shannon-Wiener index ( H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH 4 +, known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

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          Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.

          Christopher Francis, Kathryn Roberts, J. Beman … (2005)
          Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the beta- and gamma-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase alpha-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.
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            The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria.

            Graeme W Nicol, Sven Leininger, Christa Schleper … (2008)
            Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.
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              Environmental factors shaping the ecological niches of ammonia-oxidizing archaea.

              Tuba Erguder, Nico Boon, Lieven Wittebolle … (2009)
              For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Biomed Res Int
                Journal ID (iso-abbrev): Biomed Res Int
                Journal ID (publisher-id): BMRI
                Title: BioMed Research International
                Publisher: Hindawi Publishing Corporation
                ISSN (Print): 2314-6133
                ISSN (Electronic): 2314-6141
                Publication date (Print): 2015
                Publication date (Electronic): 1 February 2015
                Volume: 2015
                Electronic Location Identifier: 582938
                Affiliations
                1Department and Institute of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine, Medical University of Silesia, Jagiellońska 4, 41-200 Sosnowiec, Poland
                2Department of Microbiology, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
                Author notes
                *Mariusz Cycoń: mcycon@ 123456sum.edu.pl

                Academic Editor: Qaisar Mahmood

                Article
                DOI: 10.1155/2015/582938
                PMC ID: 4331321
                PubMed ID: 25705674
                SO-VID: 27612b8e-7aa7-4575-9fc5-4f986ad4eb35
                Copyright © Copyright © 2015 M. Cycoń and Z. Piotrowska-Seget.
                License:

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 18 August 2014
                Date revision received : 1 December 2014
                Date accepted : 1 December 2014
                Categories
                Subject: Research Article

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