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Martín-Rodríguez AJ, Fernández-Juárez V, Valeriano VD, Mihindukulasooriya I, Ceresnova L, Joffré E, Jensie-Markopoulos S, Moore ERB, Sjöling Å. A hotspot of diversity: novel Shewanella species isolated from Baltic Sea sediments delineate a sympatric species complex. Int J Syst Evol Microbiol 2024; 74. [PMID: 39150443 PMCID: PMC11329295 DOI: 10.1099/ijsem.0.006480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024] Open
Abstract
Two bacterial strains, SP1S1-4T and SP2S1-2T, were isolated from sediment samples collected in the Stockholm archipelago in November 2021. Following whole-genome sequencing, these strains were identified as tentatively belonging to two novel Shewanella genospecies, based on digital DNA-DNA hybridization, as implemented in the Type Strain Genome Server. Shewanella septentrionalis, Shewanella baltica and Shewanella hafniensis were, in this order and within a narrow genomic relatedness range, their closest genotypic relatives. Additional sampling and sequencing efforts led to the retrieval of distinct isolates that were monophyletic with SP1S1-4T and SP2S1-2T, respectively, based on phylogenomic analysis of whole-genome sequences. Comparative analyses of genome sequence data, which included blast-based average nucleotide identity, core genome-based and core proteome-based phylogenomics, in addition to MALDI-TOF MS-based protein profiling, confirmed the distinctness of the putative novel genospecies with respect to their closest genotypic relatives. A comprehensive phenotypic characterisation of SP1S1-4T and SP2S1-2T revealed only minor differences with respect to the type strains of S. septentrionalis, S. baltica and S. hafniensis. Based on the collective phylogenomic, proteomic, and phenotypic evidence presented here, we describe two novel genospecies within the genus Shewanella, for which the names Shewanella scandinavica sp. nov. and Shewanella vaxholmensis sp. nov. are proposed. The type strains are, respectively, SP2S1-2T (=CCUG 76457T=CECT 30688T), with a draft genome sequence of 5 041 805 bp and a G+C content of 46.3 mol%, and SP1S1-4T (=CCUG 76453T=CECT 30684T), with a draft genome sequence of 4 920147 bp and a G+C content of 46.0 mol%. Our findings suggest the existence of a species complex formed by the species S. baltica, S. septentrionalis, S. scandinavica sp. nov., and S. vaxholmensis sp. nov., with S. hafniensis falling in the periphery, where distinct genomic species clusters could be identified. However, this does not exclude the possibility of a continuum of genomic diversity within this sedimental ecosystem, as discussed herein with additional sequenced isolates.
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Affiliation(s)
- Alberto J Martín-Rodríguez
- Department of Clinical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Víctor Fernández-Juárez
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Valerie D Valeriano
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Indiwari Mihindukulasooriya
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Livia Ceresnova
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Enrique Joffré
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Chemistry and Molecular Biology (CMB), University of Gothenburg, Gothenburg, Sweden
| | - Susanne Jensie-Markopoulos
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Åsa Sjöling
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Chemistry and Molecular Biology (CMB), University of Gothenburg, Gothenburg, Sweden
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Ballentine WM, Dorgan KM. The Meioflume: A New System for Observing the Interstitial Behavior of Meiofauna. Integr Org Biol 2024; 6:obae016. [PMID: 38883566 PMCID: PMC11177882 DOI: 10.1093/iob/obae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 04/27/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
Meiofauna (benthic invertebrates < 1 mm in size) facilitate sediment biogeochemical cycling, alter sediment microbial community structure, and serve as an important trophic link between benthic micro- and macrofauna, yet the behaviors that mechanistically link individuals to their ecological effects are largely unknown. Meiofauna are small and sediments are opaque, making observing the in situ activities of these animals challenging. We developed the Meioflume, a small, acrylic flow tunnel filled with grains of cryolite, a transparent sand analog, to simulate the in situ conditions experienced by meiofauna in an observable lab environment. The Meioflume has a working area (28.57 mm × 10.16 mm × 1 mm) that is small enough to quickly locate fauna and clearly observe behavior but large enough that animals are not tightly confined. When connected to a syringe press, the Meioflume can produce low velocity flows consistently and evenly across the width of its working area while retaining the contents. To demonstrate its functionality in observing the behavior of meiofauna, we placed individual meiofaunal animals (a protodrilid annelid, a harpacticoid copepod, and a platyhelminth flatworm) in Meioflumes and filmed their behavioral response to a sudden initiation of porewater flow. All animals were clearly visible within the flume and could be observed responding to the onset of flow. The design and construction of the Meioflume make it an accessible, affordable tool for researchers. This experimental system could be modified to address many questions in meiofaunal ecology, such as studying behavior in response to chemical cues, allowing us to observe meiofaunal behaviors to better understand their ecological effects.
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Affiliation(s)
- W M Ballentine
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL 36528, USA
| | - K M Dorgan
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL 36528, USA
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3
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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [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] [Received: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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Broman E, Olsson M, Maciute A, Donald D, Humborg C, Norkko A, Jilbert T, Bonaglia S, Nascimento FJA. Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments. THE ISME JOURNAL 2024; 18:wrae013. [PMID: 38366020 PMCID: PMC10942774 DOI: 10.1093/ismejo/wrae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024]
Abstract
Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial-temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment-water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH4. We show that macrofauna increases CH4 fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH4 flux reduces CH4 pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH4 emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm 10691, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
| | - Markus Olsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm 10691, Sweden
| | - Adele Maciute
- Department of Marine Sciences, University of Gothenburg, Gothenburg 41390, Sweden
| | - Daniel Donald
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
| | - Christoph Humborg
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
| | - Alf Norkko
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
| | - Tom Jilbert
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
- Environmental Geochemistry Group, Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg 41390, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm 10691, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
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Nematodes As Soil Stress Indicators for Polycyclic Aromatic Hydrocarbons: a Review. Helminthologia 2022; 59:117-126. [PMID: 36118368 PMCID: PMC9444203 DOI: 10.2478/helm-2022-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/27/2022] [Indexed: 11/21/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are an important group of organic pollutants present in all parts of the environment, affecting ecosystems and human health. PAHs, which have a strong affinity for organic carbon, are found in large quantities in soil, which is one of the most important sinks for these contaminants. Their impact on the soil biotic compartments depends on a number of different factors in combination with PAH behaviour and can be assessed using soil monitoring. Soil fauna have already shown excellent properties for biomonitoring of contaminants with most promising indicator frameworks based on nematodes, which are involved in essential processes in this environment. Nematodes respond to PAHs at multiple levels, including molecular, individual and community levels. At the molecular level, this is associated with activation of metabolic pathways for xenobiotics and increased demand for energy and resources. At the individual level, this is reflected in the slowing down of various physiological processes, which has consequences at the individual and community level for sensitive taxa. In this review, the toxicity and the direct and indirect effects of PAHs on soil nematode communities are discussed. It also considers the perspectives and challenges in assessing the toxicity of PAHs and their indication using soil nematodes.
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R S PR, Gera A, K R, V RR, Mv R. Influence of salinity on the meiofaunal distribution in a hypersaline lake along the southeast coast of India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:199. [PMID: 35178589 DOI: 10.1007/s10661-022-09829-5] [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: 11/08/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The present study highlights that seasonal salinity variability plays a significant role in meiobenthic distribution with special reference to nematode assemblages. Sediment and water samples were collected from Pulicat Lake, a hypersaline lake along the southeast coast of India during two seasons (Southwest Monsoon (SWM) and Northeast Monsoon (NEM)). Based on the salinity distribution, the lake is categorized into four regions, viz., southern inlet, central region, middle inlet, and northern inlet. Meiobenthic abundance was higher during SWM (226-12,206 Ind/10 cm2) than in NEM (640-10,424 Ind/10 cm2). The meiofaunal abundance was high in the central region during both the seasons, followed by the southern, northern, and middle inlet. The nematode was the dominant meiobenthic group, followed by copepod, polychaete, and foraminifera. Due to high organic matter, the central region was dominated by deposit feeding nematode species like Halalaimus longicaudatus and Terschellingia longicaudata. The southern and northern regions were dominated by free-living nematodes Rhabditis olitoria, Mesorhabditis capitata, Mononochus bastian, Paramononchus sp., Piranchulus sp., and Diploscapter cylindricus. Oncholaimus sp., a hypersaline indicator species, was reported from the middle inlet location. Statistical analysis suggests salinity as a critical parameter for the distribution and diversity of nematodes.
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Affiliation(s)
- Pandiya Rajan R S
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, 600100, India.
| | - Anitha Gera
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, 600100, India
| | - Ramu K
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, 600100, India
| | - Ranga Rao V
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, 600100, India
| | - Ramanamurthy Mv
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, 600100, India
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Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea. mSphere 2021; 6:e0012721. [PMID: 34468165 PMCID: PMC8550262 DOI: 10.1128/msphere.00127-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Recreational boating can impact benthic ecosystems in coastal waters. Reduced height and cover of aquatic vegetation in shallow Baltic Sea inlets with high boat traffic have raised concerns about cascading effects on benthic communities in these ecosystems. Here, we characterized the diversity and composition of sediment-associated microbial and meiofaunal communities across five bays subjected to low and high degrees of boating activity and examined the community-environment relationships and association with bay morphometry. We found that recreational boating activity altered meiofauna alpha diversity and the composition of both micro- and meiobenthic communities, and there were strong correlations between community structure and morphometric variables like topographic openness, wave exposure, water surface area, and total phosphorous concentrations. Inlets with high boat traffic showed an increase of bacterial taxa like Hydrogenophilaceae and Burkholderiaceae. Several meiofauna taxa previously reported to respond positively to high levels of suspended organic matter were found in higher relative abundances in the bays with high boat traffic. Overall, our results show that morphometric characteristics of inlets are the strongest drivers of benthic diversity in shallow coastal environments. However, while the effects were small, we found significant effects of recreational boating on benthic community structure that should be considered when evaluating the new mooring projects. IMPORTANCE With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems. Here, we present the first study that uses DNA metabarcoding to assess how benthic biodiversity in shallow coastal areas is impacted by recreational boating. Our study shows a relatively small, but significant, effect of recreational boating both on meiofauna alpha diversity and meiofauna and bacterial community composition. However, both meiofauna and bacterial community composition in shallow benthic habitats is mediated to a higher degree by abiotic variables, such as topographic openness, area or size of the inlets, and wave exposure. Despite the fact that the effects were small, such impacts on benthic biodiversity should be considered in the management of coastal shallow habitats.
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Spatial and Temporal Variation in Deep-Sea Meiofauna at the LTER Observatory HAUSGARTEN in the Fram Strait (Arctic Ocean). DIVERSITY 2020. [DOI: 10.3390/d12070279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Time-series studies at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN have yielded the world’s longest time-series on deep-sea meiofauna and thus provide a decent basis to investigate the variability in deep-sea meiobenthic communities at different spatial and temporal scales. The main objective of the present study was to investigate whether the sediment-dwelling meiofauna (size range: 32–1000 µm) is controlled by small-scale local environmental conditions, rather than large-scale differences between water depths. Univariate and multivariate statistical analyses, including distance-based linear models (DistLM) and redundancy analysis (dbRDA), revealed that due to their small size, meiofauna tend to mainly respond to micro-scale (centimeter) variations in environmental conditions in surface and subsurface sediment layers. Inter-annual temporal patterns among metazoan meiofauna at higher taxon levels revealed only a weak effect of time, and merely on the rare meiofauna taxa (<2% of the total meiofauna community) at HAUSGARTEN.
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Bonaglia S, Hedberg J, Marzocchi U, Iburg S, Glud RN, Nascimento FJA. Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed. MARINE ENVIRONMENTAL RESEARCH 2020; 159:104968. [PMID: 32662428 PMCID: PMC7369627 DOI: 10.1016/j.marenvres.2020.104968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 05/03/2023]
Abstract
Oxygen depleted areas are widespread in the marine realm. Unlike macrofauna, meiofauna are abundant in hypoxic sediments. We studied to what extent meiofauna affect oxygen availability, sulfide removal and microbial communities. Meiofauna were extracted alive and added to intact sediments simulating abundance gradients previously reported in the area. A total of 324 porewater microprofiles were recorded over a 3-week incubation period and microbial community structure and cable bacteria densities were determined at the end of the experiment. At high abundances meiofauna activity deepened oxygen penetration by 85%, 59%, and 62% after 5, 14, and 22 days, respectively, compared to control sediment with scarce meiofauna. After 6 days, meiofauna increased the volume of oxidized, sulfide-free sediment by 68% and reduced sulfide fluxes from 8.8 to 0.4 mmol m-2 d-1. After 15 days, the difference with the control attenuated due to the presence of a cable bacteria population, which facilitated sulfides oxidation in all treatments. 16S rRNA gene analysis revealed that meiofauna affected microbial community structure (beta diversity). Thus, meiofauna bioturbation plays an important role in deepening oxygen penetration, counteracting euxinia and in structuring microbial diversity of hypoxic sediments. Co-existence with cable bacteria demonstrates neutralism interaction between these two ecosystem engineers.
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Affiliation(s)
- Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Nordcee, Department of Biology, University of Southern Denmark, Denmark.
| | - Johanna Hedberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ugo Marzocchi
- Department of Biosciences, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Sven Iburg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ronnie N Glud
- Nordcee, Department of Biology, University of Southern Denmark, Denmark; Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Bugge Harder C, Nyrop Albers C, Rosendahl S, Aamand J, Ellegaard-Jensen L, Ekelund F. Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters. FEMS Microbiol Ecol 2020; 95:5569652. [PMID: 31518408 DOI: 10.1093/femsec/fiz148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/12/2019] [Indexed: 11/13/2022] Open
Abstract
As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biology, Copenhagen University, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.,Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, Solvegatan 37, SE 223-62, Lund, Sweden.,Department of Plant and Soil Science, Texas Tech University, Bayer Plant Science Building, 2911 15th Street, Lubbock, TX 79409, USA
| | - Christian Nyrop Albers
- Department of Geochemistry, Geological Survey of Denmark & Greenland, Ø Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Søren Rosendahl
- Department of Biology, Copenhagen University, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark & Greenland, Ø Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Lea Ellegaard-Jensen
- Department of Geochemistry, Geological Survey of Denmark & Greenland, Ø Voldgade 10, DK-1350, Copenhagen, Denmark.,Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Flemming Ekelund
- Department of Biology, Copenhagen University, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
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11
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Bonaglia S, Broman E, Brindefalk B, Hedlund E, Hjorth T, Rolff C, Nascimento FJA, Udekwu K, Gunnarsson JS. Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments. CHEMOSPHERE 2020; 248:126023. [PMID: 32007777 DOI: 10.1016/j.chemosphere.2020.126023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
Biodegradation by microorganisms is a useful tool that helps alleviating hydrocarbon pollution in nature. Microbes are more efficient in degradation under aerobic than anaerobic conditions, but the majority of sediment by volume is generally anoxic. Incubation experiments were conducted to study the biodegradation potential of naphthalene-a common polycyclic aromatic hydrocarbon (PAH)-and the diversity of microbial communities in presence/absence of activated carbon (AC) under aerobic/anaerobic conditions. Radio-respirometry experiments with endogenous microorganisms indicated that degradation of naphthalene was strongly stimulated (96%) by the AC addition under anaerobic conditions. In aerobic conditions, however, AC had no effects on naphthalene biodegradation. Bioaugmentation tests with cultured microbial populations grown on naphthalene showed that AC further stimulated (92%) naphthalene degradation in anoxia. Analysis of the 16S rRNA gene sequences implied that sediment amendment with AC increased microbial community diversity and changed community structure. Moreover, the relative abundance of Geobacter, Thiobacillus, Sulfuricurvum, and methanogenic archaea increased sharply after amendment with AC under anaerobic conditions. These results may be explained by the fact that AC particles promoted direct interspecies electron transfer (DIET) between microorganisms involved in PAH degradation pathways. We suggest that important ecosystem functions mediated by microbes-such as hydrocarbon degradation-can be induced and that AC enrichment strategies can be exploited for facilitating bioremediation of anoxic oil-contaminated sediments and soils.
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Affiliation(s)
- Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Department of Biology, University of Southern Denmark, Odense, Denmark.
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Björn Brindefalk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Erika Hedlund
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | | | - Carl Rolff
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Klas Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden.
| | - Jonas S Gunnarsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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12
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Martínez A, Eckert EM, Artois T, Careddu G, Casu M, Curini-Galletti M, Gazale V, Gobert S, Ivanenko VN, Jondelius U, Marzano M, Pesole G, Zanello A, Todaro MA, Fontaneto D. Human access impacts biodiversity of microscopic animals in sandy beaches. Commun Biol 2020; 3:175. [PMID: 32313088 PMCID: PMC7170908 DOI: 10.1038/s42003-020-0912-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 01/25/2023] Open
Abstract
Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow “swash” zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity. Martínez et al. use DNA metabarcoding and a phylogeny-based approach to demonstrate the effects of tourist access on meiofauna diversity of beaches in Asinara National Park. Their results show that tourist frequentation decreases meiofaunal diversity at the shallow “swash” zone, and can be used to inform tourist access and management of beaches.
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Affiliation(s)
- Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy
| | - Ester M Eckert
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Giovanni Careddu
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | | | - Vittorio Gazale
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - Stefan Gobert
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Viatcheslav N Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "A. Moro", Bari, Italy
| | - Aldo Zanello
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - M Antonio Todaro
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy.
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13
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Nascimento FJA, Dahl M, Deyanova D, Lyimo LD, Bik HM, Schuelke T, Pereira TJ, Björk M, Creer S, Gullström M. Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure. Commun Biol 2019; 2:362. [PMID: 31602411 PMCID: PMC6778119 DOI: 10.1038/s42003-019-0610-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/12/2019] [Indexed: 11/08/2022] Open
Abstract
Ecological interactions between aquatic plants and sediment communities can shape the structure and function of natural systems. Currently, we do not fully understand how seagrass habitat degradation impacts the biodiversity of belowground sediment communities. Here, we evaluated indirect effects of disturbance of seagrass meadows on meiobenthic community composition, with a five-month in situ experiment in a tropical seagrass meadow. Disturbance was created by reducing light availability (two levels of shading), and by mimicking grazing events (two levels) to assess impacts on meiobenthic diversity using high-throughput sequencing of 18S rRNA amplicons. Both shading and simulated grazing had an effect on meiobenthic community structure, mediated by seagrass-associated biotic drivers and sediment abiotic variables. Additionally, shading substantially altered the trophic structure of the nematode community. Our findings show that degradation of seagrass meadows can alter benthic community structure in coastal areas with potential impacts to ecosystem functions mediated by meiobenthos in marine sediments.
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Affiliation(s)
| | - Martin Dahl
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Diana Deyanova
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Liberatus D. Lyimo
- School of Biological Sciences, University of Dodoma, Box 338, Dodoma, Tanzania
| | - Holly M. Bik
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Taruna Schuelke
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Tiago José Pereira
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Mats Björk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, LL57 2UW UK
| | - Martin Gullström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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14
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Broman E, Raymond C, Sommer C, Gunnarsson JS, Creer S, Nascimento FJA. Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem. Mol Ecol 2019; 28:3813-3829. [PMID: 31332853 PMCID: PMC6852176 DOI: 10.1111/mec.15179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/16/2022]
Abstract
Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on-going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high-throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna-macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Baltic Sea CentreStockholm UniversityStockholmSweden
| | - Caroline Raymond
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Christian Sommer
- School of Natural Sciences, Technology and Environmental StudiesSödertörn UniversityHuddingeSweden
| | - Jonas S. Gunnarsson
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Natural SciencesBangor UniversityBangorUK
| | - Francisco J. A. Nascimento
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Baltic Sea CentreStockholm UniversityStockholmSweden
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15
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D'Hondt AS, Stock W, Blommaert L, Moens T, Sabbe K. Nematodes stimulate biomass accumulation in a multispecies diatom biofilm. MARINE ENVIRONMENTAL RESEARCH 2018; 140:78-89. [PMID: 29891387 DOI: 10.1016/j.marenvres.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
While the effects of abiotic parameters on microbial tidal biofilms are relatively well-documented, the effects of grazing and/or bioturbation by meiofauna are poorly understood. We investigated the impact of a natural nematode assemblage on the biomass and microbial community structure of a multispecies diatom biofilm. Nematodes stimulated diatom biomass accumulation of the biofilm and caused a shift in diatom community structure. Higher diatom biomass accumulation in the presence of nematodes could be the result of increased diatom biomass production through nutrient regeneration resulting from grazing or bioturbation, and/or through shifts in interspecific interactions between diatoms (e.g. competition) through selective grazing. Alternatively, lower biomass in the controls may be due to higher secretion of diatom production in the form of bound extracellular polymeric substances (EPS). Our observations underscore that meiobenthos, and especially nematodes, are important for the structure and production of tidal biofilms.
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Affiliation(s)
- An-Sofie D'Hondt
- Department of Biology, Marine Biology Lab, Ghent University, 9000 Ghent, Belgium; Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Willem Stock
- Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Lander Blommaert
- Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Tom Moens
- Department of Biology, Marine Biology Lab, Ghent University, 9000 Ghent, Belgium
| | - Koen Sabbe
- Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium.
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16
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Rzeznik-Orignac J, Puisay A, Derelle E, Peru E, Le Bris N, Galand PE. Co-occurring nematodes and bacteria in submarine canyon sediments. PeerJ 2018; 6:e5396. [PMID: 30083476 PMCID: PMC6074754 DOI: 10.7717/peerj.5396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/17/2018] [Indexed: 01/17/2023] Open
Abstract
In submarine canyon sediments, bacteria and nematodes dominate the benthic biomass and play a key role in nutrient cycling and energy transfer. The diversity of these communities remains, however, poorly studied. This work aims at describing the composition of bacteria and nematode communities in the Lacaze-Duthiers submarine canyon in the north-western Mediterranean Sea. We targeted three sediment depths for two consecutive years and investigated the communities using nuclear markers (18S rRNA and 16S rRNA genes). High throughput sequencing combined to maximal information coefficient (MIC) statistical analysis allowed us to identify, for the first time, at the same small scale, the community structures and the co-occurrence of nematodes and bacteria Operational Taxonomic Units across the sediment cores. The associations detected by MIC revealed marked patterns of co-occurrences between the bacteria and nematodes in the sediment of the canyon and could be linked to the ecological requirements of individual bacteria and nematodes. For the bacterial community, Delta- and Gammaproteobacteria sequences were the most abundant, as seen in some canyons earlier, although Acidobacteria, Actinobacteria and Planctomycetes have been prevalent in other canyon sediments. The 20 identified nematode genera included bacteria feeders as Terschellingia, Eubostrichus, Geomonhystera, Desmoscolex and Leptolaimus. The present study provides new data on the diversity of bacterial and nematodes communities in the Lacaze-Duthiers canyon and further highlights the importance of small-scale sampling for an accurate vision of deep-sea communities.
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Affiliation(s)
- Jadwiga Rzeznik-Orignac
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Antoine Puisay
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France.,Criobe, Laboratoire d'Excellence "Corail", PSL Research University: EPHE-UPVD-CNRS, Papetoai, French Polynesia
| | - Evelyne Derelle
- Laboratoire de Biologie Intégrative des Organismes Marins, Sorbonne Université, CNRS, Banyuls-sur-Mer, France.,LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM, Plouzané, France
| | - Erwan Peru
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Nadine Le Bris
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Pierre E Galand
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
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17
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Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Sci Rep 2018; 8:11737. [PMID: 30082688 PMCID: PMC6078945 DOI: 10.1038/s41598-018-30179-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022] Open
Abstract
Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.
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18
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Haig SJ, Gauchotte-Lindsay C, Collins G, Quince C. Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3101-10. [PMID: 26895622 PMCID: PMC4841604 DOI: 10.1021/acs.est.5b05027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Exposure to endocrine-disrupting chemicals (EDCs), such as estrogens, is a growing issue for human and animal health as they have been shown to cause reproductive and developmental abnormalities in wildlife and plants and have been linked to male infertility disorders in humans. Intensive farming and weather events, such as storms, flash flooding, and landslides, contribute estrogen to waterways used to supply drinking water. This paper explores the impact of estrogen exposure on the performance of slow sand filters (SSFs) used for water treatment. The feasibility and efficacy of SSF bioaugmentation with estrogen-degrading bacteria was also investigated, to determine whether removal of natural estrogens (estrone, estradiol, and estriol) and overall SSF performance for drinking water treatment could be improved. Strains for SSF augmentation were isolated from full-scale, municipal SSFs so as to optimize survival in the laboratory-scale SSFs used. Concentrations of the natural estrogens, determined by gas chromatography coupled with mass spectrometry (GC-MS), revealed augmented SSFs reduced the overall estrogenic potency of the supplied water by 25% on average and removed significantly more estrone and estradiol than nonaugmented filters. A negative correlation was found between coliform removal and estrogen concentration in nonaugmented filters. This was due to the toxic inhibition of protozoa, indicating that high estrogen concentrations can have functional implications for SSFs (such as impairing coliform removal). Consequently, we suggest that high estrogen concentrations could impact significantly on water quality production and, in particular, on pathogen removal in biological water filters.
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Affiliation(s)
- Sarah-Jane Haig
- School
of Engineering, Rankine Building, University
of Glasgow, Glasgow G12 8LT, U.K.
- Phone: 734-764-6350. E-mail:
| | | | - Gavin Collins
- School
of Engineering, Rankine Building, University
of Glasgow, Glasgow G12 8LT, U.K.
- Microbial
Ecophysiology Laboratory, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - Christopher Quince
- School
of Engineering, Rankine Building, University
of Glasgow, Glasgow G12 8LT, U.K.
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19
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Ben Said O, Louati H, Soltani A, Preud'homme H, Cravo-Laureau C, Got P, Pringault O, Aissa P, Duran R. Changes of benthic bacteria and meiofauna assemblages during bio-treatments of anthracene-contaminated sediments from Bizerta lagoon (Tunisia). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15319-15331. [PMID: 25618309 DOI: 10.1007/s11356-015-4105-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
Sediments from Bizerta lagoon were used in an experimental microcosm setup involving three scenarios for the bioremediation of anthracene-polluted sediments, namely bioaugmentation, biostimulation, and a combination of both bioaugmentation and biostimulation. In order to investigate the effect of the biotreatments on the benthic biosphere, 16S rRNA gene-based T-RFLP bacterial community structure and the abundance and diversity of the meiofauna were determined throughout the experiment period. Addition of fresh anthracene drastically reduced the benthic bacterial and meiofaunal abundances. The treatment combining biostimulation and bioaugmentation was most efficient in eliminating anthracene, resulting in a less toxic sedimentary environment, which restored meiofaunal abundance and diversity. Furthermore, canonical correspondence analysis showed that the biostimulation treatment promoted a bacterial community favorable to the development of nematodes while the treatment combining biostimulation and bioaugmentation resulted in a bacterial community that advantaged the development of the other meiofauna taxa (copepods, oligochaetes, polychaetes, and other) restoring thus the meiofaunal structure. The results highlight the importance to take into account the bacteria/meiofauna interactions during the implementation of bioremediation treatment.
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Affiliation(s)
- Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia.
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France.
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia.
| | - Hela Louati
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
- Laboratoire Ecosystèmes Marins Côtiers, UMR 5119 CNRS-UM2-IFREMER-IRD-ECOSYM, Université Montpellier 2, Montpellier, France
| | - Amel Soltani
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - Hugues Preud'homme
- Laboratoire Chimie Analytique BioInorganique Environnement-UMR CNRS IPREM 5254-Helioparc, Université de Pau et des Pays de l'Adour, Pau, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - Patrice Got
- Laboratoire Ecosystèmes Marins Côtiers, UMR 5119 CNRS-UM2-IFREMER-IRD-ECOSYM, Université Montpellier 2, Montpellier, France
| | - Olivier Pringault
- Laboratoire Ecosystèmes Marins Côtiers, UMR 5119 CNRS-UM2-IFREMER-IRD-ECOSYM, Université Montpellier 2, Montpellier, France
| | - Patricia Aissa
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
| | - Robert Duran
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
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20
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Taylor JD, Cunliffe M. Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:606-613. [PMID: 25858418 DOI: 10.1111/1758-2229.12292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Previous studies have shown that the bioturbating polychaete Hediste (Nereis) diversicolor can affect the composition of bacterial communities in oil-contaminated sediments, but have not considered diversity specifically within bioturbator burrows or the impact on microbial eukaryotes. We tested the hypothesis that H. diversicolor burrows harbour different eukaryotic and bacterial communities compared with un-bioturbated sediment, and that bioturbation stimulates oil degradation. Oil-contaminated sediment was incubated with or without H. diversicolor for 30 days, after which sediment un-affected by H. diversicolor and burrow DNA/RNA samples were analysed using quantitative reverse transcription PCR (Q-RT-PCR) and high-throughput sequencing. Fungi dominated both burrow and un-bioturbated sediment sequence libraries; however, there was significant enrichment of bacterivorous protists and nematodes in the burrows. There were also significant differences between the bacterial communities in burrows compared with un-bioturbated sediment. Increased activity and relative abundance of aerobic hydrocarbon-degrading bacteria in the burrows coincided with the significant reduction in hydrocarbon concentration in the bioturbated sediment. This study represents the first detailed assessment of the effect of bioturbation on total microbial communities in oil-contaminated sediments. In addition, it further shows that bioturbation is a significant factor in determining microbial diversity within polluted sediments and plays an important role in stimulating bioremediation.
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
- Marine Biology and Ecology Research Group, Marine Institute, Plymouth University, Drake Circus, Plymouth, UK
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21
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Meiofauna increases bacterial denitrification in marine sediments. Nat Commun 2014; 5:5133. [PMID: 25318852 PMCID: PMC4218958 DOI: 10.1038/ncomms6133] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 09/02/2014] [Indexed: 11/21/2022] Open
Abstract
Denitrification is a critical process that can alleviate the effects of excessive nitrogen availability in aquatic ecosystems subject to eutrophication. An important part of denitrification occurs in benthic systems where bioturbation by meiofauna (invertebrates <1 mm) and its effect on element cycling are still not well understood. Here we study the quantitative impact of meiofauna populations of different abundance and diversity, in the presence and absence of macrofauna, on nitrate reduction, carbon mineralization and methane fluxes. In sediments with abundant and diverse meiofauna, denitrification is double that in sediments with low meiofauna, suggesting that meiofauna bioturbation has a stimulating effect on nitrifying and denitrifying bacteria. However, high meiofauna densities in the presence of bivalves do not stimulate denitrification, while dissimilatory nitrate reduction to ammonium rate and methane efflux are significantly enhanced. We demonstrate that the ecological interactions between meio-, macrofauna and bacteria are important in regulating nitrogen cycling in soft-sediment ecosystems. Excessive nutrient loading is a threat to aquatic ecosystems; however, denitrification may be key in removing large amounts of reactive nitrogen and, therefore, mitigating consequent eutrophication. Here, the authors explore how meiofauna may impact the rate of denitrification in sediments.
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22
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Stauffert M, Cravo-Laureau C, Duran R. Structure of hydrocarbonoclastic nitrate-reducing bacterial communities in bioturbated coastal marine sediments. FEMS Microbiol Ecol 2014; 89:580-93. [DOI: 10.1111/1574-6941.12359] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie; IPREM UMR CNRS 5254; Université de Pau et des Pays de l'Adour; Pau Cedex France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie; IPREM UMR CNRS 5254; Université de Pau et des Pays de l'Adour; Pau Cedex France
| | - Robert Duran
- Equipe Environnement et Microbiologie; IPREM UMR CNRS 5254; Université de Pau et des Pays de l'Adour; Pau Cedex France
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23
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Louati H, Ben Said O, Soltani A, Cravo-Laureau C, Preud'Homme H, Duran R, Aissa P, Mahmoudi E, Pringault O. Impacts of bioremediation schemes for the mitigation of a low-dose anthracene contamination on free-living marine benthic nematodes. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:201-212. [PMID: 24357236 DOI: 10.1007/s10646-013-1163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
A microcosm experiment was used to examine (1) the effects of different bioremediation schemes on degradation of anthracene and the structure of free-living marine nematodes in a lightly contaminated (4.5 μg g(-1)) sediment from Bizerte lagoon and (2) the responses of the nematode community upon an artificial spiking of a low dose anthracene (1 μg g(-1)). For that purpose sediment microcosms were incubated in laboratory for 40 days. Bioremediation techniques decreased the anthracene contamination, and interestingly, biodegradation were more efficient when anthracene was artificial supplied into the sediment suggesting that the addition of bioavailable anthracene stimulated the bacterial community to adjust towards a PAH-degrading community. Spiking with this low dose of anthracene provoked significant changes in the nematode community structure and abundance, with the elimination of specific species such as Mesacanthion diplechma, the decrease of the dominant species Oncholaimus campylocercoides and the increase in abundance of opportunistic species such as Spirinia parasitifera. This would suggest a low tolerance of the nematode community despite the presence of a weak anthracene contamination in the sediment that could have allow dominance of an anthracene tolerant nematode species. Anthracene toxicity was alleviated in biostimulation treatments, leading to a strong increase in nematode abundance, concomitantly with changes in the nematode community structure; Prochromadorella neapolitana became the most abundant species.
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Affiliation(s)
- Hela Louati
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
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Stauffert M, Duran R, Gassie C, Cravo-Laureau C. Response of archaeal communities to oil spill in bioturbated mudflat sediments. MICROBIAL ECOLOGY 2014; 67:108-119. [PMID: 24057322 DOI: 10.1007/s00248-013-0288-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, IPREM - UMR CNRS 5254, Université de Pau et des Pays de l'Adour, BP 1155, 64013, Pau Cedex, France
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Louati H, Said OB, Soltani A, Got P, Mahmoudi E, Cravo-Laureau C, Duran R, Aissa P, Pringault O. The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure. CHEMOSPHERE 2013; 93:2535-2546. [PMID: 24206831 DOI: 10.1016/j.chemosphere.2013.09.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 06/02/2023]
Abstract
Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.
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Stauffert M, Cravo-Laureau C, Jézéquel R, Barantal S, Cuny P, Gilbert F, Cagnon C, Militon C, Amouroux D, Mahdaoui F, Bouyssiere B, Stora G, Merlin FX, Duran R. Impact of oil on bacterial community structure in bioturbated sediments. PLoS One 2013; 8:e65347. [PMID: 23762350 PMCID: PMC3677869 DOI: 10.1371/journal.pone.0065347] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/24/2013] [Indexed: 02/04/2023] Open
Abstract
Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions – with tidal cycles and natural seawater – was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g−1 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Ronan Jézéquel
- Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des Eaux, Brest, France
| | - Sandra Barantal
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Philippe Cuny
- Equipe Microbiologie Environnement et Biotechnologie, Mediterranean Institute of Oceanography, Aix-Marseille Université, Marseille, France
| | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, Toulouse, France
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Cécile Militon
- Equipe Microbiologie Environnement et Biotechnologie, Mediterranean Institute of Oceanography, Aix-Marseille Université, Marseille, France
| | - David Amouroux
- Equipe Chimie Analytique Bio-Inorganique et Environnement, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Fatima Mahdaoui
- Equipe Chimie Analytique Bio-Inorganique et Environnement, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Brice Bouyssiere
- Equipe Chimie Analytique Bio-Inorganique et Environnement, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
| | - Georges Stora
- Equipe Microbiologie Environnement et Biotechnologie, Mediterranean Institute of Oceanography, Aix-Marseille Université, Marseille, France
| | - François-Xavier Merlin
- Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des Eaux, Brest, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et des Pays de l’Adour, Pau, France
- * E-mail:
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McGenity TJ, Folwell BD, McKew BA, Sanni GO. Marine crude-oil biodegradation: a central role for interspecies interactions. AQUATIC BIOSYSTEMS 2012; 8:10. [PMID: 22591596 PMCID: PMC3465203 DOI: 10.1186/2046-9063-8-10] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/25/2012] [Indexed: 05/11/2023]
Abstract
The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.
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Affiliation(s)
- Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Benjamin D Folwell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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