1
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Diver P, Ward BA, Cunliffe M. Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean. FEMS Microbiol Ecol 2024:fiae053. [PMID: 38599628 DOI: 10.1093/femsec/fiae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
Yeasts are prevalent in the open ocean, yet we have limited understanding of their ecophysiological adaptations, including their response to nitrogen availability, which can have a major role in determining the ecological potential of other planktonic microbes. In this study, we characterised the nitrogen uptake capabilities and growth responses of marine-occurring yeasts. Yeast isolates from the North Atlantic Ocean were screened for growth on diverse nitrogen substrates, and across a concentration gradient of three environmentally relevant nitrogen substrates: nitrate, ammonium, and urea. Three strains grew with enriched nitrate while two did not, demonstrating that nitrate utilisation is present but not universal in marine yeasts, consistent with existing knowledge of non-marine yeast strains. Naganishia diffluens MBA_F0213 modified the key functional trait of cell size in response to nitrogen concentration, suggesting yeast cell morphology changes along chemical gradients in the marine environment. Meta-analysis of the reference DNA barcode in public databases revealed that the genus Naganishia has a global ocean distribution, strengthening the environmental applicability of the culture-based observations. This study provides novel quantitative understanding of the ecophysiological and morphological responses of marine-derived yeasts to variable nitrogen availability in vitro, providing insight into the functional ecology of yeasts within pelagic open ocean environments.
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Affiliation(s)
- Poppy Diver
- Marine Biological Association, Plymouth, UK
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Ben A Ward
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Michael Cunliffe
- Marine Biological Association, Plymouth, UK
- School of Biological and Marine Sciences, University Plymouth, Plymouth, UK
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2
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Chrismas N, Tindall-Jones B, Jenkins H, Harley J, Bird K, Cunliffe M. Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea. New Phytol 2024; 241:2243-2257. [PMID: 37840369 DOI: 10.1111/nph.19320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023]
Abstract
Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two-way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater. Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration. Sugar-based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant-derived carbon in ectomycorrhizal symbioses.
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Affiliation(s)
- Nathan Chrismas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Beth Tindall-Jones
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Helen Jenkins
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Joanna Harley
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Kimberley Bird
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
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3
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Branscombe L, Harrison EL, Choong ZYD, Swink C, Keys M, Widdicombe C, Wilson WH, Cunliffe M, Helliwell K. Cryptic bacterial pathogens of diatoms peak during senescence of a winter diatom bloom. New Phytol 2024; 241:1292-1307. [PMID: 38037269 DOI: 10.1111/nph.19441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023]
Abstract
Diatoms are globally abundant microalgae that form extensive blooms in aquatic ecosystems. Certain bacteria behave antagonistically towards diatoms, killing or inhibiting their growth. Despite their crucial implications to diatom blooms and population health, knowledge of diatom antagonists in the environment is fundamentally lacking. We report systematic characterisation of the diversity and seasonal dynamics of bacterial antagonists of diatoms via plaque assay sampling in the Western English Channel (WEC), where diatoms frequently bloom. Unexpectedly, peaks in detection did not occur during characteristic spring diatom blooms, but coincided with a winter bloom of Coscinodiscus, suggesting that these bacteria likely influence distinct diatom host populations. We isolated multiple bacterial antagonists, spanning 4 classes and 10 bacterial orders. Notably, a diatom attaching Roseobacter Ponticoccus alexandrii was isolated multiple times, indicative of a persistent environmental presence. Moreover, many isolates had no prior reports of antagonistic activity towards diatoms. We verified diatom growth inhibitory effects of eight isolates. In all cases tested, these effects were activated by pre-exposure to diatom organic matter. Discovery of widespread 'cryptic' antagonistic activity indicates that bacterial pathogenicity towards diatoms is more prevalent than previously recognised. Finally, examination of the global biogeography of WEC antagonists revealed co-occurrence patterns with diatom host populations in marine waters globally.
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Affiliation(s)
- Laura Branscombe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Ellen L Harrison
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Zhi Yi Daniel Choong
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Courtney Swink
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Matthew Keys
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | | | - William H Wilson
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Michael Cunliffe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Katherine Helliwell
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
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4
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Timmis K, Berry D, Bonfante P, Coleman M, Cunliffe M, Danchin A, Galperin M, Huang W, Lopez P, Stewart F, Wood T. Juan Luis Ramos: An exceptional Editor of Environmental Microbiology. Environ Microbiol 2023; 25:595-596. [PMID: 36533904 DOI: 10.1111/1462-2920.16315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - David Berry
- Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Maureen Coleman
- Department of the Geophysical Sciences, University of Chicago, Illinois, USA
| | | | - Antoine Danchin
- Department of Infection, Immunity and Inflammation, Institut Cochin, Paris, France
| | - Michael Galperin
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Wei Huang
- Department of Engineering Science, University of Oxford, UK
| | - Puri Lopez
- Ecologie Systématique Evolution, UMR 8079 CNRS & Université Paris-Saclay, Orsay, France
| | | | - Tom Wood
- Departments of Chemical Engineering & Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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5
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Chrismas N, Allen R, Allen MJ, Bird K, Cunliffe M. A 17-year time-series of fungal environmental DNA from a coastal marine ecosystem reveals long-term seasonal-scale and inter-annual diversity patterns. Proc Biol Sci 2023; 290:20222129. [PMID: 36722076 PMCID: PMC9890122 DOI: 10.1098/rspb.2022.2129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Changing patterns in diversity are a feature of many habitats, with seasonality a major driver of ecosystem structure and function. In coastal marine plankton-based ecosystems, seasonality has been established through long-term time-series of bacterioplankton and protists. Alongside these groups, fungi also inhabit coastal marine ecosystems. If and how marine fungi show long-term intra- and inter-annual diversity patterns is unknown, preventing a comprehensive understanding of marine fungal ecology. Here, we use a 17-year environmental DNA time-series from the English Channel to determine long-term marine fungal diversity patterns. We show that fungal community structure progresses at seasonal and monthly scales and is only weakly related to environmental parameters. Communities restructured every 52-weeks suggesting long-term stability in diversity patterns. Some major marine fungal genera have clear inter-annual recurrence patterns, re-appearing in the annual cycle at the same period. Low relative abundance taxa that are likely non-marine show seasonal input to the coastal marine ecosystem suggesting land-sea exchange regularly takes place. Our results demonstrate long-term intra- and inter-annual marine fungal diversity patterns. We anticipate this study could form the basis for better understanding the ecology of marine fungi and how they fit in the structure and function of the wider coastal marine ecosystem.
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Affiliation(s)
- Nathan Chrismas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Ro Allen
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Michael J. Allen
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4PY, UK,Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Kimberley Bird
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
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6
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Affiliation(s)
- Michael Cunliffe
- Marine Biological Association, Plymouth, UK.,School of Biological and Marine Sciences, University Plymouth, Plymouth, UK
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7
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Cunliffe M. Evidencing the value of artist-led mental health projects. Perspect Public Health 2022; 142:309-311. [PMID: 36458492 DOI: 10.1177/17579139221103938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- M Cunliffe
- Artistic Coordinator, North Tyneside Art Studio, North Shields NE30 2AY, UK
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8
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Bonthond G, Barilo A, Allen RJ, Cunliffe M, Krueger-Hadfield SA. Fungal endophytes vary by species, tissue type, and life cycle stage in intertidal macroalgae. J Phycol 2022; 58:330-342. [PMID: 35090190 DOI: 10.1111/jpy.13237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Fungal symbionts of terrestrial plants are among the most widespread and well-studied symbioses, relatively little is known about fungi that are associated with macroalgae. To fill the gap in marine fungal taxonomy, we combined simple culture methods with amplicon sequencing to characterize the fungal communities associated with three brown (Sargassum muticum, Pelvetia canaliculata, and Himanthalia elongata) and two red (Mastocarpus stellatus and Chondrus crispus) macroalgae from one intertidal zone. In addition to characterizing novel fungal diversity, we tested three hypotheses: fungal diversity and community composition vary (i) among species distributed at different tidal heights, (ii) among tissue types (apices, mid-thallus, and stipe), and (iii) among "isomorphic" C. crispus life cycle stages. Almost 70% of our reads were classified as Ascomycota, 29% as Basidiomycota, and 1% that could not be classified to a phylum. Thirty fungal isolates were obtained, 18 of which were also detected with amplicon sequencing. Fungal communities differed by host and tissue type. Interestingly, P. canaliculata, a fucoid at the extreme high intertidal, did not show differences in fungal diversity across the thallus. As found in filamentous algal endophytes, fungal diversity varied among the three life cycle stages in C. crispus. Female gametophytes were also compositionally more dispersed as compared to the fewer variable tetrasporophytes and male gametophytes. We demonstrate the utility of combining relatively simple cultivation and sequencing approaches to characterize and study macroalgal-fungal associations and highlight the need to understand the role of fungi in near-shore marine ecosystems.
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Affiliation(s)
- Guido Bonthond
- Institute for Chemistry and Biology of the Marine environment (ICBM), Carl-von-Ossietzky University Oldenburg, Schleusenstrasse 1, Wilhelmshaven, 26382, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, Kiel, 24105, Germany
| | - Anastasiia Barilo
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Ro J Allen
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, Alabama, 35294, USA
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9
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Laundon D, Chrismas N, Bird K, Thomas S, Mock T, Cunliffe M. A cellular and molecular atlas reveals the basis of chytrid development. eLife 2022; 11:73933. [PMID: 35227375 PMCID: PMC8887899 DOI: 10.7554/elife.73933] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/01/2022] [Indexed: 12/26/2022] Open
Abstract
The chytrids (phylum Chytridiomycota) are a major fungal lineage of ecological and evolutionary importance. Despite their importance, many fundamental aspects of chytrid developmental and cell biology remain poorly understood. To address these knowledge gaps, we combined quantitative volume electron microscopy and comparative transcriptome profiling to create an 'atlas' of the cellular and molecular basis of the chytrid life cycle, using the model chytrid Rhizoclosmatium globosum. From our developmental atlas, we describe the transition from the transcriptionally inactive free-swimming zoospore to the more biologically complex germling, and show that lipid processing is multifaceted and dynamic throughout the life cycle. We demonstrate that the chytrid apophysis is a compartmentalised site of high intracellular trafficking, linking the feeding/attaching rhizoids to the reproductive zoosporangium, and constituting division of labour in the chytrid cell plan. We provide evidence that during zoosporogenesis, zoospores display amoeboid morphologies and exhibit endocytotic cargo transport from the interstitial maternal cytoplasm. Taken together, our results reveal insights into chytrid developmental biology and provide a basis for future investigations into non-dikaryan fungal cell biology.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom.,School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Nathan Chrismas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Kimberley Bird
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Seth Thomas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
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10
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Thomas S, Lengger SK, Bird KE, Allen R, Cunliffe M. Macromolecular composition and substrate range of three marine fungi across major cell types. FEMS Microbes 2022; 3:xtab019. [PMID: 37332499 PMCID: PMC10117802 DOI: 10.1093/femsmc/xtab019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/25/2021] [Indexed: 08/12/2023] Open
Abstract
Marine fungi exist as three major cell types: unicellular yeasts, filamentous hyphae and zoosporic early-diverging forms, such as the Chytridiomycota (chytrids). To begin to understand the ecological and biogeochemical influence of these cell types within the wider context of other plankton groups, cell size and macromolecular composition must be assessed across all three cell types. Using a mass-balance approach to culture, we describe quantitative differences in substrate uptake and subsequent macromolecular distribution in three model marine fungi: the yeast Metschnikowia zobellii, the filamentous Epicoccum nigrum and chytrid Rhizophydium littoreum. We compared these model cell types with select oleaginous phytoplankton of specific biotechnological interest through metanalysis. We hypothesise that fungal cell types will maintain a significantly different macromolecular composition to one another and further represent an alternative grazing material to bacterioplankton and phytoplankton for higher trophic levels. Assessment of carbon substrate range and utilisation using phenotype arrays suggests that marine fungi have a wide substrate range. Fungi also process organic matter to an elevated-lipid macromolecular composition with reduced-protein content. Because of their size and increased lipid composition compared to other plankton groups, we propose that fungi represent a compositionally distinct, energy-rich grazing resource in marine ecosystems. We propose that marine fungi could act as vectors of organic matter transfer across trophic boundaries, and supplement our existing understanding of the microbial loop and carbon transfer in marine ecosystems.
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Affiliation(s)
- Seth Thomas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Sabine K Lengger
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Kimberley E Bird
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Ro Allen
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
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11
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Abstract
The phylum Chytridiomycota (the "chytrids") is an early-diverging, mostly unicellular, lineage of fungi that consists of significant aquatic saprotrophs, parasites, and pathogens, and is of evolutionary interest because its members retain biological traits considered ancestral in the fungal kingdom. While the existence of aquatic chytrids has long been known, their fundamental biology has received relatively little attention. We are beginning to establish a detailed understanding of aquatic chytrid diversity and insights into their ecological functions and prominence. However, the underpinning biology governing their aquatic ecological activities and associated core processes remain largely understudied and therefore unresolved. Many biological questions are outstanding for aquatic chytrids. What are the mechanisms that control their development and life cycle? Which core processes underpin their aquatic influence? What can their biology tell us about the evolution of fungi and the wider eukaryotic tree of life? We propose that the field of aquatic chytrid ecology could be further advanced through the improved understanding of chytrid biology, including the development of model aquatic chytrids and targeted studies using culture-independent approaches.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
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12
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Abstract
Microbial colonization and degradation of particulate organic matter (POM) are important processes that influence the structure and function of aquatic ecosystems. Although POM is readily used by aquatic fungi and bacteria, there is a limited understanding of POM-associated interactions between these taxa, particularly for early-diverging fungal lineages. Using a model ecological system with the chitin-degrading freshwater chytrid fungus Rhizoclosmatium globosum and chitin microbeads, we assessed the impacts of chytrid fungi on POM-associated bacteria. We show that the presence of chytrids on POM alters concomitant bacterial community diversity and structure, including differing responses between chytrid life stages. We propose that chytrids can act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from POM degradation that modify bacterial POM communities. This study suggests that chytrid fungi have complex ecological roles in aquatic POM degradation not previously considered, including the regulation of bacterial colonization, community succession and subsequent biogeochemical potential.
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Affiliation(s)
- Cordelia Roberts
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Ro Allen
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Kimberley E Bird
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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13
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Laundon D, Chrismas N, Wheeler G, Cunliffe M. Chytrid rhizoid morphogenesis resembles hyphal development in multicellular fungi and is adaptive to resource availability. Proc Biol Sci 2020; 287:20200433. [PMID: 32517626 PMCID: PMC7341943 DOI: 10.1098/rspb.2020.0433] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Key to the ecological prominence of fungi is their distinctive cell biology, our understanding of which has been principally based on dikaryan hyphal and yeast forms. The early-diverging Chytridiomycota (chytrids) are ecologically important and a significant component of fungal diversity, yet their cell biology remains poorly understood. Unlike dikaryan hyphae, chytrids typically attach to substrates and feed osmotrophically via anucleate rhizoids. The evolution of fungal hyphae appears to have occurred from rhizoid-bearing lineages and it has been hypothesized that a rhizoid-like structure was the precursor to multicellular hyphae. Here, we show in a unicellular chytrid, Rhizoclosmatium globosum, that rhizoid development exhibits striking similarities with dikaryan hyphae and is adaptive to resource availability. Rhizoid morphogenesis exhibits analogous patterns to hyphal growth and is controlled by β-glucan-dependent cell wall synthesis and actin polymerization. Chytrid rhizoids growing from individual cells also demonstrate adaptive morphological plasticity in response to resource availability, developing a searching phenotype when carbon starved and spatial differentiation when interacting with particulate organic matter. We demonstrate that the adaptive cell biology and associated developmental plasticity considered characteristic of hyphal fungi are shared more widely across the Kingdom Fungi and therefore could be conserved from their most recent common ancestor.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Nathan Chrismas
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Geographical Sciences, University of Bristol, Bristol, UK
| | - Glen Wheeler
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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14
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Chrismas N, Cunliffe M. Depth-dependent mycoplankton glycoside hydrolase gene activity in the open ocean-evidence from the Tara Oceans eukaryote metatranscriptomes. ISME J 2020; 14:2361-2365. [PMID: 32494052 PMCID: PMC7608184 DOI: 10.1038/s41396-020-0687-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/09/2022]
Abstract
Mycoplankton are widespread components of marine ecosystems, yet the full extent of their functional role remains poorly known. Marine mycoplankton are likely functionally analogous to their terrestrial counterparts, including performing saprotrophy and degrading high-molecular weight organic substrates using carbohydrate-active enzymes (CAZymes). We investigated the prevalence of transcribed oceanic fungal CAZyme genes using the Marine Atlas of Tara Ocean Unigenes database. We revealed an abundance of unique transcribed fungal glycoside hydrolases in the open ocean, including a particularly high number that act upon cellulose in surface waters and the deep chlorophyll maximum (DCM). A variety of other glycoside hydrolases acting on a range of biogeochemically important polysaccharides including β-glucans and chitin were also found. This analysis demonstrates that mycoplankton are active saprotrophs in the open ocean and paves the way for future research into the depth-dependent roles of marine fungi in oceanic carbon cycling, including the biological carbon pump.
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Affiliation(s)
- Nathan Chrismas
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK. .,School of Geographical Sciences, University of Bristol, University Road, Bristol, UK.
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK. .,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK.
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15
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Dale H, Solan M, Lam P, Cunliffe M. Sediment microbial assemblage structure is modified by marine polychaete gut passage. FEMS Microbiol Ecol 2019; 95:5426820. [DOI: 10.1093/femsec/fiz047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/02/2019] [Indexed: 01/13/2023] Open
Affiliation(s)
- Harriet Dale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Martin Solan
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Marine Biology and Ecology Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS. Fungi in the Marine Environment: Open Questions and Unsolved Problems. mBio 2019; 10:e01189-18. [PMID: 30837337 PMCID: PMC6401481 DOI: 10.1128/mbio.01189-18] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.
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Affiliation(s)
- Anthony Amend
- Department of Botany, University of Hawai'i at Manoa, Honolulu, Hawaii, USA
| | - Gaetan Burgaud
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | | | - M H Gutiérrez
- Departamento de Oceanografía, Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Erik F Y Hom
- Department of Biology, University of Mississippi, Oxford, Mississippi, USA
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, USA
| | - Maiko Kagami
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan
| | - Kathryn T Picard
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C Alisha Quandt
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | | | - Mertixell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Jason Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - José Vargas-Muñiz
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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17
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Laundon D, Wheeler G, Mock T, Cunliffe M. Shining new lights on chytrid cell biology: quantitative live cell imaging of rhizoid development in an early-diverging fungus. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Davis Laundon
- 1The Marine Biological Association, Plymouth, United Kingdom
- 2University of East Anglia, Norwich, United Kingdom
| | - Glen Wheeler
- 1The Marine Biological Association, Plymouth, United Kingdom
| | - Thomas Mock
- 2University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- 3Plymouth University, Plymouth, United Kingdom
- 1The Marine Biological Association, Plymouth, United Kingdom
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18
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Chrismas N, Cunliffe M. Marine fungal dark matter in the global ocean. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nathan Chrismas
- Marine Biological Association of the UK, Plymouth, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association of the UK, Plymouth, United Kingdom
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19
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Dale H, Taylor JD, Solan M, Lam P, Cunliffe M. Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups. FEMS Microbiol Ecol 2018; 95:5247715. [DOI: 10.1093/femsec/fiy234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Harriet Dale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Joe D Taylor
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford, M5 4WT, UK
| | - Martin Solan
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Marine Biology and Ecology Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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20
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Zäncker B, Cunliffe M, Engel A. Bacterial Community Composition in the Sea Surface Microlayer Off the Peruvian Coast. Front Microbiol 2018; 9:2699. [PMID: 30498480 PMCID: PMC6249803 DOI: 10.3389/fmicb.2018.02699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/23/2018] [Indexed: 02/01/2023] Open
Abstract
The sea surface microlayer (SML) is located at the air-sea interface, with microorganisms and organic matter in the SML influencing air-sea exchange processes. Yet understanding of the SML bacterial (bacterioneuston) community composition and assembly remains limited. Availability of organic matter, UV radiation and wind speed have previously been suggested to influence the community composition of bacterioneuston. Another mechanism potentially controlling bacterioneuston dynamics is bacterioplankton attached to gel-like particles that ascend through the water column into the SML. We analyzed the bacterial community composition, Transparent Exopolymer Particles (TEP) abundance and nutrient concentrations in the surface waters of the Peruvian upwelling region. The bacterioneuston and bacterioplankton communities were similar, suggesting a close spatial coupling. Four Bacteroidetes families were significantly enriched in the SML, two of them, the Flavobacteriaceae and Cryomorphaceae, were found to comprise the majority of SML-enriched operational taxonomic units (OTUs). The enrichment of these families was controlled by a variety of environmental factors. The SML-enriched bacterial families were negatively correlated with water temperature and wind speed in the SML and positively correlated with nutrient concentrations, salinity and TEP in the underlying water (ULW). The correlations with nutrient concentrations and salinity suggest that the enriched bacterial families were more abundant at the upwelling stations.
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Affiliation(s)
- Birthe Zäncker
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, Plymouth, United Kingdom.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Plymouth, United Kingdom
| | - Anja Engel
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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21
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Taylor JD, Bird KE, Widdicome CE, Cunliffe M. Active bacterioplankton community response to dissolved 'free' deoxyribonucleic acid (dDNA) in surface coastal marine waters. FEMS Microbiol Ecol 2018; 94:5053802. [PMID: 30010743 DOI: 10.1093/femsec/fiy132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/10/2018] [Indexed: 11/14/2022] Open
Abstract
Seawater contains dissolved 'free' DNA (dDNA) that is part of a larger <0.2 µm pool of DNA (D-DNA) including viruses and uncharacterised bound DNA. Previous studies have shown that bacterioplankton readily degrade dDNA, and culture-based approaches have identified several potential dDNA-utilising taxa. This study characterised the seasonal variation in D-DNA concentrations at Station L4, a coastal marine observatory in the Western English Channel, and linked changes in concentration to cognate physicochemical and biological factors. The impact of dDNA addition on active bacterioplankton communities at Station L4 was then determined using 16S rRNA high-throughput sequencing and RNA Stable Isotope Probing (RNA SIP) with 13C-labelled diatom-derived dDNA. Compared to other major bacterioplankton orders, the Rhodobacterales actively responded to dDNA additions in amended microcosms and RNA SIP identified two Rhodobacterales populations most closely associated with the genera Halocynthiibacter and Sulfitobacter that assimilated the 13C-labelled dDNA. Here we demonstrate that dDNA is a source of dissolved organic carbon for some members of the major bacterioplankton group the Marine Roseobacter Clade. This study enhances our understanding of roles of specific bacterioplankton taxa in dissolved organic matter cycling in coastal waters with potential implications for nitrogen and phosphorus regeneration processes.
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Kimberley E Bird
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth, UK
| | | | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth, UK
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22
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Wurl O, Bird K, Cunliffe M, Landing WM, Miller U, Mustaffa NIH, Ribas‐Ribas M, Witte C, Zappa CJ. Warming and Inhibition of Salinization at the Ocean's Surface by Cyanobacteria. Geophys Res Lett 2018; 45:4230-4237. [PMID: 29937608 PMCID: PMC6001423 DOI: 10.1029/2018gl077946] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
This paper describes high-resolution in situ observations of temperature and, for the first time, of salinity in the uppermost skin layer of the ocean, including the influence of large surface blooms of cyanobacteria on those skin properties. In the presence of the blooms, large anomalies of skin temperature and salinity of 0.95°C and -0.49 practical salinity unit were found, but a substantially cooler (-0.22°C) and saltier skin layer (0.19 practical salinity unit) was found in the absence of surface blooms. The results suggest that biologically controlled warming and inhibition of salinization of the ocean's surface occur. Less saline skin layers form during precipitation, but our observations also show that surface blooms of Trichodesmium sp. inhibit evaporation decreasing the salinity at the ocean's surface. This study has important implications in the assessment of precipitation over the ocean using remotely sensed salinity, but also for a better understanding of heat exchange and the hydrologic cycle on a regional scale.
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Affiliation(s)
- O. Wurl
- Institute for Chemistry and Biology of the Marine EnvironmentCarl von Ossietzky University OldenburgWilhelmshavenGermany
| | - K. Bird
- Marine Biological Association of the United KingdomPlymouthUK
| | - M. Cunliffe
- Marine Biological Association of the United KingdomPlymouthUK
- Marine Biology and Ecology Research Centre, School of Biological and Marine SciencesPlymouth University, Drake CircusPlymouthUK
| | - W. M. Landing
- Department of Earth, Ocean, and Atmospheric ScienceFlorida State UniversityTallahasseeFLUSA
| | - U. Miller
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNYUSA
| | - N. I. H. Mustaffa
- Institute for Chemistry and Biology of the Marine EnvironmentCarl von Ossietzky University OldenburgWilhelmshavenGermany
| | - M. Ribas‐Ribas
- Institute for Chemistry and Biology of the Marine EnvironmentCarl von Ossietzky University OldenburgWilhelmshavenGermany
| | - C. Witte
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNYUSA
| | - C. J. Zappa
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNYUSA
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23
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Smale DA, Taylor JD, Coombs SH, Moore G, Cunliffe M. Community responses to seawater warming are conserved across diverse biological groupings and taxonomic resolutions. Proc Biol Sci 2018; 284:rspb.2017.0534. [PMID: 28878056 PMCID: PMC5597821 DOI: 10.1098/rspb.2017.0534] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/28/2017] [Indexed: 02/01/2023] Open
Abstract
Temperature variability is a major driver of ecological pattern, with recent changes in average and extreme temperatures having significant impacts on populations, communities and ecosystems. In the marine realm, very few experiments have manipulated temperature in situ, and current understanding of temperature effects on community dynamics is limited. We developed new technology for precise seawater temperature control to examine warming effects on communities of bacteria, microbial eukaryotes (protists) and metazoans. Despite highly contrasting phylogenies, size spectra and diversity levels, the three community types responded similarly to seawater warming treatments of +3°C and +5°C, highlighting the critical and overarching importance of temperature in structuring communities. Temperature effects were detectable at coarse taxonomic resolutions and many taxa responded positively to warming, leading to increased abundances at the community-level. Novel field-based experimental approaches are essential to improve mechanistic understanding of how ocean warming will alter the structure and functioning of diverse marine communities.
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Affiliation(s)
- Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Steve H Coombs
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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24
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25
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Taylor JD, Cunliffe M. Coastal bacterioplankton community response to diatom-derived polysaccharide microgels. Environ Microbiol Rep 2017; 9:151-157. [PMID: 27943607 DOI: 10.1111/1758-2229.12513] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Phytoplankton-derived polysaccharide microgels, including transparent exopolymer particles (TEP), are a major component of the marine organic carbon pool. Previous studies have made correlative links between phytoplankton material and bacterioplankton, and performed experiments that assess general responses to phytoplankton, yet there is a lack of direct empirical evidence of specific bacterioplankton responses to natural phytoplankton polysaccharide microgels. In this study, we used diatom produced TEP in controlled incubation experiments to determine the impact of polysaccharide microgels on a coastal bacterioplankton community. Quantification of bacterial 16S rRNA gene transcripts showed that the addition of TEP caused an increase in bacterioplankton activity. Similarly, high-throughput sequencing of RT-PCR amplified bacterial 16S rRNA gene transcripts showed that active bacterioplankton community structure and diversity also changed in response to microgels. Alteromonadales and Rhodobacterales increased in abundance in response to TEP, suggesting that both bacterioplankton taxa utilize diatom-derived microgels. However, through assessing 13 C-labelled TEP uptake via RNA Stable Isotope Probing, we show that only the Alteromonadales (genus Alteromonas) assimilated the TEP carbon. This study adds utilization of diatom-derived TEP to the metabolic repertoire of the archetypal copiotrophic bacterioplankton Alteromonas, and indicates that the Rhodobacterales may utilize TEP for other purposes (e.g. attachment sites).
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Plymouth, UK
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26
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Taylor JD, Cunliffe M. Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance. ISME J 2016; 10:2118-28. [PMID: 26943623 PMCID: PMC4989315 DOI: 10.1038/ismej.2016.24] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 01/07/2016] [Accepted: 01/21/2016] [Indexed: 11/09/2022]
Abstract
Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services.
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
- Marine Biology and Ecology Research Centre, Marine Institute, Plymouth University, Plymouth, UK
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27
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Cunliffe M. Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3. FEMS Microbiol Ecol 2015; 92:fiv150. [PMID: 26613749 DOI: 10.1093/femsec/fiv150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 11/13/2022] Open
Abstract
Purines are nitrogen-rich compounds that are widely distributed in the marine environment and are an important component of the dissolved organic nitrogen (DON) pool. Even though purines have been shown to be degraded by bacterioplankton, the identities of marine bacteria capable of purine degradation and their underlying catabolic mechanisms are currently unknown. This study shows that Ruegeria pomeroyi, a model marine bacterium and Marine Roseobacter Clade (MRC) representative, utilizes xanthine as a source of carbon and nitrogen. The R. pomeroyi genome contains putative genes that encode xanthine dehydrogenase (XDH), which is expressed during growth with xanthine. RNAseq-based analysis of the R. pomeroyi transcriptome revealed that the transcription of an XDH-initiated catabolic pathway is up-regulated during growth with xanthine, with transcription greatest when xanthine was the only available carbon source. The RNAseq-deduced pathway indicates that glyoxylate and ammonia are the key intermediates from xanthine degradation. Utilising a laboratory model, this study has identified the potential genes and catabolic pathway active during xanthine degradation. The ability of R. pomeroyi to utilize xanthine provides novel insights into the capabilities of the MRC that may contribute to their success in marine ecosystems and the potential biogeochemical importance of the group in processing DON.
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Affiliation(s)
- Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK Marine Biology and Ecology Research Centre, Marine Institute, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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Taylor JD, Cunliffe M. Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments. Environ Microbiol Rep 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Taylor JD, Cunliffe M. High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters. J Phycol 2014; 50:960-965. [PMID: 26988649 DOI: 10.1111/jpy.12228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 07/02/2014] [Indexed: 06/05/2023]
Abstract
Neustonic organisms inhabit the sea surface microlayer (SML) and have important roles in marine ecosystem functioning. Here, we use high-throughput 18S rRNA gene sequencing to characterize protist and fungal diversity in the SML at a coastal time-series station and compare with underlying plankton assemblages. Protist diversity was higher in February (pre-bloom) compared to April (spring bloom), and was lower in the neuston than in the plankton. Major protist groups, including Stramenopiles and Alveolata, dominated both neuston and plankton assemblages. Chrysophytes and diatoms were enriched in the neuston in April, with diatoms showing distinct changes in community composition between the sampling periods. Pezizomycetes dominated planktonic fungi assemblages, whereas fungal diversity in the neuston was more varied. This is the first study to utilize a molecular-based approach to characterize neustonic protist and fungal assemblages, and provides the most comprehensive diversity assessment to date of this ecosystem. Variability in the SML microeukaryote assemblage structure has potential implications for biogeochemical and food web processes at the air-sea interface.
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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
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30
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Taylor JD, Ellis R, Milazzo M, Hall-Spencer JM, Cunliffe M. Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient. FEMS Microbiol Ecol 2014; 89:670-8. [PMID: 24939799 DOI: 10.1111/1574-6941.12368] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/30/2014] [Accepted: 06/10/2014] [Indexed: 01/13/2023] Open
Abstract
Intertidal epilithic bacteria communities are important components of coastal ecosystems, yet few studies have assessed their diversity and how it may be affected by changing environmental parameters. Submarine CO2 seeps produce localised areas of CO2-enriched seawater with reduced pH levels. We utilised the seawater pH/CO2 gradient at Levante Bay (Italy) to test the hypothesis that epilithic bacteria communities are modified by exposure to seawater with the varying chemical parameters. Biofilms were sampled from three sites exposed to seawater with different pH/CO2 levels and diversity determined using high-throughput sequencing of 16S rRNA genes. Seawater pCO2 concentrations were increased from ambient at site 1 to 621 μatm at site 2 and 1654 μatm site 3, similar to the predicated future oceans beyond 2050 and 2150, respectively. Alpha diversity of total bacteria communities and Cyanobacteria communities was significantly different between sites (anova P < 0.05). Comparison between sites showed that bacteria communities and Cyanobacteria communities were significantly different (anosim P < 0.01; permanova P < 0.01). Proteobacteria, Bacteroidetes and Cyanobacteria dominated all communities; however, there were differences between sites in the relative abundance of specific orders. This study provides the most detailed assessment of intertidal epilithic bacteria diversity and shows that diversity is significantly different along a seawater pH/CO2 gradient. This information supports the evaluation of the impacts of future ocean acidification on coastal marine ecosystems.
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
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31
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Brodie J, Williamson CJ, Smale DA, Kamenos NA, Mieszkowska N, Santos R, Cunliffe M, Steinke M, Yesson C, Anderson KM, Asnaghi V, Brownlee C, Burdett HL, Burrows MT, Collins S, Donohue PJC, Harvey B, Foggo A, Noisette F, Nunes J, Ragazzola F, Raven JA, Schmidt DN, Suggett D, Teichberg M, Hall-Spencer JM. The future of the northeast Atlantic benthic flora in a high CO2 world. Ecol Evol 2014; 4:2787-98. [PMID: 25077027 PMCID: PMC4113300 DOI: 10.1002/ece3.1105] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/15/2014] [Accepted: 04/22/2014] [Indexed: 01/01/2023] Open
Abstract
Seaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will remove maerl habitat in the north. Seagrasses will proliferate, and associated epiphytes switch from calcified algae to diatoms and filamentous species. Invasive species will thrive in niches liberated by loss of native species and spread via exponential development of artificial marine structures. Combined impacts of seawater warming, ocean acidification, and increased storminess may replace structurally diverse seaweed canopies, with associated calcified and noncalcified flora, with simple habitats dominated by noncalcified, turf-forming seaweeds.
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Affiliation(s)
- Juliet Brodie
- Department of Life Sciences, The Natural History MuseumCromwell Road, London, SW7 5BD, UK
| | - Christopher J Williamson
- Department of Life Sciences, The Natural History MuseumCromwell Road, London, SW7 5BD, UK
- School of Earth and Ocean Sciences, Cardiff UniversityMain Building, Park Place, Cardiff, CF10 3YE, UK
| | - Dan A Smale
- Marine Biological Association of the UKCitadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, National Oceanography Centre, University of SouthamptonWaterfront Campus, European Way, Southampton, SO14 3ZH, UK
| | - Nicholas A Kamenos
- School of Geographical and Earth Sciences, University of GlasgowGlasgow, G12 8QQ, UK
| | - Nova Mieszkowska
- Marine Biological Association of the UKCitadel Hill, Plymouth, PL1 2PB, UK
| | - Rui Santos
- Marine Plant Ecology Research Group (ALGAE), Centre of Marine Sciences (CCMAR), University of AlgarveCampus of Gambelas, Faro, 8005-139, Portugal
| | - Michael Cunliffe
- Marine Biological Association of the UKCitadel Hill, Plymouth, PL1 2PB, UK
| | - Michael Steinke
- School of Biological Sciences, University of EssexColchester, CO4 3SQ, UK
| | - Christopher Yesson
- Department of Life Sciences, The Natural History MuseumCromwell Road, London, SW7 5BD, UK
- Institute of Zoology, Zoological Society of LondonRegent's Park, London, NW1 4RY, UK
| | - Kathryn M Anderson
- Department of Zoology, The University of British Columbia#4200-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Colin Brownlee
- Marine Biological Association of the UKCitadel Hill, Plymouth, PL1 2PB, UK
| | - Heidi L Burdett
- Department of Earth and Environmental Sciences, University of St AndrewsSt Andrews, Fife, KY16 9AL, UK
- Scottish Oceans Institute, University of St AndrewsSt Andrews, Fife, KY16 8LB, UK
| | | | - Sinead Collins
- Institute of Evolutionary Biology, University of EdinburghThe King's Building, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Penelope J C Donohue
- School of Geographical and Earth Sciences, University of GlasgowGlasgow, G12 8QQ, UK
| | - Ben Harvey
- Institute of Biology, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Andrew Foggo
- Marine Biology and Ecology Research Centre, School of Marine Sciences and Engineering, Plymouth UniversityPL4 8AA, UK
| | - Fanny Noisette
- CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff Cedex, 29688, France
- UPMC Univ. Paris 6, UMR 7144Station Biologique de Roscoff, Place Georges Teissier, Roscoff Cedex, 29688, France
| | - Joana Nunes
- Plymouth Marine LaboratoryProspect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Federica Ragazzola
- School of Earth Sciences, University of BristolWills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneyUltimo, NSW 2007, Australia
| | - Daniela N Schmidt
- School of Earth Sciences, University of BristolWills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
| | - David Suggett
- School of Biological Sciences, University of EssexColchester, CO4 3SQ, UK
| | - Mirta Teichberg
- Leibniz-Zentrum für Marine TropenökologieFahrenheitstraße 6, Bremen, D-28359, Germany
| | - Jason M Hall-Spencer
- Marine Biology and Ecology Research Centre, School of Marine Sciences and Engineering, Plymouth UniversityPL4 8AA, UK
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32
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Kadar E, Cunliffe M, Fisher A, Stolpe B, Lead J, Shi Z. Chemical interaction of atmospheric mineral dust-derived nanoparticles with natural seawater--EPS and sunlight-mediated changes. Sci Total Environ 2014; 468-469:265-271. [PMID: 24035844 DOI: 10.1016/j.scitotenv.2013.08.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/16/2013] [Accepted: 08/17/2013] [Indexed: 06/02/2023]
Abstract
Laboratory studies were conducted to investigate the interactions of nanoparticles (NPs) formed via simulated cloud processing of mineral dust with seawater under environmentally relevant conditions. The effect of sunlight and the presence of exopolymeric substances (EPS) were assessed on the: (1) colloidal stability of the nanoparticle aggregates (i.e. size distribution, zeta potential, polydispersity); (2) micromorphology and (3) Fe dissolution from particles. We have demonstrated that: (i) synthetic nano-ferrihydrite has distinct aggregation behaviour from NPs formed from mineral dusts in that the average hydrodynamic diameter remained unaltered upon dispersion in seawater (~1500 nm), whilst all dust derived NPs increased about three fold in aggregate size; (ii) relatively stable and monodisperse aggregates of NPs formed during simulated cloud processing of mineral dust become more polydisperse and unstable in contact with seawater; (iii) EPS forms stable aggregates with both the ferrihydrite and the dust derived NPs whose hydrodynamic diameter remains unchanged in seawater over 24h; (iv) dissolved Fe concentration from NPs, measured here as <3 kDa filter-fraction, is consistently >30% higher in seawater in the presence of EPS and the effect is even more pronounced in the absence of light; (v) micromorphology of nanoparticles from mineral dusts closely resemble that of synthetic ferrihydrite in MQ water, but in seawater with EPS they form less compact aggregates, highly variable in size, possibly due to EPS-mediated steric and electrostatic interactions. The larger scale implications on real systems of the EPS solubilising effect on Fe and other metals with the additional enhancement of colloidal stability of the resulting aggregates are discussed.
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Affiliation(s)
- Enikö Kadar
- Plymouth Marine Laboratory, Prospect Place, the Hoe, Plymouth PL1 3DH, UK.
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Taylor JD, Cottingham SD, Billinge J, Cunliffe M. Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters. ISME J 2013; 8:245-8. [PMID: 24132076 DOI: 10.1038/ismej.2013.178] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/04/2013] [Accepted: 09/09/2013] [Indexed: 11/09/2022]
Abstract
Phytoplankton produce large amounts of polysaccharide gel material known as transparent exopolymer particles (TEP). We investigated the potential links between phytoplankton-derived TEP and microbial community structure in the sea surface microlayer and underlying water at the English Channel time-series station L4 during a spring diatom bloom, and in two adjacent estuaries. Major changes in bacterioneuston and bacterioplankton community structure occurred after the peak of the spring bloom at L4, and coincided with the significant decline of microlayer and water column TEP. Increased abundance of Flavobacteriales and Rhodobacterales in bacterioneuston and bacterioplankton communities at L4 was significantly related to the TEP decline, indicating that both taxa could be responsible. The results suggest that TEP is an important factor in determining microbial diversity in coastal waters, and that TEP utilisation could be a niche occupied by Flavobacteriales and Rhodobacterales.
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
| | - Samuel D Cottingham
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
| | - Jack Billinge
- 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
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Lidbury I, Johnson V, Hall-Spencer JM, Munn CB, Cunliffe M. Community-level response of coastal microbial biofilms to ocean acidification in a natural carbon dioxide vent ecosystem. Mar Pollut Bull 2012; 64:1063-1066. [PMID: 22414852 DOI: 10.1016/j.marpolbul.2012.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 05/31/2023]
Abstract
The impacts of ocean acidification on coastal biofilms are poorly understood. Carbon dioxide vent areas provide an opportunity to make predictions about the impacts of ocean acidification. We compared biofilms that colonised glass slides in areas exposed to ambient and elevated levels of pCO(2) along a coastal pH gradient, with biofilms grown at ambient and reduced light levels. Biofilm production was highest under ambient light levels, but under both light regimes biofilm production was enhanced in seawater with high pCO(2). Uronic acids are a component of biofilms and increased significantly with high pCO(2). Bacteria and Eukarya denaturing gradient gel electrophoresis profile analysis showed clear differences in the structures of ambient and reduced light biofilm communities, and biofilms grown at high pCO(2) compared with ambient conditions. This study characterises biofilm response to natural seabed CO(2) seeps and provides a baseline understanding of how coastal ecosystems may respond to increased pCO(2) levels.
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Affiliation(s)
- Ian Lidbury
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
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35
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Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MSM, Vuilleumier S, Han J, Peters L, Mikhailova N, Teshima H, Tapia R, Kyrpides N, Ivanova N, Pagani I, Cheng JF, Goodwin L, Han C, Hauser L, Land ML, Lapidus A, Lucas S, Pitluck S, Woyke T, Stein L, Murrell JC. Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 2011; 193:7001-2. [PMID: 22123758 PMCID: PMC3232845 DOI: 10.1128/jb.06267-11] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 10/10/2011] [Indexed: 12/18/2022] Open
Abstract
Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.
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Affiliation(s)
- Rich Boden
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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36
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Abstract
Aquatic surface microlayers are unique microbial ecosystems found at the air-water interface of all open water bodies and are often referred to as the neuston. Unambiguous interpretation of the microbiology of aquatic surface microlayers relies on robust sampling, for which several methods are available. All have particular advantages and disadvantages that make them more or less suited to this task. A key feature of surface microlayers is their role in regulating air-water gas exchange, which affords them a central role in global biogeochemistry that is only now being fully appreciated. The microbial populations in surface microlayers can impact air-water gas exchange through specific biogeochemical processes mediated by particular microbial groups such as methanotrophs or through more general metabolic activity such as the balance of primary production vs. heterotrophy. There have been relatively few studies of surface microlayers that have utilized molecular ecology techniques. The emerging consensus view is that aquatic surface microlayers are aggregate-enriched biofilm environments containing complex microbial communities that are ecologically distinct from those present in the subsurface water immediately below. Future research should focus on unravelling the complex interactions between microbial diversity and the ecosystem function of surface microlayers in order to better understand the important but complex role of microorganisms in Earth system processes.
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Affiliation(s)
- Michael Cunliffe
- Marine Biological Association of the United Kingdom, Plymouth, UK.
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37
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Lobelle D, Cunliffe M. Early microbial biofilm formation on marine plastic debris. Mar Pollut Bull 2011; 62:197-200. [PMID: 21093883 DOI: 10.1016/j.marpolbul.2010.10.013] [Citation(s) in RCA: 444] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 10/15/2010] [Accepted: 10/27/2010] [Indexed: 05/17/2023]
Abstract
An important aspect of the global problem of plastic debris pollution is plastic buoyancy. There is some evidence that buoyancy is influenced by attached biofilms but as yet this is poorly understood. We submerged polyethylene plastic in seawater and sampled weekly for 3 weeks in order to study early stage processes. Microbial biofilms developed rapidly on the plastic and coincided with significant changes in the physicochemical properties of the plastic. Submerged plastic became less hydrophobic and more neutrally buoyant during the experiment. Bacteria readily colonised the plastic but there was no indication that plastic-degrading microorganisms were present. This study contributes to improved understanding of the fate of plastic debris in the marine environment.
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Affiliation(s)
- Delphine Lobelle
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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38
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Abstract
Aquatic surface microlayers are unique microbial ecosystems found at the air-water interface of all open water bodies and are often referred to as the neuston. Unambiguous interpretation of the microbiology of aquatic surface microlayers relies on robust sampling, for which several methods are available. All have particular advantages and disadvantages that make them more or less suited to this task. A key feature of surface microlayers is their role in regulating air-water gas exchange, which affords them a central role in global biogeochemistry that is only now being fully appreciated. The microbial populations in surface microlayers can impact air-water gas exchange through specific biogeochemical processes mediated by particular microbial groups such as methanotrophs or through more general metabolic activity such as the balance of primary production vs. heterotrophy. There have been relatively few studies of surface microlayers that have utilized molecular ecology techniques. The emerging consensus view is that aquatic surface microlayers are aggregate-enriched biofilm environments containing complex microbial communities that are ecologically distinct from those present in the subsurface water immediately below. Future research should focus on unravelling the complex interactions between microbial diversity and the ecosystem function of surface microlayers in order to better understand the important but complex role of microorganisms in Earth system processes.
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Affiliation(s)
- Michael Cunliffe
- Marine Biological Association of the United Kingdom, Plymouth, UK.
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39
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40
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Cunliffe M, Murrell JC. Eukarya 18S rRNA gene diversity in the sea surface microlayer: implications for the structure of the neustonic microbial loop. ISME J 2009; 4:455-8. [DOI: 10.1038/ismej.2009.133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Cunliffe M, Salter M, Mann PJ, Whiteley AS, Upstill-Goddard RC, Murrell JC. Dissolved organic carbon and bacterial populations in the gelatinous surface microlayer of a Norwegian fjord mesocosm. FEMS Microbiol Lett 2009. [PMID: 19732151 DOI: 10.1111/j.1574‐6968.2009.01751.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The sea surface microlayer is the interfacial boundary layer between the marine environment and the troposphere. Surface microlayer samples were collected during a fjord mesocosm experiment to study microbial assemblage dynamics within the surface microlayer during a phytoplankton bloom. Transparent exopolymer particles were significantly enriched in the microlayer samples, supporting the concept of a gelatinous surface film. Dissolved organic carbon and bacterial cell numbers (determined by flow cytometry) were weakly enriched in the microlayer samples. However, the numbers of Bacteria 16S rRNA genes (determined by quantitative real-time PCR) were more variable, probably due to variable numbers of bacterial cells attached to particles. The enrichment of transparent exopolymer particles in the microlayer and the subsequent production of a gelatinous biofilm have implications on air-sea gas transfer and the partitioning of organic carbon in surface waters.
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Affiliation(s)
- Michael Cunliffe
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
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42
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Cunliffe M, Salter M, Mann PJ, Whiteley AS, Upstill-Goddard RC, Murrell JC. Dissolved organic carbon and bacterial populations in the gelatinous surface microlayer of a Norwegian fjord mesocosm. FEMS Microbiol Lett 2009; 299:248-54. [PMID: 19732151 DOI: 10.1111/j.1574-6968.2009.01751.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The sea surface microlayer is the interfacial boundary layer between the marine environment and the troposphere. Surface microlayer samples were collected during a fjord mesocosm experiment to study microbial assemblage dynamics within the surface microlayer during a phytoplankton bloom. Transparent exopolymer particles were significantly enriched in the microlayer samples, supporting the concept of a gelatinous surface film. Dissolved organic carbon and bacterial cell numbers (determined by flow cytometry) were weakly enriched in the microlayer samples. However, the numbers of Bacteria 16S rRNA genes (determined by quantitative real-time PCR) were more variable, probably due to variable numbers of bacterial cells attached to particles. The enrichment of transparent exopolymer particles in the microlayer and the subsequent production of a gelatinous biofilm have implications on air-sea gas transfer and the partitioning of organic carbon in surface waters.
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Affiliation(s)
- Michael Cunliffe
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
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43
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Affiliation(s)
- Michael Cunliffe
- Department of Biological Sciences, University of Warwick, Coventry, UK
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44
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Abstract
Spinal surgery is performed in children of all age groups. Some of these children will have significant, other medical problems. For most, surgery will be performed in the prone position. Blood loss may be high for some types of surgery, and patients will benefit from use of a blood-sparing technique. Many patients will require spinal cord monitoring to assess cord function and to prevent neurological deficit.
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Affiliation(s)
- N Soundararajan
- Jackson Rees Department of Paediatric Anaesthesia, Royal Liverpool Children's Hospital - Alder Hey, Eaton Road, Liverpool L12 2AP, UK
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45
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Dearlove OR, Ram AD, Natsagdoy S, Humphrey G, Cunliffe M, Potter F. Hyponatraemia after postoperative fluid management in children. Br J Anaesth 2007; 97:897-8; author reply 898. [PMID: 17098726 DOI: 10.1093/bja/ael298] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Cunliffe M, Kawasaki A, Fellows E, Kertesz MA. Effect of inoculum pretreatment on survival, activity and catabolic gene expression of Sphingobium yanoikuyae B1 in an aged polycyclic aromatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol 2006; 58:364-72. [PMID: 17117981 DOI: 10.1111/j.1574-6941.2006.00167.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The survival and effectiveness of a bioaugmentation strain in its target environment depend not only on physicochemical parameters in the soil but also on the physiological state of the inoculated organism. This study examined the effect of variations in inoculum pretreatment on the survival, metabolic activity (measured as rRNA content) and polycyclic aromatic hydrocarbon (PAH)-catabolic gene expression of Sphingobium yanoikuyae B1 in an aged PAH-contaminated soil. RNA denaturing gradient gel electrophoresis analysis showed stable colonization of PAH-contaminated soil by S. yanoikuyae B1 after four pretreatments (growth in complex or minimal medium, starvation, or acclimation to phenanthrene). By contrast, extractable CFUs decreased with time for all four treatments, and significantly faster for Luria Bertani-grown inocula, suggesting that these cells adhered strongly to soil particles while remaining metabolically active. Pretreatment of the inoculum had a dramatic effect on the expression of genes specific to the PAH-degradation pathway. The highest levels of bphC and xylE expression were seen for inocula that had been precultivated on complex medium, and degradation of PAHs was significantly enhanced in soils treated with these inocula. The results suggest that using complex media instead of minimal media for cultivating bioaugmentation inocula may improve the subsequent efficiency of contaminant biodegradation in the soil.
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Affiliation(s)
- Michael Cunliffe
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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47
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Cunliffe M, Kertesz MA. Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly PAH-contaminated soils. Environ Pollut 2006; 144:228-37. [PMID: 16524654 DOI: 10.1016/j.envpol.2005.12.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 11/15/2005] [Accepted: 12/11/2005] [Indexed: 05/07/2023]
Abstract
Sphingobium yanoikuyae B1 is able to degrade a range of polycyclic aromatic hydrocarbons (PAHs) and as a sphingomonad belongs to one of the dominant genera found in PAH-contaminated soils. We examined the ecological effect that soil inoculation with S. yanoikuyae B1 has on the native bacterial community in three different soils: aged PAH-contaminated soil from an industrial site, compost freshly contaminated with PAHs and un-contaminated compost. Survival of S. yanoikuyae B1 was dependent on the presence of PAHs, and the strain was unable to colonize un-contaminated compost. Inoculation with S. yanoikuyae B1 did not cause extensive changes in the native bacterial community of either soil, as assessed by denaturing gel electrophoresis, but its presence led to an increase in the population level of two other species in the aged contaminated soil community and appeared to have an antagonistic affect on several members of the contaminated compost community, indicating niche competition.
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Affiliation(s)
- Michael Cunliffe
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
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48
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49
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Cunliffe M, Kertesz MA. Autecological properties of soil sphingomonads involved in the degradation of polycyclic aromatic hydrocarbons. Appl Microbiol Biotechnol 2006; 72:1083-9. [PMID: 16568318 DOI: 10.1007/s00253-006-0374-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 02/03/2006] [Accepted: 02/07/2006] [Indexed: 11/27/2022]
Abstract
Autecological properties that are thought to be important for polycyclic aromatic hydrocarbon (PAH)-degradation by bacteria in contaminated soils include the ability to utilize a broad range of carbon sources, efficient biofilm formation, cell-surface hydrophobicity, surfactant production, motility, and chemotaxis. Sphingomonas species are common PAH-degraders, and a selection of PAH-degrading sphingomonad strains isolated from contaminated soils was therefore characterized in terms of these properties. All the sphingomonads tested were relatively hydrophilic and were able to grow as biofilms on a phenanthrene-coated surface, though biofilm formation under other conditions was variable. Sphingobium yanoikuyae B1 was able to utilize the greatest range of carbon sources, though it was not chemotaxic towards any of the substrates tested. Other sphingomonad strains were considerably less flexible in their catabolic range. None of the strains produced detectable surfactant and swimming motility varied between the strains. Examination of the total Sphingomonas community in the soils tested showed that one of the isolates studied was present at significant levels, suggesting that it can thrive under PAH-contaminated conditions despite the lack of many of the tested characteristics. We conclude that these properties are not essential for survival and persistence of Sphingomonas in PAH-contaminated soils.
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Affiliation(s)
- Michael Cunliffe
- Faculty of Life Sciences, University of Manchester, 1.800 Stopford Bldg, Oxford Road, Manchester, M13 9PT, UK
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