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Mocek-Płóciniak A, Mencel J, Zakrzewski W, Roszkowski S. Phytoremediation as an Effective Remedy for Removing Trace Elements from Ecosystems. PLANTS (BASEL, SWITZERLAND) 2023; 12:1653. [PMID: 37111876 PMCID: PMC10141480 DOI: 10.3390/plants12081653] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
The pollution of soil by trace elements is a global problem. Conventional methods of soil remediation are often inapplicable, so it is necessary to search intensively for innovative and environment-friendly techniques for cleaning up ecosystems, such as phytoremediation. Basic research methods, their strengths and weaknesses, and the effects of microorganisms on metallophytes and plant endophytes resistant to trace elements (TEs) were summarised and described in this manuscript. Prospectively, bio-combined phytoremediation with microorganisms appears to be an ideal, economically viable and environmentally sound solution. The novelty of the work is the description of the potential of "green roofs" to contribute to the capture and accumulation of many metal-bearing and suspended dust and other toxic compounds resulting from anthropopressure. Attention was drawn to the great potential of using phytoremediation on less contaminated soils located along traffic routes and urban parks and green spaces. It also focused on the supportive treatments for phytoremediation using genetic engineering, sorbents, phytohormones, microbiota, microalgae or nanoparticles and highlighted the important role of energy crops in phytoremediation. Perceptions of phytoremediation on different continents are also presented, and new international perspectives are presented. Further development of phytoremediation requires much more funding and increased interdisciplinary research in this direction.
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Affiliation(s)
- Agnieszka Mocek-Płóciniak
- Department of Soil Science and Microbiology, Poznan University of Life Sciences, Szydłowska 50, 60-656 Poznan, Poland
| | - Justyna Mencel
- Department of Soil Science and Microbiology, Poznan University of Life Sciences, Szydłowska 50, 60-656 Poznan, Poland
| | - Wiktor Zakrzewski
- Regional Chemical and Agricultural Station in Poznan, Sieradzka 29, 60-163 Poznan, Poland
| | - Szymon Roszkowski
- Department of Geriatrics, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Jagiellonska 13/15, 85-067 Bydgoszcz, Poland
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2
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Madakka M, Jayaraju N, Shirisha J. An integrated analysis of sinkholes in Kadapa region, Andra Pradesh, India: Implication to pedology. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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3
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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4
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Lebre PH, Bottos E, Makhalanyane TP, Hogg I, Cowan DA. Islands in the sand: are all hypolithic microbial communities the same? FEMS Microbiol Ecol 2021; 97:5928546. [PMID: 33068395 DOI: 10.1093/femsec/fiaa216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Hypolithic microbial communities (hypolithons) are complex assemblages of phototrophic and heterotrophic organisms associated with the ventral surfaces of translucent minerals embedded in soil surfaces. Past studies on the assembly, structure and function of hypolithic communities have tended to use composite samples (i.e. bulked hypolithic biomass) with the underlying assumption that samples collected from within a 'homogeneous' locality are phylogenetically homogeneous. In this study, we question this assumption by analysing the prokaryote phylogenetic diversity of multiple individual hypolithons: i.e. asking the seemingly simple question of 'Are all hypolithons the same'? Using 16S rRNA gene-based phylogenetic analysis of hypolithons recovered for a localized moraine region in the Taylor Valley, McMurdo Dry Valleys, Antarctica, we demonstrate that these communities are heterogeneous at very small spatial scales (<5 m). Using null models of phylogenetic turnover, we showed that this heterogeneity between hypolithons is probably due to stochastic effects such as dispersal limitations, which is entirely consistent with the physically isolated nature of the hypolithic communities ('islands in the sand') and the almost complete absence of a liquid continuum as a mode of microbial transport between communities.
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Affiliation(s)
- Pedro H Lebre
- Centre for Microbial Ecology and Genomic, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Eric Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Colombia, BC V2C 0C8, Canada
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomic, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Ian Hogg
- Canadian High Arctic Research Station, rue Uvajuq place, Cambridge Bay, Nunavut, CP 2150, Canada
| | - Don A Cowan
- Centre for Microbial Ecology and Genomic, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
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5
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Changes in soil bacterial community diversity following the removal of invasive feral pigs from a Hawaiian tropical montane wet forest. Sci Rep 2019; 9:14681. [PMID: 31604976 PMCID: PMC6789016 DOI: 10.1038/s41598-019-48922-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/06/2019] [Indexed: 12/01/2022] Open
Abstract
Nonnative, invasive feral pigs (Sus scrofa) modify habitats by disturbing soils and vegetation, which can alter biogeochemical processes. Soil microbial communities drive nutrient cycling and therefore also play important roles in shaping ecosystem structure and function, but the responses of soil microbes to nonnative ungulate removal remains poorly studied. We examined changes in the soil bacterial community over a ~25 year chronosequence of feral pig removal in tropical montane wet forests on the Island of Hawai’i. We extracted bacterial eDNA from soil samples collected inside and outside of ungulate exclosures along this chronosequence and sequenced the eDNA using the Illumina platform. We found that ungulate removal increased diversity of soil bacteria, with diversity scores positively correlated with time since removal. While functional and phylogenetic diversity were not significantly different between pig present and pig removed soils, soil bulk density, which decreases following the removal of feral pigs, was a useful predictor of dissimilarity among sites and correlated to changes in functional diversity. Additionally, increases in soil porosity, potassium, and calcium were correlated to increases in functional diversity. Finally, sites with greater mean annual temperatures were shown to have higher scores of both functional and phylogenetic diversity. As such, we conclude that feral pigs influence overall bacterial community diversity directly while influencing functional diversity indirectly through alterations to soil structure and nutrients. Comparatively, phylogenetic differences between communities are better explained by mean annual temperature as a climatic predictor of community dissimilarity.
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Harrison E, Hall JPJ, Brockhurst MA. Migration promotes plasmid stability under spatially heterogeneous positive selection. Proc Biol Sci 2019; 285:rspb.2018.0324. [PMID: 29794045 DOI: 10.1098/rspb.2018.0324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023] Open
Abstract
Bacteria-plasmid associations can be mutualistic or antagonistic depending on the strength of positive selection for plasmid-encoded genes, with contrasting outcomes for plasmid stability. In mutualistic environments, plasmids are swept to high frequency by positive selection, increasing the likelihood of compensatory evolution to ameliorate the plasmid cost, which promotes long-term stability. In antagonistic environments, plasmids are purged by negative selection, reducing the probability of compensatory evolution and driving their extinction. Here we show, using experimental evolution of Pseudomonas fluorescens and the mercury-resistance plasmid, pQBR103, that migration promotes plasmid stability in spatially heterogeneous selection environments. Specifically, migration from mutualistic environments, by increasing both the frequency of the plasmid and the supply of compensatory mutations, stabilized plasmids in antagonistic environments where, without migration, they approached extinction. These data suggest that spatially heterogeneous positive selection, which is common in natural environments, coupled with migration helps to explain the stability of plasmids and the ecologically important genes that they encode.
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Affiliation(s)
- Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 1AE, UK
| | - James P J Hall
- Department of Animal and Plant Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Science, University of Sheffield, Sheffield S10 2TN, UK
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7
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France MT, Forney LJ. The Relationship between Spatial Structure and the Maintenance of Diversity in Microbial Populations. Am Nat 2019; 193:503-513. [PMID: 30912968 DOI: 10.1086/701799] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Spatial structure is pervasive in the microbial world, yet we know little about how it influences the evolution of microbial populations. It is thought that spatial structure limits the scale of competitive interactions and protracts selective sweeps. This may allow microbial populations to simultaneously explore multiple evolutionary paths. But how structured a microbial population must be before this effect is realized is not known. We used empirical and simulation studies to explore the relationship between spatial structure and the maintenance of diversity. The degree of spatial structure experienced by Escherichia coli metapopulations was manipulated by varying the migration rate between its component subpopulations. Each subpopulation was inoculated with an equal number of two equally fit genotypes, and their frequencies in 12 subpopulations were determined during 150 generations of evolution. We observed that the frequency of the "loser" genotypes decreased exponentially as the migration rate between the subpopulations was increased and that higher frequencies of the loser genotypes were maintained in structured metapopulations. These results demonstrate that structured microbial populations can evolve along multiple evolutionary trajectories even when migration rates between the subpopulations are relatively high.
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Lima GDP, Meyer JR, Khosla K, Dunfield KE, Parker BL. Spatial variability of microbial communities in a fractured sedimentary rock matrix impacted by a mixed organics plume. JOURNAL OF CONTAMINANT HYDROLOGY 2018; 218:110-119. [PMID: 30342835 DOI: 10.1016/j.jconhyd.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/27/2018] [Accepted: 10/03/2018] [Indexed: 05/20/2023]
Abstract
Dissolved phase contaminants, transported by diffusion into the low permeability matrix of fractured sedimentary rock, pose a challenge to groundwater cleanup efforts because this stored mass may persist even when the upgradient source zone is removed. In this context, if contaminant biodegradation takes place within the low permeability matrix, plume persistence may be substantially reduced. Therefore, it is important to characterize microbial communities within the low permeability, rock matrix pores, instead of only from groundwater samples, which represent biomass from fast flowing fractures. This research relies on depth-discrete data from both core and groundwater samples collected from two locations representing a mid-plume and plume front condition within an aged, mixed organic contaminant plume in a sedimentary rock aquifer. Results from multiple analyte measurements on rock and groundwater indicate that biodegradation in the lower permeability matrix of fractured sedimentary rocks and the microbial consortia is spatially variable due to differences in hydrochemistry, redox conditions, and contaminant concentrations. Dechlorinating microorganisms were detected in the sandstone matrix at both locations, but the detected microbial diversity calculated with PCR-DGGE was significantly higher in samples collected from the core located closer to the source zone, where contaminant concentrations are higher and contaminant compositions more diverse, compared to samples from the plume front location.
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Affiliation(s)
- Gláucia da P Lima
- G(360) Institute for Groundwater Research at the University of Guelph, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
| | - Jessica R Meyer
- G(360) Institute for Groundwater Research at the University of Guelph, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
| | - Kamini Khosla
- School of Environmental Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
| | - Beth L Parker
- G(360) Institute for Groundwater Research at the University of Guelph, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
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9
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Almeida CMR, Oliveira T, Reis I, Gomes CR, Mucha AP. Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments. MARINE ENVIRONMENTAL RESEARCH 2017; 132:68-78. [PMID: 29122290 DOI: 10.1016/j.marenvres.2017.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 10/09/2017] [Accepted: 10/13/2017] [Indexed: 05/12/2023]
Abstract
Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas, contributing for an efficient risk management strategy of these coastal zones.
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Affiliation(s)
- C Marisa R Almeida
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Tânia Oliveira
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Izabela Reis
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Carlos R Gomes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Ana P Mucha
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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10
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Bouhajja E, Agathos SN, George IF. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnol Adv 2016; 34:1413-1426. [PMID: 27825829 DOI: 10.1016/j.biotechadv.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 12/23/2022]
Abstract
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.
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Affiliation(s)
- Emna Bouhajja
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium
| | - Spiros N Agathos
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech University, 100119 San Miguel de Urcuquí, Ecuador
| | - Isabelle F George
- Université Libre de Bruxelles, Laboratoire d'Ecologie des Systèmes Aquatiques, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
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11
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Michelland R, Thioulouse J, Kyselková M, Grundmann GL. Bacterial Community Structure at the Microscale in Two Different Soils. MICROBIAL ECOLOGY 2016; 72:717-724. [PMID: 27418177 DOI: 10.1007/s00248-016-0810-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.
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Affiliation(s)
- Rory Michelland
- Université de Lyon, 69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Jean Thioulouse
- Université de Lyon, 69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Martina Kyselková
- Institute of Soil Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Genevieve L Grundmann
- Université de Lyon, 69622, Lyon, France.
- Université Lyon 1, Villeurbanne, France.
- CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France.
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12
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O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol 2016; 18:2039-51. [PMID: 26914164 DOI: 10.1111/1462-2920.13231] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/17/2016] [Indexed: 01/16/2023]
Abstract
Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.
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Affiliation(s)
- Sarah L O'Brien
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Sean M Gibbons
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Graduate Program in Biophysical Sciences, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Computation Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Department of Ecology and Evolution, Department of Surgery, University of Chicago, 1101 E. 57th St., Chicago, IL, 606037, USA
| | - Eric R Johnston
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Julie D Jastrow
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Department of Ecology and Evolution, Department of Surgery, University of Chicago, 1101 E. 57th St., Chicago, IL, 606037, USA.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.,College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Folker Meyer
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Computation Institute, University of Chicago, Chicago, IL, 60637, USA
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13
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Kim M, Or D. Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces. PLoS One 2016; 11:e0147394. [PMID: 26807803 PMCID: PMC4726620 DOI: 10.1371/journal.pone.0147394] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/04/2016] [Indexed: 12/02/2022] Open
Abstract
Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils.
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Affiliation(s)
- Minsu Kim
- Soil and Terrestrial Environmental Physics (STEP), Department of Environmental Systems Sciences (USYS), ETH Zürich, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics (STEP), Department of Environmental Systems Sciences (USYS), ETH Zürich, 8092 Zürich, Switzerland
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Koskella B, Vos M. Adaptation in Natural Microbial Populations. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054458] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California 94720;
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Penryn Campus, Cornwall TR10 9FE, United Kingdom;
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Bourceret A, Leyval C, de Fouquet C, Cébron A. Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants. PLoS One 2015; 10:e0142851. [PMID: 26599438 PMCID: PMC4657893 DOI: 10.1371/journal.pone.0142851] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/26/2015] [Indexed: 12/03/2022] Open
Abstract
Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH) biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi), and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging) revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron.
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Affiliation(s)
- Amélia Bourceret
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-lès-Nancy, France
- Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Corinne Leyval
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-lès-Nancy, France
- Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Chantal de Fouquet
- MINES ParisTech, Centre de Géosciences Géostatistique, Ecole Nationale Supérieure des Mines de Paris, 35 Rue Saint-Honoré, 77305 Fontainebleau, France
| | - Aurélie Cébron
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-lès-Nancy, France
- Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
- * E-mail:
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Goix S, Mombo S, Schreck E, Pierart A, Lévêque T, Deola F, Dumat C. Field isotopic study of lead fate and compartmentalization in earthworm-soil-metal particle systems for highly polluted soil near Pb recycling factory. CHEMOSPHERE 2015; 138:10-17. [PMID: 26025429 DOI: 10.1016/j.chemosphere.2015.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/13/2015] [Accepted: 05/03/2015] [Indexed: 06/04/2023]
Abstract
Earthworms are important organisms in soil macrofauna and play a key role in soil functionality, and consequently in terrestrial ecotoxicological risk assessments. Because they are frequently observed in soils strongly polluted by metals, the influence of earthworm bioturbation on Pb fate could therefore be studied through the use of Pb isotopes. Total Pb concentrations and isotopic composition ((206)Pb, (207)Pb and (208)Pb) were then measured in earthworms, casts and bulk soils sampled at different distance from a lead recycling factory. Results showed decreasing Pb concentrations with the distance from the factory whatever the considered matrix (bulk soils, earthworm bodies or cast samples) with higher concentrations in bulk soils than in cast samples. The bivariate plot (208)Pb/(206)Pb ratios versus (206)Pb/(207)Pb ratios showed that all samples can be considered as a linear mixing between metallic process particulate matter (PM) and geochemical Pb background. Calculated anthropogenic fraction of Pb varied between approximately 84% and 100%. Based on Pb isotopic signatures, the comparison between casts, earthworms and bulk soils allowed to conclude that earthworms preferentially ingest the anthropogenic lead fraction associated with coarse soil organic matter. Actually, soil organic matter was better correlated with Pb isotopic ratios than with Pb content in soils. The proposed hypothesis is therefore a decrease of soil organic matter turnover due to Pb pollution with consequences on Pb distribution in soils and earthworm exposure. Finally, Pb isotopes analysis constitutes an efficient tool to study the influence of earthworm bioturbation on Pb cycle in polluted soils.
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Affiliation(s)
- Sylvaine Goix
- Université de Toulouse, INP-ENSAT, Av. Agrobiopôle, 31326 Castanet-Tolosan, France; UMR 5245 CNRS-INP-UPS, EcoLab (Laboratoire d'écologie fonctionnelle et Environnement), Avenue de l'Agrobiopôle, BP 32607, 31326 Castanet-Tolosan, France; Géosciences Environnement Toulouse (GET), Observatoire Midi Pyrénées, Université de Toulouse, CNRS, IRD, 14 Avenue E. Belin, F-31400 Toulouse, France
| | - Stéphane Mombo
- Université de Toulouse, INP-ENSAT, Av. Agrobiopôle, 31326 Castanet-Tolosan, France; UMR 5245 CNRS-INP-UPS, EcoLab (Laboratoire d'écologie fonctionnelle et Environnement), Avenue de l'Agrobiopôle, BP 32607, 31326 Castanet-Tolosan, France
| | - Eva Schreck
- Géosciences Environnement Toulouse (GET), Observatoire Midi Pyrénées, Université de Toulouse, CNRS, IRD, 14 Avenue E. Belin, F-31400 Toulouse, France
| | - Antoine Pierart
- Université de Toulouse, INP-ENSAT, Av. Agrobiopôle, 31326 Castanet-Tolosan, France; UMR 5245 CNRS-INP-UPS, EcoLab (Laboratoire d'écologie fonctionnelle et Environnement), Avenue de l'Agrobiopôle, BP 32607, 31326 Castanet-Tolosan, France
| | - Thibaut Lévêque
- Université de Toulouse, INP-ENSAT, Av. Agrobiopôle, 31326 Castanet-Tolosan, France; UMR 5245 CNRS-INP-UPS, EcoLab (Laboratoire d'écologie fonctionnelle et Environnement), Avenue de l'Agrobiopôle, BP 32607, 31326 Castanet-Tolosan, France
| | - Frédéric Deola
- STCM, Société de Traitements Chimiques des Métaux, 30 Avenue de Fondeyre, 31200 Toulouse, France
| | - Camille Dumat
- Université de Toulouse, INP-ENSAT, Av. Agrobiopôle, 31326 Castanet-Tolosan, France; Certop UMR5044-Centre d'Etude et de Recherche Travail, Organisation, Pouvoir, France.
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McCann CM, Gray ND, Tourney J, Davenport RJ, Wade M, Finlay N, Hudson-Edwards KA, Johnson KL. Remediation of a historically Pb contaminated soil using a model natural Mn oxide waste. CHEMOSPHERE 2015; 138:211-217. [PMID: 26073590 DOI: 10.1016/j.chemosphere.2015.05.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/05/2015] [Accepted: 05/17/2015] [Indexed: 06/04/2023]
Abstract
A natural Mn oxide (NMO) waste was assessed as an in situ remediation amendment for Pb contaminated sites. The viability of this was investigated using a 10 month lysimeter trial, wherein a historically Pb contaminated soil was amended with a 10% by weight model NMO. The model NMO was found to have a large Pb adsorption capacity (qmax 346±14 mg g(-1)). However, due to the heterogeneous nature of the Pb contamination in the soils (3650.54-9299.79 mg kg(-1)), no treatment related difference in Pb via geochemistry could be detected. To overcome difficulties in traditional geochemical techniques due to pollutant heterogeneity we present a new method for unequivocally proving metal sorption to in situ remediation amendments. The method combines two spectroscopic techniques; namely electron probe microanalysis (EPMA) and X-ray photoelectron spectroscopy (XPS). Using this we showed Pb immobilisation on NMO, which were Pb free prior to their addition to the soils. Amendment of the soil with exogenous Mn oxide had no effect on microbial functioning, nor did it perturb the composition of the dominant phyla. We conclude that NMOs show excellent potential as remediation amendments.
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Affiliation(s)
- Clare M McCann
- Newcastle University, School of Civil Engineering and Geosciences, Newcastle upon Tyne NE1 7RU, United Kingdom.
| | - Neil D Gray
- Newcastle University, School of Civil Engineering and Geosciences, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Janette Tourney
- Durham University, School of Engineering and Computing Sciences, Durham DH1 3LE, United Kingdom
| | - Russell J Davenport
- Newcastle University, School of Civil Engineering and Geosciences, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Matthew Wade
- Newcastle University, School of Civil Engineering and Geosciences, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nina Finlay
- Durham University, School of Engineering and Computing Sciences, Durham DH1 3LE, United Kingdom
| | - Karen A Hudson-Edwards
- Department of Earth and Planetary Sciences, Birkbeck, University of London, Malet St., London WC1E 7HX, United Kingdom
| | - Karen L Johnson
- Durham University, School of Engineering and Computing Sciences, Durham DH1 3LE, United Kingdom
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Cheeke TE, Schütte UM, Hemmerich CM, Cruzan MB, Rosenstiel TN, Bever JD. Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes. Mol Ecol 2015; 24:2580-93. [PMID: 25827202 DOI: 10.1111/mec.13178] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/28/2015] [Accepted: 03/18/2015] [Indexed: 02/06/2023]
Abstract
Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes.
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Affiliation(s)
- Tanya E Cheeke
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97207, USA; Department of Biology, Indiana University, Bloomington, IN, 47405, USA; Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Teixeira C, Almeida CMR, Nunes da Silva M, Bordalo AA, Mucha AP. Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 493:757-765. [PMID: 25000571 DOI: 10.1016/j.scitotenv.2014.06.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 06/03/2023]
Abstract
UNLABELLED Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. CAPSULE ABSTRACT Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity.
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Affiliation(s)
- Catarina Teixeira
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - C Marisa R Almeida
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Marta Nunes da Silva
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Adriano A Bordalo
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Ana P Mucha
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
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Meli M, Palmqvist A, Forbes VE, Groeneveld J, Grimm V. Two pairs of eyes are better than one: Combining individual-based and matrix models for ecological risk assessment of chemicals. Ecol Modell 2014. [DOI: 10.1016/j.ecolmodel.2013.07.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Chen Q, Wang H, Yang B, He F. The combined effects of atrazine and lead (Pb): relative microbial activities and herbicide dissipation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 102:93-99. [PMID: 24580827 DOI: 10.1016/j.ecoenv.2014.01.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 12/10/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
The experiment was conducted to investigate the effects of single and combined pollution from different concentrations of atrazine (field rate, FR, 2.0 mg kg(-1) and 5 times FR, 10 mg kg(-1)) and lead (Pb) (300 mg kg(-1) and 600 mg kg(-1)) on enzyme activity, basal soil respiration (BSR), and net nitrogen (N) mineralization (NNM) in soil after exposure for 0, 7, 14, 21, and 28 days. In addition, residual atrazine was measured in the samples of combined contamination. Results showed that the notable effects of either or both contaminants on the microbial activity and biological processes. Enzyme activity data demonstrated that the order of sensitivity to contamination was urease>invertase>catalase. BSR was strongly stimulated by atrazine/Pb at the early exposure (0-7 days for single contaminant and 7-14 days for combined contaminants). The stimulation effects on BSR were higher at low concentrations of the contamination (FR and Pb300). The combined treatments of 5FR+Pb600 inhibit BSR and NNM. Overall, the parameters associated with N cycling (urease and NNM) were more sensitive than others. Both Pb concentrations (300 and 600 mg/kg) had little influence on the dissipation of high concentrations of atrazine (5FR) during the 28-day-incubation. This study has provided useful information on potential ecotoxicology effects of combined contamination of atrazine and Pb on relative microbial biological process.
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Affiliation(s)
- Qinglin Chen
- School of Resources and Environment, University of Jinan, Jinan 250022, China; Shandong Provincial Engineering Technology Research Center for Ecological Carbon Sink and Capture Utilization, Jinan 250022, China
| | - Hui Wang
- School of Resources and Environment, University of Jinan, Jinan 250022, China; Shandong Provincial Engineering Technology Research Center for Ecological Carbon Sink and Capture Utilization, Jinan 250022, China.
| | - Baoshan Yang
- School of Resources and Environment, University of Jinan, Jinan 250022, China; Shandong Provincial Engineering Technology Research Center for Ecological Carbon Sink and Capture Utilization, Jinan 250022, China
| | - Fei He
- School of Resources and Environment, University of Jinan, Jinan 250022, China; Shandong Provincial Engineering Technology Research Center for Ecological Carbon Sink and Capture Utilization, Jinan 250022, China
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Vos M, Wolf AB, Jennings SJ, Kowalchuk GA. Micro-scale determinants of bacterial diversity in soil. FEMS Microbiol Rev 2013; 37:936-54. [DOI: 10.1111/1574-6976.12023] [Citation(s) in RCA: 338] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/08/2013] [Accepted: 03/15/2013] [Indexed: 11/29/2022] Open
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Nakatsu CH, Barabote R, Thompson S, Bruce D, Detter C, Brettin T, Han C, Beasley F, Chen W, Konopka A, Xie G. Complete genome sequence of Arthrobacter sp. strain FB24. Stand Genomic Sci 2013; 9:106-16. [PMID: 24501649 PMCID: PMC3910542 DOI: 10.4056/sigs.4438185] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.
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Affiliation(s)
- Cindy H Nakatsu
- Department of Agronomy, Purdue University, West Lafayette, IN
| | | | - Sue Thompson
- Los Alamos National Laboratories, Los Alamos, NM
| | - David Bruce
- Los Alamos National Laboratories, Los Alamos, NM
| | - Chris Detter
- Los Alamos National Laboratories, Los Alamos, NM
| | | | - Cliff Han
- Los Alamos National Laboratories, Los Alamos, NM
| | | | - Weimin Chen
- Department of Agronomy, Purdue University, West Lafayette, IN
| | | | - Gary Xie
- Los Alamos National Laboratories, Los Alamos, NM
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Kang S, Van Nostrand JD, Gough HL, He Z, Hazen TC, Stahl DA, Zhou J. Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. FEMS Microbiol Ecol 2013; 86:200-14. [DOI: 10.1111/1574-6941.12152] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 05/19/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sanghoon Kang
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; Norman; OK; USA
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; Norman; OK; USA
| | - Heidi L. Gough
- Department of Civil and Environmental Engineering; University of Washington; Seattle; WA; USA
| | - Zhili He
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; Norman; OK; USA
| | - Terry C. Hazen
- Department of Earth and Planetary Sciences; University of Tennessee; Knoxville; TN; USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering; University of Washington; Seattle; WA; USA
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Martí E, Sierra J, Cáliz J, Montserrat G, Vila X, Garau MA, Cruañas R. Ecotoxicity of Cr, Cd, and Pb on two Mediterranean soils. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2013; 64:377-87. [PMID: 23212577 DOI: 10.1007/s00244-012-9841-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 11/05/2012] [Indexed: 06/01/2023]
Abstract
Three potentially toxic elements [chromium (Cr), lead (Pb), and cadmium (Cd)] were tested to assess their effects on two soils of different properties and origin. The soils were a granitic soil (Haplic Arenosol), which meets the requirements of OECD ecotoxicity testing, and a calcareous soil (Calcaric Regosol) with properties often found in the Mediterranean areas. The metal concentrations used ranged from 0.001 to 5,000 mg kg(-1) soil. The effects on soil microbial activity and community composition (respirometry and polymerase chain reaction-denaturing gradient gel electrophoresis analysis), as well as the effects on plant germination and elongation (Lactuca sativa), were assessed. The toxicity of the soil water extracts was also evaluated by the growth inhibition of algal populations (Pseudokirschneriella subcapitata). Cr showed the highest level of toxicity to soil organisms in the assays performed because this element remains in soil as anionic form and is less retained by the soil solid matrix than Cd and Pb. The lowest observed-adverse effect level for Cr ranged from approximately 0.1 mg kg(-1) [substrate induced respiration (SIR) test for the granitic soil] to 10 mg kg(-1) (basal respiration and SIR tests for the calcareous soil). For Pb (SIR) and Cd (SIR and alga tests), these levels were approximately 100 mg kg(-1). Germination and algal tests showed higher sensitivity in Regosol soil than in Arenosol soil for Cr due to differences in the bioavailability between the soils. In the cases or areas where alkaline soils are abundant, these should also be considered in laboratory ecotoxicity testing to avoid underestimation of ecotoxicological risks.
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Affiliation(s)
- Esther Martí
- Laboratori d'Edafologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, 08028, Spain.
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26
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Structure analysis of bacterial community and their heavy-metal resistance determinants in the heavy-metal-contaminated soil sample. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0123-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Puspita ID, Kamagata Y, Tanaka M, Asano K, Nakatsu CH. Are uncultivated bacteria really uncultivable? Microbes Environ 2012; 27:356-66. [PMID: 23059723 PMCID: PMC4103542 DOI: 10.1264/jsme2.me12092] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/20/2012] [Indexed: 11/16/2022] Open
Abstract
Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.
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Affiliation(s)
- Indun Dewi Puspita
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17 Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido 062–8517,
Japan
| | - Michiko Tanaka
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Kozo Asano
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Cindy H. Nakatsu
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907,
USA
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Caliz J, Montserrat G, Martí E, Sierra J, Cruañas R, Garau MA, Triadó-Margarit X, Vila X. The exposition of a calcareous Mediterranean soil to toxic concentrations of Cr, Cd and Pb produces changes in the microbiota mainly related to differential metal bioavailability. CHEMOSPHERE 2012; 89:494-504. [PMID: 22658943 DOI: 10.1016/j.chemosphere.2012.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 04/25/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
The involvement of the bacterial community of an agricultural Mediterranean calcareous soil in relation to several heavy metals has been studied in microcosms under controlled laboratory conditions. Soil samples were artificially polluted with Cr(VI), Cd(II) and Pb(II) at concentrations ranging from 0.1 to 5000 mg kg(-1) and incubated along 28 d. The lowest concentrations with significant effects in soil respirometry were 10 mg kg(-1) Cr and 1000 mg kg(-1) Cd and Pb. However, only treatments showing more than 40% inhibition of respirometric activity led to significant changes in bacterial composition, as indicated by PCR-DGGE analyses. Presumable Cr- and Cd-resistant bacteria were detected in polluted microcosms, but development of the microbiota was severely impaired at the highest amendments of both metals. Results also showed that bioavailability is an important factor determining the impact of the heavy metals assayed, and even an inverted potential toxicity ranking could be achieved if their soluble fraction is considered instead of the total concentration. Moreover, multiresistant bacteria were isolated from Cr-polluted soil microcosms, some of them showing the capacity to reduce Cr(VI) concentrations between 26% and 84% of the initial value. Potentially useful strains for bioremediation were related to Arthrobacter crystallopoietes, Stenotrophomonas maltophilia and several species of Bacillus.
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Affiliation(s)
- Joan Caliz
- Institute of Aquatic Ecology, University of Girona, Avda Montilivi s/n, Girona 17071, Spain
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Almeida R, Mucha AP, Teixeira C, Bordalo AA, Almeida CMR. Biodegradation of petroleum hydrocarbons in estuarine sediments: metal influence. Biodegradation 2012; 24:111-23. [DOI: 10.1007/s10532-012-9562-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/28/2012] [Indexed: 10/28/2022]
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Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile. Extremophiles 2012; 16:523-38. [PMID: 22555750 DOI: 10.1007/s00792-012-0452-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/02/2012] [Indexed: 02/07/2023]
Abstract
Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.
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Batıoğlu-Pazarbaşı M, Baelum J, Johnsen AR, Sørensen SR, Albrechtsen HJ, Aamand J. Centimetre-scale vertical variability of phenoxy acid herbicide mineralization potential in aquifer sediment relates to the abundance of tfdA genes. FEMS Microbiol Ecol 2012; 80:331-41. [DOI: 10.1111/j.1574-6941.2012.01300.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Jacob Baelum
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
| | - Anders R. Johnsen
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
| | - Sebastian R. Sørensen
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
| | - Hans-Jørgen Albrechtsen
- DTU Environment; Department of Environmental Engineering; Technical University of Denmark; Kgs. Lyngby; Denmark
| | - Jens Aamand
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
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Factors driving potential ammonia oxidation in Canadian arctic ecosystems: does spatial scale matter? Appl Environ Microbiol 2011; 78:346-53. [PMID: 22081570 DOI: 10.1128/aem.06132-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is a major process in nitrogen cycling, and it plays a key role in nitrogen limited soil ecosystems such as those in the arctic. Although mm-scale spatial dependency of ammonia oxidizers has been investigated, little is known about the field-scale spatial dependency of aerobic ammonia oxidation processes and ammonia-oxidizing archaeal and bacterial communities, particularly in arctic soils. The purpose of this study was to explore the drivers of ammonia oxidation at the field scale in cryosols (soils with permafrost within 1 m of the surface). We measured aerobic ammonia oxidation potential (both autotrophic and heterotrophic) and functional gene abundance (bacterial amoA and archaeal amoA) in 279 soil samples collected from three arctic ecosystems. The variability associated with quantifying genes was substantially less than the spatial variability observed in these soils, suggesting that molecular methods can be used reliably evaluate spatial dependency in arctic ecosystems. Ammonia-oxidizing archaeal and bacterial communities and aerobic ammonia oxidation were spatially autocorrelated. Gene abundances were spatially structured within 4 m, whereas biochemical processes were structured within 40 m. Ammonia oxidation was driven at small scales (<1m) by moisture and total organic carbon, whereas gene abundance and other edaphic factors drove ammonia oxidation at medium (1 to 10 m) and large (10 to 100 m) scales. In these arctic soils heterotrophs contributed between 29 and 47% of total ammonia oxidation potential. The spatial scale for aerobic ammonia oxidation genes differed from potential ammonia oxidation, suggesting that in arctic ecosystems edaphic, rather than genetic, factors are an important control on ammonia oxidation.
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Knecht K, Schroth MH, Schulin R, Nowack B. Development and evaluation of micro push-pull tests to investigate micro-scale processes in porous media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:6460-6467. [PMID: 21710991 DOI: 10.1021/es2009727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Soils and sediments are porous media characterized by heterogeneities across a wide range of spatial scales. Physical, chemical, and biological properties have been found to show great variation even at subcentimeter scales. Here we present a new micro technique for the in situ study of chemical and microbiological reactions in water-saturated porous media at the mm-scale. This technique combines micro suction cups with the principle of single-well injection-withdrawal tests ("push-pull" tests). Push-pull tests have been used extensively on larger scales in groundwater research to obtain quantitative information of physical, chemical, and microbiological characteristics of an aquifer. The micro push-pull technique presented here was developed and validated using a thin-slab chamber filled with sand. A porous micro cup was used to inject about 250 μL of a test solution into the water-saturated sand pack and then to slowly extract about 850 μL water from the same point. The extraction-phase breakthrough curves of the solutes were modeled considering advection, dispersion, and molecular diffusion without fitting any parameters. As an example we quantified the degradation of citrate injected into the water-saturated sand pack inoculated with denitrifying bacteria. The results show that the new technique can be used to assess local microbial degradation processes under in situ conditions on the micro scale.
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Affiliation(s)
- Kajsa Knecht
- Institute of Terrestrial Ecosystems, ETH Zurich, Zurich, Switzerland
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Morimoto S, Hayatsu M, Takada Hoshino Y, Nagaoka K, Yamazaki M, Karasawa T, Takenaka M, Akiyama H. Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fields with different soil types. Microbes Environ 2011; 26:248-53. [PMID: 21576844 DOI: 10.1264/jsme2.me11127] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R(2)=0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R(2)=0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.
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Affiliation(s)
- Sho Morimoto
- National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki 305–8604, Japan.
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Hybholt TK, Aamand J, Johnsen AR. Quantification of centimeter-scale spatial variation in PAH, glucose and benzoic acid mineralization and soil organic matter in road-side soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:1085-1091. [PMID: 21396755 DOI: 10.1016/j.envpol.2011.02.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/28/2011] [Accepted: 02/11/2011] [Indexed: 05/30/2023]
Abstract
The aim of the study was to determine centimeter-scale spatial variation in mineralization potential in diffusely polluted soil. To this end we employed a 96-well microplate method to measure the mineralization of 14C-labeled organic compounds in deep-well microplates and thereby compile mineralization curves for 348 soil samples of 0.2-cm3. Centimeter-scale spatial variation in organic matter and the mineralization of glucose, benzoic acid, and PAHs (phenanthrene and pyrene) was determined for urban road-side soil sampled as arrays (7×11cm) of 96 subsamples. The spatial variation in mineralization was visualized by means of 2-D contour maps and quantified by means of semivariograms. The geostatistical analysis showed that the easily degradable compounds (glucose and benzoic acid) exhibited little spatial variation in mineralization potential, whereas the mineralization was highly heterogeneous for the PAH compounds that require specialized degraders. The spatial heterogeneity should be taken into account when estimating natural attenuation rates.
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Affiliation(s)
- Trine K Hybholt
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350 Copenhagen K, Denmark
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Keil D, Meyer A, Berner D, Poll C, Schützenmeister A, Piepho HP, Vlasenko A, Philippot L, Schloter M, Kandeler E, Marhan S. Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils. FEMS Microbiol Ecol 2011; 77:95-106. [PMID: 21410493 DOI: 10.1111/j.1574-6941.2011.01091.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type denitrifiers to scales >14 m for nirK-type denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type denitrifiers increased in high LUI, but decreased for biogeochemical properties, suggesting that biotic and/or abiotic factors other than those measured are driving the spatial distribution of these microorganisms at the plot scale. Furthermore, ammonia oxidizers (amoA ammonia-oxidizing archaea and amoA ammonia-oxidizing bacteria) and nitrate reducers (napA and narG) showed spatial coexistence, whereas niche partitioning was found between nirK- and nirS-type denitrifiers. Together, our results indicate that spatial analysis is a useful tool to characterize the distribution of different functional microbial guilds with respect to soil biogeochemical properties and land-use management. In addition, spatial analyses allowed us to identify distinct distribution ranges indicating the coexistence or niche partitioning of N-cycling communities in grassland soil.
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Affiliation(s)
- Daniel Keil
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany
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37
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The isolation of heavy-metal resistant culturable bacteria and resistance determinants from a heavy-metal-contaminated site. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0145-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Fuma S, Ishii N, Takeda H, Doi K, Kawaguchi I, Shikano S, Tanaka N, Inamori Y. Effects of acute gamma-irradiation on community structure of the aquatic microbial microcosm. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2010; 101:915-922. [PMID: 20615589 DOI: 10.1016/j.jenvrad.2010.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 06/03/2010] [Accepted: 06/11/2010] [Indexed: 05/29/2023]
Abstract
To characterise indirect effects of ionising radiation on aquatic microbial communities, effects of acute gamma-irradiation were investigated in a microcosm consisting of populations of green algae (Chlorella sp. and Scenedesmus sp.) and a blue-green alga (Tolypothrix sp.) as producer; a ciliate protozoan (Cyclidium glaucoma), rotifers (Lecane sp. and Philodina sp.) and an oligochaete (Aeolosoma hemprichi) as consumer; and more than four species of bacteria as decomposers. Population changes in the constituent organisms were observed over 160 days after irradiation. Prokaryotic community structure was also examined by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Principle response curve analysis revealed that the populations of the microcosm as a whole were not significantly affected at 100Gy while they were adversely affected at 500-5000Gy in a dose-dependent manner. However, some effects on each population, including each bacterial population detected by DGGE, did not depend on radiation doses, and some populations in the irradiated microcosm were larger than those of the control. These unexpected results are regarded as indirect effects through interspecies interactions, and possible mechanisms are proposed originating from population changes in other organisms co-existing in the microcosm. For example, some indirect effects on consumers and decomposers likely arose from interspecies competition within each trophic level. It is also likely that prey-predator relationships between producers and consumers caused some indirect effects on producers.
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Affiliation(s)
- Shoichi Fuma
- Environmental Radiation Effects Research Group, National Institute of Radiological Sciences,Chiba, Japan.
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39
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Microbial community structures in anoxic freshwater lake sediment along a metal contamination gradient. ISME JOURNAL 2010; 5:543-58. [PMID: 20811473 DOI: 10.1038/ismej.2010.132] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Contamination, such as by heavy metals, has frequently been implicated in altering microbial community structure. However, this association has not been extensively studied for anaerobic communities, or in freshwater lake sediments. We investigated microbial community structure in the metal-contaminated anoxic sediments of a eutrophic lake that were impacted over the course of 80 years by nearby zinc-smelting activities. Microbial community structure was inferred for bacterial, archaeal and eukaryotic populations by evaluating terminal restriction fragment length polymorphism (TRFLP) patterns in near-surface sediments collected in triplicate from five areas of the lake that had differing levels of metal contamination. The majority of the fragments in the bacterial and eukaryotic profiles showed no evidence of variation in association with metal contamination levels, and diversity revealed by these profiles remained consistent even as metal concentrations varied from 3000 to 27,000 mg kg(-1) total Zn, 0.125 to 11.2 μ pore water Zn and 0.023 to 5.40 μM pore water As. Although most archaeal fragments also showed no evidence of variation, the prevalence of a fragment associated with mesophilic Crenarchaeota showed significant positive correlation with total Zn concentrations. This Crenarchaeota fragment dominated the archaeal TRFLP profiles, representing between 35% and 79% of the total measured peak areas. Lake DePue 16S rRNA gene sequences corresponding to this TRFLP fragment clustered with anaerobic and soil mesophilic Crenarchaeota sequences. Although Crenarchaeota have been associated with metal-contaminated groundwater and soils, this is a first report (to our knowledge) documenting potential increased prevalence of Crenarchaeota associated with elevated levels of metal contamination.
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Bayle S, Malhautier L, Degrange V, Godon JJ, Fanlo JL. Structural and functional responses of sewage microbial communities used for the treatment of a complex mixture of volatile organic compounds (VOCs). J Appl Microbiol 2009; 107:85-96. [DOI: 10.1111/j.1365-2672.2009.04190.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Solé A, Diestra E, Esteve I. Confocal laser scanning microscopy image analysis for cyanobacterial biomass determined at microscale level in different microbial mats. MICROBIAL ECOLOGY 2009; 57:649-656. [PMID: 18982381 DOI: 10.1007/s00248-008-9463-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2008] [Accepted: 09/23/2008] [Indexed: 05/27/2023]
Abstract
We recently published a new method based on determining cyanobacterial biomass by confocal laser scanning microscopy image analysis (CLSM-IA) (Solé et al., Ultramicrosc 107:669-673, 2007). CLSM-IA allows biomass calculation for microorganisms of a small size, since the limit of the technique's resolution is that generated by a voxel, the smallest unit of a three-dimensional digital image, equivalent to 1.183 x 10(-3) mgC/cm(3) of sediment. This method is especially suitable for the quantitative analysis of a large number of CLSM images generated from benthic sediments in which complex populations of cyanobacteria are abundant, such as microbial mats. In order to validate the new CLSM approach, mats with varying structural characteristics were studied. We have grouped them into three types: Microcoleus mats (laminated), sandy mats (nonlaminated and composed of well-sorted quartz sands), and oil-polluted mats. In this work, we applied CLSM-IA in natural [the Ebro delta and Sant Jordi colony (Spain), Salins-de-Giraud and Etang de Berre (France), and Orkney Islands (Scotland)] and artificial [mesocosms (Israel)] microbial mats. A total of 4,103 confocal images were obtained in order to determine total and individual cyanobacteria biomass profiles, at microscale level. The data presented in this paper show the efficacy of the method, as it can be applied to highly diverse mat samples.
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Affiliation(s)
- A Solé
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
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Baldwin BR, Nakatsu CH, Nebe J, Wickham GS, Parks C, Nies L. Enumeration of aromatic oxygenase genes to evaluate biodegradation during multi-phase extraction at a gasoline-contaminated site. JOURNAL OF HAZARDOUS MATERIALS 2009; 163:524-530. [PMID: 18706759 DOI: 10.1016/j.jhazmat.2008.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 06/30/2008] [Accepted: 07/01/2008] [Indexed: 05/26/2023]
Abstract
Multi-phase extraction (MPE) is commonly used at petroleum-contaminated sites to volatilize and recover hydrocarbons from the vadose and saturated zones in contaminant source areas. Although primarily a physical treatment technology, the induced subsurface air flow can potentially increase oxygen supply and promote aerobic biodegradation of benzene, toluene, ethylbenzene, and xylenes (BTEX), the contaminants of concern at gasoline-contaminated sites. In this study, real-time PCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles were used to elucidate the impact of MPE operation on the aquifer microbial community structure and function at a gasoline-contaminated site. Prior to system activation, ring-hydroxylating toluene monooxygenase (RMO) and naphthalene dioxygenase (NAH) gene copies were on the order of 10(6) to 10(10)copies L(-1) in groundwater samples obtained from BTEX-impacted wells. Aromatic oxygenase genes were not detected in groundwater samples obtained during continuous MPE indicating decreased populations of BTEX-utilizing bacteria. During periods of pulsed MPE, total aromatic oxygenase gene copies were not significantly different than prior to system activation, however, shifts in aromatic catabolic genotypes were noted. The consistent detection of RMO, NAH, and phenol hydroxylase (PHE), which catabolizes further oxidation of hydroxylated BTEX metabolites indicated the potential for aerobic biodegradation of dissolved BTEX during pulsed MPE.
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Drenovsky RE, Feris KP, Batten KM, Hristova K. New and Current Microbiological Tools for Ecosystem Ecologists: Towards a Goal of Linking Structure and Function. AMERICAN MIDLAND NATURALIST 2008. [DOI: 10.1674/0003-0031(2008)160[140:nacmtf]2.0.co;2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Slater FR, Bruce KD, Ellis RJ, Lilley AK, Turner SL. Heterogeneous selection in a spatially structured environment affects fitness tradeoffs of plasmid carriage in pseudomonads. Appl Environ Microbiol 2008; 74:3189-97. [PMID: 18378654 PMCID: PMC2394952 DOI: 10.1128/aem.02383-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 03/21/2008] [Indexed: 11/20/2022] Open
Abstract
Environmental conditions under which fitness tradeoffs of plasmid carriage are balanced to facilitate plasmid persistence remain elusive. Periodic selection for plasmid-encoded traits due to the spatial and temporal variation typical in most natural environments (such as soil particles, plant leaf and root surfaces, gut linings, and the skin) may play a role. However, quantification of selection pressures and their effects is difficult at a scale relevant to the bacterium in situ. The present work describes a novel experimental system for such fine-scale quantification, with conditions designed to mimic the mosaic of spatially variable selection pressures present in natural surface environments. The effects of uniform and spatially heterogeneous mercuric chloride (HgCl(2)) on the dynamics of a model community of plasmid-carrying, mercury-resistant (Hg(r)) and plasmid-free, mercury-sensitive (Hg(s)) pseudomonads were compared. Hg resulted in an increase in the surface area occupied by, and therefore an increase in the fitness of, Hg(r) bacteria relative to Hg(s) bacteria. Uniform and heterogeneous Hg distributions were demonstrated to result in different community structures by epifluorescence microscopy, with heterogeneous Hg producing spatially variable selection landscapes. The effects of heterogeneous Hg were only apparent at scales of a few hundred micrometers, emphasizing the importance of using appropriate analysis methods to detect effects of environmental heterogeneity on community dynamics. Heterogeneous Hg resulted in negative frequency-dependent selection for Hg(r) cells, suggesting that sporadic selection may facilitate the discontinuous distribution of plasmids through host populations in complex, structured environments.
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Affiliation(s)
- Frances R Slater
- The Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, United Kingdom
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45
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Microbial Diversity, Life Strategies, and Adaptation to Life in Extreme Soils. SOIL BIOLOGY 2008. [DOI: 10.1007/978-3-540-74231-9_2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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46
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Jacobson AR, Dousset S, Andreux F, Baveye PC. Electron microprobe and synchrotron x-ray fluorescence mapping of the heterogeneous distribution of copper in high-copper vineyard soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:6343-6349. [PMID: 17948777 DOI: 10.1021/es070707m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The response of microorganisms to metal contamination of soils varies significantly from one investigation to another. One explanation is that metals are heterogeneously distributed at spatial scales relevant to microbes and that microoorganisms are able to avoid zones of intense contamination. This article aims to assess the microscale distribution of Cu in a vineyard soil. The spatial distribution of Cu was measured at two resolutions (0.3 mm and 20 microm) in thin sections of the surface 4 cm of undisturbed soil by electron microprobe and synchrotron X-ray microfluo-rescence spectroscopy. Bulk physicochemical analyses of Cu, pH, organic matter, texture, and mineralogy were performed. The results indicate that the Cu distribution is strongly heterogeneous at both scales of observation. Entire regions of the thin sections are virtually devoid of Cu, whereas highly localized "hotspots" have Cu signal intensities thousands of times higher than background. The distribution of Rb, or Al and Si, indicators of clay minerals, or Fe (iron (hydr)oxides), show that Cu is not preferentially associated with these mineral phases. Instead, Cu hotspots are associated with particulate organic matter. These observations suggest modification of current sampling protocols, and design of ecotoxicological experiments involving microorganisms, for contaminated soils.
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Affiliation(s)
- Astrid R Jacobson
- Laboratory of Geoenvironmental Science and Engineering, Bradfield Hall, Cornell University, Ithaca, New York 14853-1901, USA.
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47
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Tong Z, Bischoff M, Nies L, Applegate B, Turco RF. Impact of fullerene (C60) on a soil microbial community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:2985-91. [PMID: 17533868 DOI: 10.1021/es061953l] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The nascent state of the nanoproduct industry calls for important early assessment of environmental impacts before significant releases have occurred. Clearly, the impact of manufactured nanomaterials on key soil processes must be addressed so that an unbiased discussion concerning the environmental consequences of nanotechnology can take place. In this study, soils were treated with either 1 microg C60 g(-1) soil in aqueous suspension (nC60) or 1000 microg C60 g(-1) soil in granularform, a control containing equivalent tetrahydrofuran residues as generated during nC60 formation process or water and incubated for up to 180 days. Treatment effects on soil respiration, both basal and glucose-induced, were evaluated. The effects on the soil microbial community size was evaluated using total phospholipid derived phosphate. The impact on community structure was evaluated using both fatty acid profiles and following extraction of total genomic DNA, by DGGE after PCR amplification of total genomic DNA using bacterial variable V3 region targeted primers. In addition, treatment affects on soil enzymatic activities for beta-glucosidase, acid-phosphatase, dehydrogenase, and urease were followed. Our observations show that the introduction of fullerene, as either C60 or nC60, has little impact on the structure and function of the soil microbial community and microbial processes.
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Affiliation(s)
- Zhonghua Tong
- College of Agriculture, Laboratory for Soil Microbiology, School of Civil Engineering, Ecological Engineering Science Group, Department of Food Science, Purdue University, West Lafayette, Indiana 47907, USA
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Accinelli C, Koskinen WC, Becker JM, Sadowsky MJ. Environmental fate of two sulfonamide antimicrobial agents in soil. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:2677-82. [PMID: 17348682 DOI: 10.1021/jf063709j] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Veterinary antimicrobial agents have been detected in a number of environmental samples, including agricultural soils. In this study, we investigated the persistence and sorption of the sulfonamides sulfamethazine (SMZ) and sulfachloropyridine (SCP) in soil and their potential effects on soil microorganisms. The sulfonamides dissipated more rapidly from the silt loam soil as compared to the sandy soil. Average half-lives of SMZ and SPC among the two soils were 18.6 and 21.3 days, respectively. The presence of liquid swine slurry (5% v/w) decreased sulfonamide persistence in the silt loam soil. The lower persistence of the antimicrobials in liquid swine slurry-amended soil was likely due to higher microbial activity, as compared to unamended soil, and/or to the greater bioavailability of the sulfonamides to degrading microorganisms, as estimated by sorption isotherms. Concentrations of SMZ and SPC up to 100 microg g-1 had no effect on antimicrobial degradation rates and soil microorganisms. These studies suggest that higher sulfonamide concentrations would be necessary to affect the main processes controlling their environmental fates in soil, but at the concentrations normally found in the environment, there would be little or no effects.
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Affiliation(s)
- Cesare Accinelli
- Department of Agro-Environmental Science and Technology, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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