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Tang CH, Buskey EJ. Compositional change of bacterial communities in oil-polluted seawater amid varying degrees of nanoplankton bacterivory. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124723. [PMID: 39142426 DOI: 10.1016/j.envpol.2024.124723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/28/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024]
Abstract
Petroleum hydrocarbons are being released into the marine environment continuously. They will undergo weathering and may eventually be biodegraded by bacteria and other microbes. While nanoplankton (2-20 μm) are the major consumers of marine bacteria, their effect on the process of biodegradation of oil hydrocarbons is still debated. A 14-day microcosm experiment was conducted to investigate the effects of crude oil hydrocarbons on nanoplankton bacterivory and bacterial community in coastal waters. The coefficients of population growth (0.56-1.80 d-1 for all treatments considered) and grazing mortality (0.38-1.65 d-1 for all treatment considered) of bacteria estimated with the dilution method did not differ among the treatments of control (Ctrl), low dose chemically dispersed oil (LDOil, 2 μL L-1 of crude oil), and high dose chemically dispersed oil (HDOil, 8 μL L-1 of crude oil). Bacterial abundance ranged between 0.21-0.86 × 106 cells mL-1 on average for all treatments. The lack of drastic increases in the cell density of bacterial cells in the oil-loaded treatments was observed throughout the experiment period. Sequencing analysis of the 16S rRNA gene revealed the progressive changes in the community compositions of bacteria in all treatments. The relatively high abundance of oil-degrading bacteria, including Cycloclasticus and Alcanivorax on Days 3-14 of the experiment reflected the presence of biodegradation of oil in the LDOil and HDOil treatments. Throughout the 14 days, the community composition of bacteria in the LDOil and HDOil treatments became more similar and they both differed from that in the Ctrl treatment. This study concluded that, in oil-polluted seawater, the changes in the bacterial community composition were mainly resulting from the addition of chemically dispersed crude oil.
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Affiliation(s)
- Chi Hung Tang
- Marine Science Institute, The University of Texas at Austin, Texas, USA; School of Science and Technology, Hong Kong Metropolitan University, Hong Kong S.A.R., China.
| | - Edward J Buskey
- Marine Science Institute, The University of Texas at Austin, Texas, USA
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Nieto EE, Jurburg SD, Steinbach N, Festa S, Morelli IS, Coppotelli BM, Chatzinotas A. DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories. MICROBIOME 2024; 12:146. [PMID: 39113100 PMCID: PMC11305082 DOI: 10.1186/s40168-024-01865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/26/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation. RESULTS Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. CONCLUSION Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.
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Affiliation(s)
- Esteban E Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
| | - Stephanie D Jurburg
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nicole Steinbach
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Irma S Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
- Comisión de Investigaciones Científicas de La Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2. mSystems 2023; 8:e0117422. [PMID: 36786610 PMCID: PMC10134887 DOI: 10.1128/msystems.01174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Strain inoculation (bioaugmentation) is a potentially useful technology to provide microbiomes with new functionalities. However, there is limited understanding of the genetic factors contributing to successful establishment of inoculants. This work aimed to characterize the genes implicated in proliferation of the monoaromatic compound-degrading Pseudomonas veronii 1YdBTEX2 in nonsterile polluted soils. We generated two independent mutant libraries by random minitransposon-delivered marker insertion followed by deep sequencing (Tn-seq) with a total of 5.0 × 105 unique insertions. Libraries were grown in multiple successive cycles for up to 50 generations either in batch liquid medium or in two types of soil microcosms with different resident microbial content (sand or silt) in the presence of toluene. Analysis of gene insertion abundances at different time points (passed generations of metapopulation growth), in comparison to proportions at start and to in silico generated randomized insertion distributions, allowed to define ~800 essential genes common to both libraries and ~2,700 genes with conditional fitness effects in either liquid or soil (195 of which resulted in fitness gain). Conditional fitness genes largely overlapped among all growth conditions but affected approximately twice as many functions in liquid than in soil. This indicates soil to be a more promiscuous environment for mutant growth, probably because of additional nutrient availability. Commonly depleted genes covered a wide range of biological functions and metabolic pathways, such as inorganic ion transport, fatty acid metabolism, amino acid biosynthesis, or nucleotide and cofactor metabolism. Only sparse gene sets were uncovered whose insertion caused fitness decrease exclusive for soils, which were different between silt and sand. Despite detectable higher resident bacteria and potential protist predatory counts in silt, we were, therefore, unable to detect any immediately obvious candidate genes affecting P. veronii biological competitiveness. In contrast to liquid growth conditions, mutants inactivating flagella biosynthesis and motility consistently gained strong fitness advantage in soils and displayed higher growth rates than wild type. In conclusion, although many gene functions were found to be important for growth in soils, most of these are not specific as they affect growth in liquid minimal medium more in general. This indicates that P. veronii does not need major metabolic reprogramming for proliferation in soil with accessible carbon and generally favorable growth conditions. IMPORTANCE Restoring damaged microbiomes is still a formidable challenge. Classical widely adopted approaches consist of augmenting communities with pure or mixed cultures in the hope that these display their intended selected properties under in situ conditions. Ecological theory, however, dictates that introduction of a nonresident microbe is unlikely to lead to its successful proliferation in a foreign system such as a soil microbiome. In an effort to study this systematically, we used random transposon insertion scanning to identify genes and possibly, metabolic subsystems, that are crucial for growth and survival of a bacterial inoculant (Pseudomonas veronii) for targeted degradation of monoaromatic compounds in contaminated nonsterile soils. Our results indicate that although many gene functions are important for proliferation in soil, they are general factors for growth and not exclusive for soil. In other words, P. veronii is a generalist that is not a priori hindered by the soil for its proliferation and would make a good bioaugmentation candidate.
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Marxsen J, Rütz NK, Schmidt SI. Organic carbon and nutrients drive prokaryote and metazoan communities in a floodplain aquifer. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kim B, Perez-Calleja P, Li M, Nerenberg R. Effect of predation on the mechanical properties and detachment of MABR biofilms. WATER RESEARCH 2020; 186:116289. [PMID: 32836146 DOI: 10.1016/j.watres.2020.116289] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/30/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
The membrane-aerated biofilm reactor (MABR) is an emerging wastewater treatment technology that uses O2-supplying membranes as a biofilm support. Because O2 is supplied from the biofilm base instead of the bulk liquid, MABR biofilms have distinct microbial community structures and behavior. Past research showed that protozoan predation in MABR biofilms can greatly increase biofilm porosity, producing a void layer at the base of the biofilm. We hypothesized that this void layer could weaken the biofilm and promote sloughing, and investigated this with heterotrophic MABR biofilms. A rheometer was used to measure biofilm mechanical strength, and MABR flow cells were used to explore detachment. MABRs supplied with cycloheximide, a protozoan inhibitor, were used as controls. Predation increased the internal void ratio from 6 ± 7% to 50 ± 16%. The storage modulus was 1,780 ± 1,180 Pa with predation condition, compared to 9,800 ± 4,290 Pa for the control. Similarly, the loss modulus was 1,580 ± 729 Pa with predation and 363 ± 189 Pa for the control. When subjected to an increased flow, the biofilm loss was 44 ± 24% for the flow cell with predation, while only 7 ± 9% for the control. This research shows that predation can have an important impact on biofilm porosity in MABRs, reducing the mechanical strength and increasing detachment. Understanding this phenomenon can help develop more effective biofilm control strategies in MABRs.
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Affiliation(s)
- B Kim
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - P Perez-Calleja
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA.
| | - M Li
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA.
| | - R Nerenberg
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA.
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Richardson E, Dacks JB. Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight. Microorganisms 2019; 7:microorganisms7060178. [PMID: 31248111 PMCID: PMC6617064 DOI: 10.3390/microorganisms7060178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/17/2022] Open
Abstract
Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world’s largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.
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Affiliation(s)
- Elisabeth Richardson
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada.
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Di Lorenzo T, Cifoni M, Fiasca B, Di Cioccio A, Galassi DMP. Ecological risk assessment of pesticide mixtures in the alluvial aquifers of central Italy: Toward more realistic scenarios for risk mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:161-172. [PMID: 29981516 DOI: 10.1016/j.scitotenv.2018.06.345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
In this study we used the data of an extensive pesticide monitoring survey that took place in 11 alluvial aquifers of central Italy from 2010 to 2015 to explore 4 different scenarios of risk. The Scenarios 1 and 2 were used to depict the risk of failing to meet the good groundwater chemical status as defined by the Water Framework Directive. The Scenarios 3 and 4 were used to assess for the first time the ecological risk in groundwater bodies, defined as the likelihood of hazard to the groundwater communities stably residing in the 11 alluvial aquifers that may be affected by pesticide contamination. The ecological risk was assessed through a new procedure called GERAp (Groundwater Ecological Risk Assessment due to pesticides). The main results of this study highlighted that: 1) the Scenario 1 provided information of little use for risk managers; 2) more realistic information was provided by using the highest concentrations measured in the six-year monitoring period and considering the ecological risk in a combined scenario (Scenarios 2 and 4); 3) the achievement of the good chemical status by 2027 in 3 aquifers will be likely much more difficult than in the others because the ecosystem services, such as pesticide biodegradation, are likely less efficient in the 3 groundwater bodies; 4) some pesticides that were banned in Europe in 2009 should be kept monitored in the next surveys because they showed a persistent occurrence in the 11 aquifers; 5) DDT forms, Dieldrin and Heptachlor are expected to damage groundwater communities at concentrations that are lower than the present legal limits.
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Affiliation(s)
- Tiziana Di Lorenzo
- Institute of Ecosystem Study of the CNR, National Research Council of Italy, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy.
| | - Marco Cifoni
- Gran Sasso-Laga National Park, Via Del Convento 1, 67010 Assergi, L'Aquila, Italy
| | - Barbara Fiasca
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, Coppito, 67100 L'Aquila, Italy
| | - Alessia Di Cioccio
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, Coppito, 67100 L'Aquila, Italy
| | - Diana Maria Paola Galassi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, Coppito, 67100 L'Aquila, Italy
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Mercury bioremediation by mercury resistance transposon-mediated in situ molecular breeding. Appl Microbiol Biotechnol 2018; 102:3037-3048. [DOI: 10.1007/s00253-018-8847-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
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Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev 2018; 42:293-323. [DOI: 10.1093/femsre/fuy006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel 2000, Switzerland
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, Canada
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Straße, 67663 Kaiserslautern, Germany
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Avenida Viel 1497, Santiago, Chile
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, 37073 Göttingen, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, United States of America
| | - Julia Walochnik
- Molecular Parasitology, Institute of Tropical Medicine, Medical University, 1090 Vienna, Austria
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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Schmidt SI, Cuthbert MO, Schwientek M. Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 592:215-227. [PMID: 28319709 DOI: 10.1016/j.scitotenv.2017.03.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
Micro scale processes are expected to have a fundamental role in shaping groundwater ecosystems and yet they remain poorly understood and under-researched. In part, this is due to the fact that sampling is rarely carried out at the scale at which microorganisms, and their grazers and predators, function and thus we lack essential information. While set within a larger scale framework in terms of geochemical features, supply with energy and nutrients, and exchange intensity and dynamics, the micro scale adds variability, by providing heterogeneous zones at the micro scale which enable a wider range of redox reactions. Here we outline how understanding micro scale processes better may lead to improved appreciation of the range of ecosystems functions taking place at all scales. Such processes are relied upon in bioremediation and we demonstrate that ecosystem modelling as well as engineering measures have to take into account, and use, understanding at the micro scale. We discuss the importance of integrating faunal processes and computational appraisals in research, in order to continue to secure sustainable water resources from groundwater.
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Affiliation(s)
- Susanne I Schmidt
- Centre for Systems Biology, University of Birmingham, Birmingham, UK.
| | - Mark O Cuthbert
- Connected Waters Initiative Research Centre, UNSW Australia, 110 King Street, Manly Vale 2093, Australia; Department of Geography, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marc Schwientek
- Center of Applied Geoscience, University of Tübingen, 72074 Tübingen, Germany
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Hirakata Y, Oshiki M, Kuroda K, Hatamoto M, Kubota K, Yamaguchi T, Harada H, Araki N. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge. Microbes Environ 2016; 31:279-87. [PMID: 27431197 PMCID: PMC5017804 DOI: 10.1264/jsme2.me16067] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Predation by protists is top-down pressure that regulates prokaryotic abundance, community function, structure, and diversity in natural and artificial ecosystems. Although the effects of predation by protists have been studied in aerobic ecosystems, they are poorly understood in anoxic environments. We herein studied the influence of predation by Metopus and Caenomorpha ciliates—ciliates frequently found in anoxic ecosystems—on prokaryotic community function, structure, and diversity. Metopus and Caenomorpha ciliates were cocultivated with prokaryotic assemblages (i.e., anaerobic granular sludge) in an up-flow anaerobic sludge blanket (UASB) reactor for 171 d. Predation by these ciliates increased the methanogenic activities of granular sludge, which constituted 155% of those found in a UASB reactor without the ciliates (i.e., control reactor). Sequencing of 16S rRNA gene amplicons using Illumina MiSeq revealed that the prokaryotic community in the UASB reactor with the ciliates was more diverse than that in the control reactor; 2,885–3,190 and 2,387–2,426 operational taxonomic units (>97% sequence similarities), respectively. The effects of predation by protists in anaerobic engineered systems have mostly been overlooked, and our results show that the influence of predation by protists needs to be examined and considered in the future for a better understanding of prokaryotic community structure and function.
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Affiliation(s)
- Yuga Hirakata
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
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14
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Albers CN, Feld L, Ellegaard-Jensen L, Aamand J. Degradation of trace concentrations of the persistent groundwater pollutant 2,6-dichlorobenzamide (BAM) in bioaugmented rapid sand filters. WATER RESEARCH 2015; 83:61-70. [PMID: 26125500 DOI: 10.1016/j.watres.2015.06.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/14/2015] [Accepted: 06/15/2015] [Indexed: 05/12/2023]
Abstract
Groundwater is an important drinking water resource. Yet, this resource is threatened by pollution from chemicals, such as pesticides and their degradation products. To investigate the potential for remediation of groundwater polluted by trace concentrations of the pesticide residue 2,6-dichlorobenzamide (BAM), we established a pilot waterworks including two sand filters. The waterworks treated groundwater polluted with 0.2 μg/L BAM at flow conditions typical for rapid sand filters. Bioaugmentation of the sand filter with a specific BAM-degrading bacterium (Aminobacter sp. MSH1) resulted in significant BAM degradation to concentrations below the legal threshold level (0.1 μg/L), and this without adverse effects on other sand filter processes such as ammonium and iron oxidation. However, efficient degradation for more than 2-3 weeks was difficult to maintain due to loss of MSH1-bacteria, especially during backwashing. By limiting backwash procedures, the period of degradation was prolonged, but bacteria (and hence degradation activity) were still lost with time. Protozoa were observed to grow in the filters to a density that contributed significantly to the general loss of bacteria from the filters. Additionally, the concentration of easily assimilable organic carbon (AOC) in the remediated water may have been too low to sustain a sufficient population of degrader bacteria in the filter. This study shows that scaling up is not trivial and shortcomings in transferring degradation rates obtained in batch experiments to a rapid sand filter system are discussed. Further optimization is necessary to obtain and control more temporally stable systems for water purification. However, for the first time outside the laboratory and at realistic conditions a potential for the biodegradation of recalcitrant micropollutants in bioaugmented rapid sand filters is shown.
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Affiliation(s)
- Christian Nyrop Albers
- Dept. Geochemistry, Geological Survey of Denmark & Greenland, Øster Voldgade 10, DK-1350 Copenhagen, Denmark.
| | - Louise Feld
- Dept. Geochemistry, Geological Survey of Denmark & Greenland, Øster Voldgade 10, DK-1350 Copenhagen, Denmark
| | - Lea Ellegaard-Jensen
- Dept. Geochemistry, Geological Survey of Denmark & Greenland, Øster Voldgade 10, DK-1350 Copenhagen, Denmark
| | - Jens Aamand
- Dept. Geochemistry, Geological Survey of Denmark & Greenland, Øster Voldgade 10, DK-1350 Copenhagen, Denmark
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15
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Sauret C, Böttjer D, Talarmin A, Guigue C, Conan P, Pujo-Pay M, Ghiglione JF. Top-Down Control of Diesel-Degrading Prokaryotic Communities. MICROBIAL ECOLOGY 2015; 70:445-458. [PMID: 25805213 DOI: 10.1007/s00248-015-0596-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/08/2015] [Indexed: 06/04/2023]
Abstract
Biostimulation through the addition of inorganic nutrients has been the most widely practiced bioremediation strategy in oil-polluted marine waters. However, little attention has so far been paid to the microbial food web and the impact of top-down control that directly or indirectly influences the success of the bioremediation. We designed a mesocosm experiment using pre-filtered (<50 μm) surface seawater from the Bay of Banyuls-sur-Mer (North-Western Mediterranean Sea) and examined the top-down effect exerted by heterotrophic nanoflagellates (HNF) and virus-like particles (VLP) on prokaryotic abundance, activity and diversity in the presence or absence of diesel fuel. Prokaryotes, HNF and VLP abundances showed a predator-prey succession, with a co-development of HNF and VLP. In the polluted system, we observed a stronger impact of viral lysis on prokaryotic abundances than in the control. Analysis of the diversity revealed that a bloom of Vibrio sp. occurred in the polluted mesocosm. That bloom was rapidly followed by a less abundant and more even community of predation-resistant bacteria, including known hydrocarbon degraders such as Oleispira spp. and Methylophaga spp. and opportunistic bacteria such as Percisivirga spp., Roseobacter spp. and Phaeobacter spp. The shift in prokaryotic dominance in response to viral lysis provided clear evidence of the 'killing the winner' model. Nevertheless, despite clear effects on prokaryotic abundance, activity and diversity, the diesel degradation was not impacted by top-down control. The present study investigates for the first time the functioning of a complex microbial network (including VLP) using a nutrient-based biostimulation strategy and highlights some key processes useful for tailoring bioremediation.
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Affiliation(s)
- Caroline Sauret
- UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, 66650, Banyuls-sur-mer, France
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16
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Meckenstock RU, Elsner M, Griebler C, Lueders T, Stumpp C, Aamand J, Agathos SN, Albrechtsen HJ, Bastiaens L, Bjerg PL, Boon N, Dejonghe W, Huang WE, Schmidt SI, Smolders E, Sørensen SR, Springael D, van Breukelen BM. Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7073-81. [PMID: 26000605 DOI: 10.1021/acs.est.5b00715] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.
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Affiliation(s)
- Rainer U Meckenstock
- †University of Duisburg-Essen, Biofilm Centre, Universitätsstrasse 5, 45141 Essen, Germany
| | - Martin Elsner
- ○Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Christian Griebler
- ○Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tillmann Lueders
- ○Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Christine Stumpp
- ○Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jens Aamand
- ‡Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, 1350 Copenhagen K, Denmark
| | - Spiros N Agathos
- §Laboratory of Bioengineering; Earth and Life Institute (ELI); Université Catholique de Louvain; Place Croix du Sud 2, L7.05.19, B-1348 Louvain-la-Neuve, Belgium
| | - Hans-Jørgen Albrechtsen
- ∥Department of Environmental Engineering, Miljoevej, building 113, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Leen Bastiaens
- ⊥Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Poul L Bjerg
- ∥Department of Environmental Engineering, Miljoevej, building 113, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Nico Boon
- ∇University of Gent, LabMET, Coupure Links 653, 9000 Ghent, Belgium
| | - Winnie Dejonghe
- ⊥Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Wei E Huang
- ◆Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Susanne I Schmidt
- ¶CSB Centre for Systems Biology, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Erik Smolders
- ∞Division Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Sebastian R Sørensen
- ‡Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, 1350 Copenhagen K, Denmark
| | - Dirk Springael
- ∞Division Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Boris M van Breukelen
- #Department of Earth Sciences, VU University Amsterdam, De Boelelaan 1085, NL-1081 HV Amsterdam, The Netherlands
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Saleem M, Moe LA. Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice. Trends Biotechnol 2014; 32:529-37. [PMID: 25192971 DOI: 10.1016/j.tibtech.2014.08.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/16/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes.
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Affiliation(s)
- Muhammad Saleem
- Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY 40546-0312, USA.
| | - Luke A Moe
- Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY 40546-0312, USA
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18
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Cortés-Pérez S, Rodríguez-Zaragoza S, Mendoza-López MR. Trophic structure of amoeba communities near roots of Medicago sativa after contamination with fuel oil no. 6. MICROBIAL ECOLOGY 2014; 67:430-442. [PMID: 24158688 DOI: 10.1007/s00248-013-0305-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 09/30/2013] [Indexed: 06/02/2023]
Abstract
Root exudation increases microbial activity, selecting bacterial and fungal communities that metabolize organic matter such as hydrocarbons. However, a strong contamination pulse of hydrocarbons around plant roots may reorganize the soil's microbial trophic structure toward amoebae feeding on bacteria. We conducted a microcosm experiment to elucidate the effect of Medicago sativa on the trophic structure of naked amoebae after a strong pulse of pollution (50,000 ppm of fuel oil no. 6, which is a mixture of long chains ranging from C10 to C28). Plants were seeded 24 h after contamination and species of amoebae in the microcosms were identified at 1, 30, and 60 days after pollution. Several species from three trophic groups of naked amoeba were still alive 24 h after the hydrocarbon pulse. Non-planted microcosms harbored three trophic groups after 60 days, while planted ones nourished four groups. The bacterivore group was the most diverse in all microcosms, followed by protist-eaters and omnivores. The quantity of amoebae was significantly higher (3.4×10(3) organisms/g soil) in the planted pots than in the non-planted ones (1.3×10(3) organisms/g soil after 30 days of pollution (P ≤ 0.01). The shortest hydrocarbon chains (C10-C14) disappeared or diminished in all microcosms, and the longest ones increased in the planted ones. M. sativa thus exerted a positive effect on species richness, quantity, and the composition of amoebae trophic groups in contaminated soil. This indirect effect on bacterial predators is another key factor underlying hydrocarbon assimilation by living organisms during phytoremediation.
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Affiliation(s)
- Sandra Cortés-Pérez
- Laboratorio de Microbiología, UBIPRO, Fes-Iztacala UNAM, Av. De los Barrios #1 Col. Los Reyes Iztacala, Tlalnepantla Edo., México, C.P. 54090, Mexico,
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19
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Holmes DE, Giloteaux L, Williams KH, Wrighton KC, Wilkins MJ, Thompson CA, Roper TJ, Long PE, Lovley DR. Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater. THE ISME JOURNAL 2013; 7:1286-98. [PMID: 23446832 PMCID: PMC3695288 DOI: 10.1038/ismej.2013.20] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/07/2013] [Accepted: 01/10/2013] [Indexed: 11/09/2022]
Abstract
The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, Morrill Science Center IVN, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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20
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Risse-Buhl U, Herrmann M, Lange P, Akob DM, Pizani N, Schönborn W, Totsche KU, Küsel K. Phagotrophic Protist Diversity in the Groundwater of a Karstified Aquifer - Morphological and Molecular Analysis. J Eukaryot Microbiol 2013; 60:467-79. [DOI: 10.1111/jeu.12054] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/29/2013] [Accepted: 04/10/2013] [Indexed: 01/24/2023]
Affiliation(s)
- Ute Risse-Buhl
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
| | - Martina Herrmann
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
| | - Patricia Lange
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
- Department of Hydrogeology; Institute of Geosciences, Friedrich Schiller University Jena; Burgweg 11 07749 Jena Thuringia Germany
| | - Denise M. Akob
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
| | - Natalia Pizani
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
| | - Wilfried Schönborn
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
| | - Kai Uwe Totsche
- Department of Hydrogeology; Institute of Geosciences, Friedrich Schiller University Jena; Burgweg 11 07749 Jena Thuringia Germany
| | - Kirsten Küsel
- Limnology/Aquatic Geomicrobiology Research Group; Institute of Ecology, Friedrich Schiller University Jena; Dornburger Straße 159 07743 Jena Thuringia Germany
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21
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Sauret C, Christaki U, Moutsaki P, Hatzianestis I, Gogou A, Ghiglione JF. Influence of pollution history on the response of coastal bacterial and nanoeukaryote communities to crude oil and biostimulation assays. MARINE ENVIRONMENTAL RESEARCH 2012; 79:70-8. [PMID: 22743577 DOI: 10.1016/j.marenvres.2012.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/03/2012] [Accepted: 05/20/2012] [Indexed: 05/25/2023]
Abstract
Pollution history has often been proposed to explain site-dependent bioremediation efficiencies, but this hypothesis has been poorly explored. Here, bacteria and their heterotrophic nanoflagellates (HNF) predators originating from pristine and chronically oil-polluted coastal sites were subjected to crude oil ± nutrients or emulsifier amendments. The addition of crude oil had a more visible effect on bacteria originating from the pristine site with a higher increase in the activity of given OTU and inactivation of other petroleum-sensitive bacteria, as revealed by DNA and RNA-based comparison. Such changes resulted in a delay in microbial growth and in a lower bacterial degradation of the more complex hydrocarbons. Biostimulation provoked a selection of different bacterial community assemblages and stirred metabolically active bacteria. This resulted in a clear increase of the peak of bacteria and their HNF predators and higher oil degradation, irrespective of the pollution history of the site.
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Affiliation(s)
- Caroline Sauret
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne LOMIC, Avenue Fontaulé, F-66651 Banyuls-sur-Mer, France
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22
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Gertler C, Näther DJ, Cappello S, Gerdts G, Quilliam RS, Yakimov MM, Golyshin PN. Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study. FEMS Microbiol Ecol 2012; 81:520-36. [DOI: 10.1111/j.1574-6941.2012.01377.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/23/2012] [Accepted: 03/20/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christoph Gertler
- School of Biological Sciences; Environment Centre for Wales; Bangor University; Bangor; Gwynedd; UK
| | | | - Simone Cappello
- Istituto per Ambiente Marino Costiere; IAMC-CNR; Sezione di Messina; Italy
| | - Gunnar Gerdts
- Alfred Wegener Institute Foundation for Polar and Marine Research; Biologische Anstalt Helgoland; Helgoland; Germany
| | - Richard S. Quilliam
- School of Environment, Natural Resources & Geography; Bangor University; Bangor; Gwynedd; UK
| | - Michail M. Yakimov
- Istituto per Ambiente Marino Costiere; IAMC-CNR; Sezione di Messina; Italy
| | - Peter N. Golyshin
- School of Biological Sciences; Environment Centre for Wales; Bangor University; Bangor; Gwynedd; UK
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Gertler C, Näther DJ, Gerdts G, Malpass MC, Golyshin PN. A mesocosm study of the changes in marine flagellate and ciliate communities in a crude oil bioremediation trial. MICROBIAL ECOLOGY 2010; 60:180-91. [PMID: 20393846 DOI: 10.1007/s00248-010-9660-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 03/19/2010] [Indexed: 05/13/2023]
Abstract
Protozoan grazers play an important role in controlling the density of crude-oil degrading marine communities as has been evidenced in a number of microcosm experiments. However, small bioreactors contain a low initial titre of protozoa and the growth of hydrocarbon-depleting bacteria is accompanied by the fast depletion of mineral nutrients and oxygen, which makes microcosms rather unsuitable for simulating the sequence of events after the oil spill in natural seawater environment. In the present study, the population dynamics of marine protozoan community have been analysed in a 500 l mesocosm experiment involving bioaugmented oil booms that contained oil sorbents and slow-release fertilisers. A significant increase in numbers of marine flagellates and ciliates on biofilms of oil-degrading microbes was microscopically observed as early as 8 days after the start of the experiment, when protozoa exhibited a population density peak making up to 3,000 cells ml(-1). Further, the protozoan density varied throughout the experiment, but never dropped below 80 cells ml(-1). An 18S rRNA gene-based fingerprinting analysis revealed several changes within the eukaryotic community over the whole course of the experiment. Initial growth of flagellates and small ciliates was followed by a predominance of larger protozoa. According to microscopic observations and SSU rRNA molecular analyses, most predominant were the ciliates belonging to Euplotidae and Scuticociliatia. This is the first study to characterise the eukaryotic communities specifically in a large-scale oil bioremediation trial using both microscopy-based and several molecular techniques.
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Affiliation(s)
- Christoph Gertler
- School of Biological Sciences, Bangor University, Bangor Gwynedd, UK.
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24
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Näslund J, Nascimento FJA, Gunnarsson JS. Meiofauna reduces bacterial mineralization of naphthalene in marine sediment. ISME JOURNAL 2010; 4:1421-30. [DOI: 10.1038/ismej.2010.63] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Subramanyam E, Mohandoss S, Shin HW. Synthesis, characterization, and evaluation of antifouling polymers of 4-acryloyloxybenzaldehyde with methyl methacrylate. J Appl Polym Sci 2009. [DOI: 10.1002/app.29313] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kim YM, Jeon JR, Murugesan K, Kim EJ, Chang YS. Biodegradation of 1,4-dioxane and transformation of related cyclic compounds by a newly isolated Mycobacterium sp. PH-06. Biodegradation 2008; 20:511-9. [DOI: 10.1007/s10532-008-9240-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 12/04/2008] [Indexed: 11/29/2022]
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Brad T, van Breukelen BM, Braster M, van Straalen NM, Röling WFM. Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer. FEMS Microbiol Ecol 2008; 65:534-43. [PMID: 18616584 DOI: 10.1111/j.1574-6941.2008.00533.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Heterogeneity in eukaryotic and bacteria community structure in surface and subsurface sediment samples downgradient of the Banisveld landfill (The Netherlands) was studied using a culturing-independent molecular approach. Along a transect covering the part of the aquifer most polluted by landfill leachate, sediment was sampled at 1-m depth intervals, until a depth of 5.5 m, at four distances from the landfill. Two drillings were placed in a nearby clean area as a reference. Denaturing gradient gel electrophoresis banding patterns revealed high bacterial and eukaryotic diversity and complex community structures. Bacteria and eukaryotic community profiles in polluted samples grouped different from those in clean samples. Bacteria community profiles in surface samples clustered together and separately from subsurface community profiles. Subsurface bacteria profiles clustered in a location-specific manner. Eukaryotic community structure did not significantly relate to distance from the landfill or depth. No significant spatial autocorrelation of bacteria or eukaryotic communities was observed over 1-m depth intervals per sampling location. Spatial heterogeneity in sediment-associated bacterial communities appears to be much larger than in groundwater. We discuss how on the one hand, spatial heterogeneity may complicate the assessment of microbial community structure and functioning, while on the other it may provide better opportunities for natural attenuation.
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Affiliation(s)
- Traian Brad
- Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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28
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Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate. Appl Environ Microbiol 2008; 74:3959-68. [PMID: 18469120 DOI: 10.1128/aem.02820-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sediment-associated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of the Basidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellate Heteromita globosa (Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 10(2) to 10(3) cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.
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Dalby AP, Kormas KA, Christaki U, Karayanni H. Cosmopolitan heterotrophic microeukaryotes are active bacterial grazers in experimental oil-polluted systems. Environ Microbiol 2007; 10:47-56. [PMID: 17903218 DOI: 10.1111/j.1462-2920.2007.01428.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the population dynamics and prevailing 18S rDNA phylotypes of microeukaryotes (<or= 10 microm) in microcosms containing seawater from either an unpolluted oligotrophic site or a chronically oil-polluted mesotrophic site of the Aegean Sea, amended with crude oil (100 p.p.m. final concentration) and crude oil plus emulsifier (10 p.p.m. final concentration). The addition of oil alone did not result in an important increase of bacteria or their predators, while the addition of oil and emulsifiers caused an important increase in bacteria followed by nanoflagellate predator response. We observed an important shift in the microeukaryotic community structure, which was characterized by the dominance of the same heterotrophic nanoflagellates in all oil-polluted treatments. Thus, the resulting 18S rDNA phylotypes were dominated (48.1-82.4%) by Paraphysomonas foraminifera in all treatments containing crude oil and crude oil plus emulsifier. The origin of the seawater, i.e. unpolluted versus chronically oil-polluted, had no effect on the dominant eukaryote, suggesting that the ubiquitous P. foraminifera is an effective opportunist in oil-polluted aquatic systems. The next dominant phylotypes were Monosiga brevicollis (<or= 27.0%) and Pseudobodo tremulans (<or= 23.1%). However, the addition of the emulsifier increased the dominance of P. foraminifera but decreased that of M. brevicollis and P. tremulans. Our study revealed that these dominant oil-tolerant eukaryotes, which are commonly found in the marine environments, are important grazers of bacteria and as such their dynamics should be taken into account in bioremediation practices in situ.
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Affiliation(s)
- Andrew P Dalby
- Institute of Oceanography, Hellenic Centre for Marine Research, PO Box 712, 190 13 Anavissos, Greece
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Priya M, Haridas A, Manilal VB. Anaerobic protozoa and their growth in biomethanation systems. Biodegradation 2007; 19:179-85. [PMID: 17492357 DOI: 10.1007/s10532-007-9124-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 04/13/2007] [Indexed: 11/28/2022]
Abstract
This study was to investigate growth of protozoa and its influence on biodegradation in anaerobic treatment systems. It was done by specifically controlling and monitoring growth of protozoa versus degradation in continuous stirred anaerobic reactors and batch anaerobic reactors. Occurrence of a diverse protozoa population such as the ciliates, Prorodon, Vorticella, Cyclidium, Spathidium, Loxodes, Metopus were observed in stable anaerobic systems and the flagellates, Rhynchomonas, Naeglaria, Amoeboflagellates, Tetramitus, Trepomonas and Bodo during increased VFA concentration and affected periods of biomethanation. The abundance of ciliates in the anaerobic system had significant correlation with the reduction of MLSS, increased rate of COD removal and higher methane production. The results of this study thus tend to relate increased anaerobic degradation with the abundance of protozoa, mainly ciliates, which indicate their possible involvement in the process. Present study also reveals that performance of anaerobic process can be assessed by monitoring the protozoa population in the system.
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Affiliation(s)
- M Priya
- Process Engineering and Environmental Technology Division, Regional Research Laboratory, CSIR, Thiruvananthapuram, 695019, India
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Pogue AJ, Gilbride KA. Impact of protozoan grazing on nitrification and the ammonia- and nitrite-oxidizing bacterial communities in activated sludge. Can J Microbiol 2007; 53:559-71. [PMID: 17668014 DOI: 10.1139/w07-027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In activated sludge, protozoa feed on free-swimming bacteria and suspended particles, inducing flocculation and increasing the turnover rate of nutrients. In this study, the effect of protozoan grazing on nitrification rates under various conditions in municipal activated sludge batch reactors was examined, as was the spatial distribution of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) within the activated sludge. The reactors were monitored for ammonia, nitrite, nitrate, and total nitrogen concentrations, and bacterial numbers in the presence and absence of cycloheximide (a protozoan inhibitor), allylthiourea (an inhibitor of ammonia oxidation), and EDTA (a deflocculating agent). The accumulations of nitrate, nitrite, and ammonia were lower in batches without than with protozoa grazing. Inhibition of ammonia oxidation also decreased the amount of nitrite and nitrate accumulation. Inhibiting protozoan grazing along with ammonia oxidation further decreased the amounts of nitrite and nitrate accumulated. Induction of deflocculation led to high nitrate accumulation, indicating high levels of nitrification; this effect was lessened in the absence of protozoan grazing. Using fluorescent in situ hybridization and confocal laser scanning microscopy, AOB and NOB were found clustered within the floc, and inhibiting the protozoa, inhibiting ammonia oxidation, or inducing flocculation did not appear to lower the number of AOB and NOB present or affect their position within the floc. These results suggest that the AOB and NOB are present but less active in the absence of protozoa.
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Affiliation(s)
- Amy J Pogue
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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Tso SF, Taghon GL. Protozoan grazing increases mineralization of naphthalene in marine sediment. MICROBIAL ECOLOGY 2006; 51:460-9. [PMID: 16645923 DOI: 10.1007/s00248-006-9058-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 01/13/2006] [Accepted: 01/14/2006] [Indexed: 05/08/2023]
Abstract
Bacterial decomposition of organic matter is frequently enhanced when protozoa are present. Various mechanisms have been proposed to account for this phenomenon, including effects associated with grazing by protozoa (such as increased recycling of limiting nutrients, removal of senescent cells, or reduction of competition among bacteria) and indirect effects of grazers (such as excretion of bacterial growth factors). Few studies have examined the role of protozoa in bacterial degradation of xenobiotic compounds in sediment containing a natural community of microbes. The effect of protozoa on mineralization of naphthalene was investigated in this study. Laboratory experiments were conducted using field-contaminated estuarine sediment, with the indigenous microbial populations. Mineralization of naphthalene was up to four times greater in treatments with actively grazing protozoa than in treatments containing the grazing inhibitor cytochalasin B. Control experiments confirmed that the grazing inhibitor was not toxic to ciliates but did prevent them from grazing. The grazing inhibitor did not affect growth rates of a mixed culture of sediment bacteria or a pure polycyclic-aromatic-hydrocarbon-degrading strain. Once grazing had been inhibited, supplementing treatments with inorganic N and P, glucose, or additional protozoa failed to stimulate naphthalene mineralization. Naphthalene-degrading bacteria were four to nine times less abundant when protozoan grazing was suppressed. We suggest that protozoa enhance naphthalene mineralization by selectively grazing on those sediment bacteria that ordinarily would outcompete naphthalene-degrading bacteria.
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Affiliation(s)
- Suk-Fong Tso
- Institute of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901-8521, USA
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Abstract
Hundreds of millions of litres of petroleum enter the environment from both natural and anthropogenic sources every year. The input from natural marine oil seeps alone would be enough to cover all of the world's oceans in a layer of oil 20 molecules thick. That the globe is not swamped with oil is testament to the efficiency and versatility of the networks of microorganisms that degrade hydrocarbons, some of which have recently begun to reveal the secrets of when and how they exploit hydrocarbons as a source of carbon and energy.
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Affiliation(s)
- Ian M Head
- School of Civil Engineering and Geosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK.
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Mattison RG, Taki H, Harayama S. The soil flagellate Heteromita globosa accelerates bacterial degradation of alkylbenzenes through grazing and acetate excretion in batch culture. MICROBIAL ECOLOGY 2005; 49:142-150. [PMID: 15690226 DOI: 10.1007/s00248-003-0226-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 06/01/2004] [Indexed: 05/24/2023]
Abstract
The impact of grazing by soil flagellates Heteromita globosa on aerobic biodegradation of benzene by Pseudomonas strain PS+ was examined in batch culture. Growth of H. globosa on these bacteria obeyed Monod kinetics (mu(max), 0.17 +/- 0.03 h(-1); K(s), 1.1 +/- 0.2 x 10(7) bacteria mL(-1)) and was optimal at a bacteria/ flagellate ratio of 2000. Carbon mass balance showed that 5.2% of total [ring-U-(14)C]benzene fed to bacteria was subsequently incorporated into flagellate biomass. Growth-inhibiting concentrations (IC50) of alkylbenzenes (benzene, toluene, ethylbenzene) were inversely related with their octanol/ water partitioning coefficients, and benzene was least toxic for bacteria and flagellates with IC50 values of 4392 (+/- 167) microM and 2770 (+/- 653) microM, respectively. The first-order rate constant for benzene degradation (k1, 0.48 +/- 0.12 day(-1)) was unaffected by the presence or absence of flagellates in cultures. However, the rate of benzene degradation by individual bacteria averaged three times higher in the presence of flagellates (0.73 +/- 0.13 fmol cell(-1) h(-1)) than in their absence (0.26 +/- 0.03 fmol cell(-1) h(-1)). Benzene degradation also coincided with higher levels of dissolved oxygen and a higher rate of nitrate reduction in the presence of flagellates (p < 0.02). Grazing by flagellates may have increased the availability of dissolved oxygen to a smaller surviving population of bacteria engaged in the aerobic reactions initiating benzene degradation. In addition, flagellates may also have increased the rate of nitrate reduction through the excretion of acetate as an additional electron donor for these bacteria. Indeed, acetate was shown to progressively accumulate in cultures where flagellates grazed on heat-killed bacteria. This study provided evidence that grazing flagellates stimulate bacterial degradation of alkylbenzenes and provide a link for carbon cycling to consumers at higher trophic levels. This may have important implications for bioremediation processes.
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Affiliation(s)
- R G Mattison
- Marine Biotechnology Institute Co., Ltd., 3-75-1 Heita, Kamaishi City, Iwate 026-0001, Japan.
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Coupe SJ, Smith HG, Newman AP, Puehmeier T. Biodegradation and microbial diversity within permeable pavements. Eur J Protistol 2003. [DOI: 10.1078/0932-4739-00027] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Kinner NE, Harvey RW, Shay DM, Metge DW, Warren A. Field evidence for a protistan role in an organically-contaminated aquifer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2002; 36:4312-4318. [PMID: 12387403 DOI: 10.1021/es020611m] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The association between protists, bacteria, and dissolved organic carbon (DOC) in an oxygen-depleted, 6 km-long wastewater contaminant plume within a sandy aquifer (Cape Cod, MA) was investigated by comparing abundance patterns along longitudinal and vertical transects and at a control site. Strong linear correlations were observed between unattached bacterial abundance and DOC for much of the upgradient-half of the plume (0.1-2.5 km downgradient from the source) that is characterized by quasi-steady state chemistry. However, a logarithmic decrease was observed between the number of protists supported per mg of DOC and the estimated age of the DOC within the plume. The relatively labile dissolved organic contaminants that characterize the groundwater sampled from the plume < or = 0.1 km downgradient from the contaminant source appeared to indirectly support 3-4 times as many protists (per mg of DOC) as the older, more recalcitrant DOC in the alkylbenzene sulfonate (ABS)-contaminated zone at 3 km downgradient (approximately 30 years travel time). Substantive numbers of protists (>10(4)/cm3) were recovered from suboxic zones of the plume. The higher than expected ratios of protists to unattached bacteria (10 to 100:1) observed in much of the plume suggest that protists may be grazing upon both surface-associated and unattached bacterial communities to meet their nutritional requirements. In closed bottle incubation experiments, the presence of protists caused an increase in bacterial growth rate, which became more apparent at higher amendments of labile DOC (3-20 mgC/L). The presence of protists resulted in an increase in the apparent substrate saturation level for the unattached bacterial community, suggesting an important role for protists in the fate of more-labile aquifer organic contaminants.
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Affiliation(s)
- Nancy E Kinner
- Bedrock Bioremediation Center, University of New Hampshire, Durham 03824, USA.
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Mattison RG, Taki H, Harayama S. The bacterivorous soil flagellate Heteromita globosa reduces bacterial clogging under denitrifying conditions in sand-filled aquifer columns. Appl Environ Microbiol 2002; 68:4539-45. [PMID: 12200311 PMCID: PMC124123 DOI: 10.1128/aem.68.9.4539-4545.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An exopolymer (slime)-producing soil bacterium Pseudomonas sp. (strain PS+) rapidly clogged sand-filled columns supplied with air-saturated artificial groundwater containing glucose (500 mg liter(-1)) as a sole carbon source and nitrate (300 mg liter(-1)) as an alternative electron acceptor. After 80 days of operation under denitrifying conditions, the effective porosity and saturated hydraulic conductivity (permeability) of sand in these columns had fallen by 2.5- and 26-fold, respectively. Bacterial biofilms appeared to induce clogging by occluding pore spaces with secreted exopolymer, although there may also have been a contribution from biogas generated during denitrification. The bacterivorous soil flagellate Heteromita globosa minimized reductions in effective porosity (1.6-fold) and permeability (13-fold), presumably due to grazing control of biofilms. Grazing may have limited growth of bacterial biomass and hence the rate of exopolymer and biogas secretion into pore spaces. Evidence for reduction in biogas production is suggested by increased nitrite efflux from columns containing flagellates, without a concomitant increase in nitrate consumption. There was no evidence that flagellates could improve flow conditions if added once clogging had occurred (60 days). Presumably, bacterial biofilms and their secretions were well established at that time. Nevertheless, this study provides evidence that bacterivorous flagellates may play a positive role in maintaining permeability in aquifers undergoing remediation treatments.
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Affiliation(s)
- Richard G Mattison
- Marine Biotechnology Institute Co., Ltd., Kamaishi Laboratories, Kamaishi City, Iwate 026-0001, Japan.
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Harvey RW, Mayberry N, Kinner NE, Metge DW, Novarino F. Effect of growth conditions and staining procedure upon the subsurface transport and attachment behaviors of a groundwater protist. Appl Environ Microbiol 2002; 68:1872-81. [PMID: 11916707 PMCID: PMC123859 DOI: 10.1128/aem.68.4.1872-1881.2002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transport and attachment behaviors of Spumella guttula (Kent), a nanoflagellate (protist) found in contaminated and uncontaminated aquifer sediments in Cape Cod, Mass., were assessed in flowthrough and static columns and in a field injection-and-recovery transport experiment involving an array of multilevel samplers. Transport of S. guttula harvested from low-nutrient (10 mg of dissolved organic carbon per liter), slightly acidic, granular (porous) growth media was compared to earlier observations involving nanoflagellates grown in a traditional high-nutrient liquid broth. In contrast to the highly retarded (retardation factor of approximately 3) subsurface transport previously reported for S. guttula, the peak concentration of porous-medium-grown S. guttula traveled concomitantly with that of a conservative (bromide) tracer. About one-third of the porous-medium-grown nanoflagellates added to the aquifer were transported at least 2.8 m downgradient, compared to only approximately 2% of the broth-grown nanoflagellates. Flowthrough column studies revealed that a vital (hydroethidine [HE]) staining procedure resulted in considerably less attachment (more transport) of S. guttula in aquifer sediments than did a staining-and-fixation procedure involving 4',6'-diamidino-2-phenylindole (DAPI) and glutaraldehyde. The calculated collision efficiency (approximately 10(-2) for porous-medium-grown, DAPI-stained nanoflagellates) was comparable to that observed earlier for the indigenous community of unattached groundwater bacteria that serve as prey. The attachment of HE-labeled S. guttula onto aquifer sediment grains was independent of pH (over the range from pH 3 to 9) suggesting a primary attachment mechanism that may be fundamentally different from that of their prey bacteria, which exhibit sharp decreases in fractional attachment with increasing pH. The high degree of mobility of S. guttula in the aquifer sediments has important ecological implications for the protistan community within the temporally changing plume of organic contaminants in the Cape Cod aquifer.
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