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      Microbial changes linked to the accelerated degradation of the herbicide atrazine in a range of temperate soils

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          Abstract

          Accelerated degradation is the increased breakdown of a pesticide upon its repeated application, which has consequences for the environmental fate of pesticides. The herbicide atrazine was repeatedly applied to soils previously untreated with s-triazines for >5 years. A single application of atrazine, at an agriculturally relevant concentration, was sufficient to induce its rapid dissipation. Soils, with a range of physico-chemical properties and agricultural histories, showed similar degradation kinetics, with the half-life of atrazine decreasing from an average of 25 days after the first application to <2 days after the second. A mathematical model was developed to fit the atrazine-degrading kinetics, which incorporated the exponential growth of atrazine-degrading organisms. Despite the similar rates of degradation, the repertoire of atrazine-degrading genes varied between soils. Only a small portion of the bacterial community had the capacity for atrazine degradation. Overall, the microbial community was not significantly affected by atrazine treatment. One soil, characterised by low pH, did not exhibit accelerated degradation, and atrazine-degrading genes were not detected. Neutralisation of this soil restored accelerated degradation and the atrazine-degrading genes became detectable. This illustrates the potential for accelerated degradation to manifest when conditions become favourable. Additionally, the occurrence of accelerated degradation under agriculturally relevant concentrations supports the consideration of the phenomena in environmental risk assessments.

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          The online version of this article (doi:10.1007/s11356-017-8377-y) contains supplementary material, which is available to authorized users.

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          The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria.

          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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            Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens.

            We describe a novel adaptation of the TaqMan PCR assay which potentially allows for highly sensitive detection of any eubacterial species with simultaneous species identification. Our system relies on a unique multiprobe design in which a single set of highly conserved sequences encoded by the 16S rRNA gene serves as the primer pair and is used in combination with both an internal highly conserved sequence, the universal probe, and an internal variable region, the species-specific probe. A pre-PCR ultrafiltration step effectively decontaminates or removes background DNA. The TaqMan system described reliabAly detected 14 common bacterial species with a detection limit of 50 fg. Further, highly sensitive and specific pathogen detection was demonstrated with a prototype species-specific probe designed to detect Staphylococcus aureus. This assay has broad potential in the clinical arena for rapid and specific diagnosis of infectious diseases.
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              From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation.

              Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.
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                Author and article information

                Contributors
                +44 (0) 7766448455 , rachel.yale@hse.gov.uk
                Melanie.Sapp@uni-duesseldorf.de
                chris.sinclair@fera.co.uk
                james.moir@york.ac.uk
                Journal
                Environ Sci Pollut Res Int
                Environ Sci Pollut Res Int
                Environmental Science and Pollution Research International
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0944-1344
                1614-7499
                20 January 2017
                20 January 2017
                2017
                : 24
                : 8
                : 7359-7374
                Affiliations
                [1 ]CRD, Mallard House, 3 Peasholme Green, York, YO1 7PX UK
                [2 ]GRID grid.5685.e, Department of Biology, , University of York, ; Heslington, York, YO10 5DD UK
                [3 ]GRID grid.470556.5, , FERA Science Ltd., ; Sand Hutton, York, YO41 1LZ UK
                [4 ]GRID grid.411327.2, , Heinrich-Heine-Universität Düsseldorf, ; Universitätsstrasse 1, 40225 Düsseldorf, NRW Germany
                Author notes

                Responsible editor: Zhihong Xu

                Article
                8377
                10.1007/s11356-017-8377-y
                5383679
                28108915
                23fdc0ee-bb3b-4db0-8fef-da02cbe23179
                © The Author(s) 2017

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                : 17 August 2016
                : 3 January 2017
                Funding
                Funded by: FERA Seedcorn
                Categories
                Research Article
                Custom metadata
                © Springer-Verlag Berlin Heidelberg 2017

                General environmental science
                microbial communities,atrazine,risk assessment,fate modelling,soil ph,adaptation

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