title: Fifty important research questions in microbial ecology.
abstract: Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
authors.affiliation: School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK.
authors.forename: Rachael E
authors.initials: RE
authors.lastname: Antwis
authors.affiliation: School of Science and the Environment, Manchester Metropolitan University, Manchester, Greater Manchester M1 5GD, UK.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Griffiths
authors.affiliation: Institute of Zoology, Zoological Society of London, London, London NW1 4RY, UK.
authors.forename: Xavier A
authors.initials: XA
authors.lastname: Harrison
authors.affiliation: School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK.
authors.forename: Paz
authors.initials: P
authors.lastname: Aranega-Bou
authors.affiliation: Silwood Park, Faculty of Natural Sciences, Imperial College London, London, London SW7 2AZ, UK.
authors.forename: Andres
authors.initials: A
authors.lastname: Arce
authors.affiliation: School of Biosciences, Cardiff University, Cardiff, South Glamorgan CF10 3XQ, UK.
authors.forename: Aimee S
authors.initials: AS
authors.lastname: Bettridge
authors.affiliation: School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd LL57 2DG, UK.
authors.forename: Francesca L
authors.initials: FL
authors.lastname: Brailsford
authors.affiliation: School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK.
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Menezes
authors.affiliation: Biosciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Devaynes
authors.affiliation: Department of Virology, University of Helsinki, Helsinki 00014, Finland.
authors.forename: Kristian M
authors.initials: KM
authors.lastname: Forbes
authors.affiliation: School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK.
authors.forename: Ellen L
authors.initials: EL
authors.lastname: Fry
authors.affiliation: School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Goodhead
authors.affiliation: Department of Biology, University of York, York, North Yorkshire YO10 5DD, UK.
authors.forename: Erin
authors.initials: E
authors.lastname: Haskell
authors.affiliation: Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK.
authors.forename: Chloe
authors.initials: C
authors.lastname: Heys
authors.affiliation: School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK.
authors.forename: Chloe
authors.initials: C
authors.lastname: James
authors.affiliation: School of Biosciences, Cardiff University, Cardiff, South Glamorgan CF10 3XQ, UK.
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Johnston
authors.affiliation: Biosciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK.
authors.forename: Gillian R
authors.initials: GR
authors.lastname: Lewis
authors.affiliation: Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK.
authors.forename: Zenobia
authors.initials: Z
authors.lastname: Lewis
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Macey
authors.affiliation: Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK.
authors.forename: Alan
authors.initials: A
authors.lastname: McCarthy
authors.affiliation: School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2DG, UK.
authors.forename: James E
authors.initials: JE
authors.lastname: McDonald
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
authors.forename: Nasmille L
authors.initials: NL
authors.lastname: Mejia-Florez
authors.affiliation: Scottish Natural Heritage, Inverness IV3 8NW, UK.
authors.forename: David
authors.initials: D
authors.lastname: O'Brien
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire CB2 1TN, UK.
authors.forename: Chloé
authors.initials: C
authors.lastname: Orland
authors.affiliation: Animal and Plant Health Unit, European Food Safety Authority, Parma 43126, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Pautasso
authors.affiliation: School of Biology, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK.
authors.forename: William D K
authors.initials: WDK
authors.lastname: Reid
authors.affiliation: School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK.
authors.forename: Heather A
authors.initials: HA
authors.lastname: Robinson
authors.affiliation: Lancaster Environment Centre, Lancaster University, Lancaster, Lancashire LA1 4YW, UK.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Wilson
authors.affiliation: Conservation Science Group, Department of Zoology, University of Cambridge, Cambridge, Cambridgeshire CB2 1TN, UK.
authors.forename: William J
authors.initials: WJ
authors.lastname: Sutherland
mesh_terms: D001419:Bacteria / Q000254:growth & development*; D005075:Biological Evolution; D003141:Communicable Diseases; D004463:Ecology; D017753:Ecosystem; D059022:Food Safety; D006801:Humans; D064307:Microbiota
keywords: environmental processes; evolutionary processes; functional diversity; host–microbiome interactions; priority setting, research agenda