bacteria, archaea and eukaryotes

52 Pages·2017·3.44 MB·English

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Archaea and the nitrogen cycle
Archaea in activated sludge systems
Genome segregation in heat-loving archaea
The symbiosis that changed the world
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E d i t o r i a l
Welcome to the August edition of Microbiology Today, and one
in which we consider the role of archaea and their impact on
microbiology since their reclassification in the 1970s. The Archaea
are a fascinating set of microbes that can thrive in unusual
environments, including some of the most extreme places on
the planet. They can survive in extremes of temperature, pH and
pressure, and are found in many places including the deep sea, ure
ct
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volcanoes and within the guts of animals and humans. e
ol
h
W
A
rchaea have historically been of the role of archaea in the activated has revealed a surprising deep-sea link
given a back seat in terms of sludge process. This essential treatment to eukaryotic origins.
research and publicity, perhaps of wastewater is relatively affordable CRISPR-Cas adaptive immune
because of the generally accepted and produces high-quality effluent. The systems have been the focus of much
premise that there are no archaeal activated sludge is known to contain scientific and media attention recently. In
pathogens, and so much of the research a majority of bacteria, and the role of this article, Qunxin She and Wenyuan Han
has focused on their involvement in archaea, integral within the process, explain how these systems are unevenly
methane and ammonia cycling. There are is still incompletely understood. There distributed amongst bacteria, possibly
also difficulties associated in culturing is evidence that methanogens and due to the presence and pressure from
these microbes in the lab, and as culture- ammonia-oxidising archaea contribute archaeal viruses driving the selection of
independent techniques improve, to the activated sludge in a fundamental one or more CRISPR-Cas within archaea.
research evolves and more information way, and there is a growing recognition They also discuss how Cas accessory
about these microbes emerges. Archaea that more work is needed to understand proteins might modulate the functionality
have significant roles in aspects of global the diversity and function of archaea within CRISPR-Cas systems.
ecology, and the collection of articles in within activated sludge. James Chong writes the Comment
this edition highlights how widespread In our third piece, Daniela Barillà piece, highlighting the hazards (including
and successful these organisms are. explains the importance of genome explosions) that can be associated with
Our first piece, written by Graeme segregation in archaea that thrive in working with archaea. He ponders why
Nicol, gives an insight into the role temperatures of over 80 °C. Building on there are no archaeal pathogens, and
of archaea in the nitrogen cycle. The work from archaeal pioneer Wolfram the answer suggests there may be many
presence of large numbers of ammonia- Zillig, researchers are now discovering complexities at play. Evidence proposes
oxidising archaea in oceans and soils new information on the roles of both that archaea could be functioning as
has shifted global understanding chromosome segregation and three- opportunistic pathogens in a range
of how nitrification works. Graeme component plasmid segregation of health conditions. As in so many
discusses how the application of fertiliser machinery, relevant to all life on Earth. microbiological studies, the analytical
during the 20th century has led to an Laura Eme and Thijs Ettema pose methods employed may have, until
accelerated nitrogen cycle, causing the question of archaeal involvement in recently, given a skewed picture. Improved
damage to the environment. He then eukaryotic evolution. Did chloroplasts and techniques could lead to new questions
outlines how ammonia-oxidising archaea mitochondria arise from endosymbiosis about the status of these microbes.
could be utilised to alleviate some of between plants, cyanobacteria
these pollution problems. and alphaproteobacteria? Or did Rowena Jenkins
The second article has been fusion between an archaeon and an Editor
contributed by Marta Filipa Simões and alphaproteobacterium lead to eukaryotic [email protected]
André Antunes, and provides details cells? The availability of sequence data
Microbiology Today Aug 17 | www.microbiologysociety.org 97
C o n t e n t s
Microbiology
TODAY
Articles
106 Archaea and the nitrogen cycle
Graeme Nicol
The important role of archaea in a global context.
110 Archaea in activated sludge systems
Marta Filipa Simões and André Antunes
The phylogenetic and functional diversity in wastewater.
114 Genome segregation in heat-loving
archaea
Daniela Barillà
Intriguing perspectives on genome segregation.
118 The symbiosis that changed the world
Laura Eme and Thijs J. G. Ettema
Our microbial history revealed.
122 Archaea and CRISPR biology
Qunxin She and Wenyuan Han
An adaptive immune system found in archaea.
44:3 August 2017
Features Regulars
130 Microbiology Society strategy changes 97 Editorial
Responding to feedback and the launch of a new strategy. 100 Council 2017
101 From the President
131 Good news:
102 From the Chief Executive
the Member Directory is coming
103 News
An online directory for members.
126 Annual Conference
132 Publishing 128 Focused Meetings
The latest on the Society’s publishing activities. 142 Reviews
134 Outreach Editor Rowena Jenkins
Managing Editor Ruth Paget
Information on Antibiotics Unearthed and TeaTime Science.
Editorial Board David Bhella, Helen Brown, Emma Denham,
Lorena Fernández-Martínez, Rebecca Hall, Freya Harrison, James Redfern,
136 Policy – Infection diagnosis in the UK Alison Sinclair, Nicola Stonehouse
Address Microbiology Society, Charles Darwin House, 12 Roger Street,
UK Standards for Microbiology Investigations guidelines.
London WC1N 2JU T [phone] E [email protected]
Design Ian Atherton, Corbicula Design (www.corbiculadesign.co.uk)
137 ECM Forum update –
Printed by Charlesworth Press, Wakefield
Conference highlights and prize winners © 2017 Microbiology Society
ISSN 1464-0570
Rebecca Hall gives us an overview of ECM activities. The views expressed by contributors do not necessarily reflect official policy of the Society; nor can
the claims of advertisers be guaranteed.
138 Schoolzone – Meet the Microbes
Society member Naomi Osborne’s fun e-book.
FSC Logo
140 Membership Q&A
Introducing Adrindam Mitra from Adamas University. Cover: Cold-loving archaea. Coloured transmission electron micrograph of
a section through the archaeon Methanococcoides burtonii. The cell walls
143 Comment – appear red, while the granular cell contents include scattered genetic
Archaea: closet pathogens? material. These psychrophilic (cold-loving) archaea were discovered in 1992
in Ace Lake, Antarctica, and can survive in temperatures as low as –2.5 °C.
James Chong
As methanogenic microbes, they are able to form methane from carbon
Why are there no known archaeal pathogens? dioxide and hydrogen. Dr M. Rohde, GBF/Science Photo Library
Council 2017
Executive Officers
President – Professor Neil Gow
School of Medicine, Medical Sciences and Nutrition, Polwarth Building, Foresterhill, Aberdeen AB25 2ZD; [email protected]
General Secretary – Professor Maggie Smith
Department of Biology, Wentworth Way, University of York, York YO10 5DD; [email protected]
Treasurer – Professor Christopher Morton Thomas
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT; [email protected]
Chairs of Committees
Communications Committee – Dr David Bhella
MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH; [email protected]
Early Career Microbiologists’ Forum Executive Committee – Dr Helen Brown
School of Dentistry, Cardiff University, Cardiff CF14 4XY
Finance and Operations Committee – Professor Christopher Morton Thomas
See ‘Treasurer’ above
Policy Committee – Dr Pat Goodwin
c/o Microbiology Society, Charles Darwin House, 12 Roger Street, London WC1N 2JU
Professional Development Committee – Dr David Whitworth
Institute of Biological, Environmental and Rural Sciences Room S22, Cledwyn Building, Aberystwyth University, Ceredigion SY23 3FG; [email protected]
Publishing Committee – Professor Charles Dorman
Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, College Green, Dublin 2, Ireland; [email protected]
Scientific Conferences Committee – Dr Karen Robinson
Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham NG7 2RD
Elected Members
Professor Paul Kellam
Imperial College London, Faculty of Medicine, St Mary’s Campus, Norfolk Place, London W2 1PG; & Kymab Ltd; [email protected]
Professor Stephen Oliver
Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA
Professor David Pearce
Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne NE1 8ST;
[email protected]
Professor George Salmond
Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW
Dr Mike Skinner
Section of Virology, Imperial College London, Faculty of Medicine, St Mary’s Campus, Norfolk Place, London W2 1PG; [email protected]
Professor Nicola Stonehouse
School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT; [email protected]
100 Microbiology Today Aug 17 | www.microbiologysociety.org
From the President
The age of the earliest origins of (microbial) life
on Earth extend to at least four billion years ago.
There is renewed debate on exactly how and when
the three major extant groups of life forms on
Earth (bacteria, archaea and eukaryotes) evolved
and diverged.
B
ut, whatever the consensus major divisions of life. We used to was interesting was that expression
emerges, it is clear that all of life think of these organisms as being of these ancient thioredoxin proteins
is microbiological in origin and all restricted to the more extreme could, to a greater or lesser extent,
plants and animals depend on microbial environments and ecosystems. While render modern E. coli phage-immune.
collaborations and endosymbiosis for it is true that these organisms include The reason for mentioning this is that
their existence. This issue celebrates notable thermophilic and halotolerant the study of ancient microbes, and the
the Archaea – one of the three basic cell species (see the review on thermophilic understanding of how they evolved
types on Earth, and one perhaps that few archaea by Daniela Barillà), it has turned into modern ones, might provide novel
members of the general public will have out that archaea are very much more insights and opportunities to develop
ever heard of. widely distributed than first thought. desirable properties, such as virus
The late Carl Woese, a pioneer of The importance of these organisms in resistance in plants and animals.
16S ribosomal DNA sequencing, was many guises is set out in this issue. See, Archaea are one such group of microbes
first to recognise the distinction between for example, the articles by Graeme that have not been fully explored in terms
the Archaea and other prokaryotes, Nicol describing the contributions that of their ecology and utility.
publishing the seminal paper on this archaea make to soil nitrification and Elsewhere in this issue you can
topic in 1977. Therefore, Woese revealed other aspects of the nitrogen cycle, and catch up on Microbiology Society
a new view of the world showing that to the biodegradation of sewage (article news, with an overview by Laura Crick
the basic arrangement and evolution of by Marta Filipa Simões and André on conferences and meetings and
life forms on Earth comes from three Antunes). There is also an interesting information about the new Membership
basic microbial prototypes. This refined account of how the CRISPR-Cas system Directory from Paul Easton. The Early
and extended the previous paradigm is linked to archaea (article by Qunxin Career Microbiologists’ Forum is now
published in 1962 by Roger Stanier and She and Wenyuan Han). Please also read gearing up and has quickly become
C. B. van Niel who first established the the commentary by James Chong on the integrated into the central machination
division of prokaryotes and eukaryotes apparent absence of pathogenic archaeal of the Microbiology Society (see article
based in part on whether they had a species. by Rebecca Hall). There are other Society
membrane-bound nucleus. Although we I wonder if you read the recent updates from Benjamin Thompson, and
have only known of their very existence article in Cell Reports by Asuncion also Hannah Forrest with information
for less than 40 years, it is clear that the Delgado from Jose Sanchez-Ruiz’s lab, on schools activities and the Antibiotics
Archaea are an ancient and fascinating who showed that a ‘fossil’ bacterial Unearthed project.
independent group of organisms (see in protein (thioredoxin) could be expressed
this issue the article on p. 118 by Laura in a contemporary bacterium (Escherichia Neil Gow
Eme and Thijs Ettema). coli) and modify its properties. President
This issue rightly celebrates the Bacteriophages need to recruit this redox [email protected]
Archaea as the least well known of the protein for their replication, and what
Microbiology Today Aug 17 | www.microbiologysociety.org 101
From the Chief Executive
It has been a great privilege to attend a number of meetings
in Ireland over the past few months, where I have seen some
of the fascinating work being carried out by Microbiology
Society members there. In Belfast, Dublin, Wexford, Cork and
Kildare, there has been some amazing microbiology on display,
and it has been shared in a community that gets the best out
of its members by being supportive and friendly.
I
n May, it was a real pleasure to visit was organised by a long-time member sense of community. The Society’s Irish
Johnstown Castle in County Wexford, of the Society, John McGrath, together Division has a long history of organising
one of the homes of Teagasc – the with Katrina Macintosh, Jason Chin, meetings that are not just scientifically
Agriculture and Food Development John Quinn and Vincent O’Flaherty, who stimulating, but which also make an
Authority. Society member Fiona is Chair of the Society’s Irish Division. effort to support early career members.
Brennan organised a stimulating There was a great range of offered Members in Ireland routinely attend
workshop on harnessing the power of papers from Ireland and further afield, meetings on subjects that are a long
plant and soil microbiomes. As well as and it was wonderful to learn more about way from their own research interests,
scientists, the event was attended by the diverse roles played by microbes in because they feel part of a vibrant and
policy-makers and funders from Science agricultural systems. supportive community.
Foundation Ireland, the Department The 33rd International Specialised We are a Society of communities, and
of Agriculture and the Environment Symposium on Yeast (ISSY33) was those communities can be taxonomically
Protection Agency. It was great to be able organised under the auspices of the defined – like the Virology, Prokaryotic
to present the emerging findings from International Commission on Yeasts, with and Eukaryotic Divisions – or defined
the Microbiology Society’s policy report the support of the Microbiology Society. by career stage like the Early Career
on microbiomes, ahead of the main It was held in June at University College Microbiologists’ Forum, or by other
report’s publication in the autumn. Cork, the home of its driving force – John interests, like the Policy Committee. The
Then, in June, I had enormous fun Morrissey – who is Chair of the Society’s Irish Division is the only geographically
at University College Dublin, where PhD Eukaryotic Division. It explored the ways based group of members the Society
students in the School of Biology and in which yeasts can be used for industrial has. But when we consulted you recently
Environmental Science presented their applications, and included a keynote as Council prepares a new five-year
work at the annual Seminar Day. The lecture from Steve Oliver, a member of strategy, there was a strong sense from
postgraduate representatives – Tamsin, the Society’s Council, on how yeasts can the members that you want us to do
Sam and Laura – kindly asked me to be used as a model of human diseases. more at a local level.
be one of the judges. The winner of the And very soon, I will be back in I am very keen to hear from you
Carmel Humphries Memorial Medal Ireland for another of the Society’s about what this means to you, and how
was Maeve Long, whose work on the Focused Meetings at Maynooth in County the Society can connect and empower
endomembrane system referred to Kildare, on Antimicrobial Resistance your local community in the way the Irish
Shigella toxin and was both fascinating and One Health. Organised by Fiona Division does so effectively.
and impressive. Walsh and Thuy Thi Do, it has a lot to live
Later in the month, the first of the up to after the success of all the other Peter Cotgreave
Society’s Focused Meetings for 2017 was meetings! Chief Executive
held in Belfast, on Microbial Resources One of the things that always strikes [email protected]
for Agricultural and Food Security. It me when I visit members in Ireland is the
102 Microbiology Today Aug 17 | www.microbiologysociety.org
News
Policy briefing: Annual Conference 2018
Antimicrobial
Our full exhibition and sponsorship packages for
Resistance Annual Conference 2018 can now be found online. We
have a number of opportunities with a range of prices
The latest in the Society’s series
to suit all budgets, but stand space is limited so contact
of short policy briefings focuses
us as soon as possible to reserve your preferred area.
on the topic of Antimicrobial
Remember to note in your diaries that Annual
Resistance (AMR). The briefing
Conference 2018 will differ from previous years and
was sent to policy-makers in
takes place from Tuesday 10 April to Friday 13 April –
the UK and Ireland, and sets out
don’t forget when booking travel and accommodation.
the key issues around AMR and
Read more about Annual Conference 2018 on
the actions needed to mitigate
page 126.
it. You can download it here:
www.microbiologysociety.org/
briefings
Focused Meetings 2017
Thank you to those who attended, presented and spoke at our two ICC Birmingham
Focused Meetings that took place in June this year – ISSY33 and
Microbial Resources for Agricultural and Food Security. These two
Support for your invited speaker costs
successful meetings brought together like-minded researchers, and
were only the first of a busy Focused Meetings programme for 2017. Our Society-Supported Conference Grants can cover
Find out more about what’s still to come on page 128. speaker costs at your microbiological event for up
to £2,000. This grant can be used towards the cost
of accommodation and travel. Round 1 of our 2018
awards closes on 15 December 2017. Details can
be found online: www.microbiologysociety.org/
SSconferencegrants
Deaths
It is with great sadness that the Society announces
the passing of one of our members, Professor Martin
Allday, who was internationally renowned for his work
Society Champion activities on the biology of the Epstein–Barr virus. Professor
Allday joined the Society in 1982.
Our Champions have been busy organising events in their Please contact [email protected] if
local areas – find out more about what they’ve been up to at you wish to notify the Society of the death of a member
www.microbiologysociety.org/champions whose details can be included in this section.
Microbiology Today Aug 17 | www.microbiologysociety.org 103
Grant deadlines
Date Grant
1 September 2017 Travel Grants – for eligible members wishing to present at conferences or attend training events
on or after 1 October.
Careers Conference Grant – to support Undergraduate Student Members wishing to attend the
Royal Society of Biology Biosciences Careers Festival.
30 September 2017 ECM Forum Event Fund – for ECM members requiring sponsorship for local events.
1 October 2017 Education and Outreach Grants – for eligible members requiring support for projects to
communicate or teach microbiology.
Research Visit Grants – for eligible members wishing to make a research visit to a collaborator.
International Development Fund – for eligible members wishing to contribute to the
development of microbiology in low- and lower-middle-income countries.
Volunteers for Glasgow Antibiotics
Unearthed pop-up event
The Antibiotics Unearthed team will be at the Glasgow
Botanic Gardens on Thursday 7 September 2017 with
our interactive pop-up stand, and we are looking for
volunteers to help out.
The stand will include a variety of hands-on
activities for visitors to engage with the issue of
antimicrobial resistance and drug discovery. Members
of the public are encouraged to collect a soil sample
and prepare it for scientific analysis at the pop-up.
If you are interested in volunteering, please
contact the Antibiotics Unearthed team at
[email protected]
Antibiotics Unearthed events in 2015 and 2016.
104 Microbiology Today Aug 17 | www.microbiologysociety.org