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Microbial Musings – December 2020

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Microbial Musings – December 2020 EDITORIAL Thomas, Microbiology 2020;166:1107–1109 DOI 10.1099/mic.0.001019 OPEN ACCESS Microbial Musings – December 2020 Gavin H. Thomas* As we end this extraordinary year, the importance of micro- resistance (AMR)’ to our ‘Antimicrobials and AMR’ theme. biology continues to be demonstrated in our daily lives in Next month I will be announcing a significant number of new ways that we would never have predicted 12 months ago. This editors to handle submissions within our revised topic areas. month in the UK, the identification of a new variant of severe The first paper from this issue to highlight is one that would acute respiratory syndrome coronavirus 2 (SARS- CoV-2) fit nicely into the new Plant microbiology and soil health through the continuing work of the COVID-19 Genomics topic, as it is around the biology of two Bacillus species strains Consortium (@CovidGenomicsUK) led to an almost imme- that are currently used as biocontrol agents in China, and diate change in government policy, and while the manifesta- more specifically are used to protect oil seed rape crop from tions of the new variant are being uncovered, it is an example a pathogenic fungal infections. The work from Alex Mullins of evolution occurring in real time in front of the eyes of the (@AlexJMullins), collaborating with Eshwar Mahenthiral- general public. The development and delivery of multiple new ingam and Gordon Webster at the University of Cardiff, UK, vaccines against the virus are a true illustration that biology and colleagues at the Oil Crops Research Institute of Chinese has the potential to be the greatest technology of the 21st Academy of Agricultural Sciences, Wuhan, PR China, aimed century. to use genome sequencing to learn more about these strains, As we look forward to the situation improving slowly across and the authors were immediately able to place them into the the globe through 2021, I want to highlight some exciting species Bacillus velezensis [1]. With this information to hand, changes at the journal as we move into its 74th year. One Mullins and colleagues compared the genomes of their strains problem with having a journal with a title that is literally with those of a large number of other B. velezensis strains as broad as the whole subject, is that sometime authors can and noted the precociousness of their strains for producing feel that they should look for a more specialized publication. natural products. Experimentally they demonstrated that the To address this, we have entirely reworked the topic areas lipopeptide iturin A, which both their strains have the biosyn- in which we are looking for submissions. From January thetic cluster for, can kill the fungi that their strains protect 2021 we will have 10 new topic areas (Table 1), which are against, making this a likely component of the biocontrol aimed to help identify and build new communities around process. However, they suspect that their strains produce a the journal and the Microbiology Society. To support this mixture of natural products that they could see encoded on move, we have appointed four new Senior Editors to help their genomes, some of which have been detected previously our leadership team to lead and develop these communities. biochemically [2], which may indicate why this species more For our ‘Microbial cell surfaces’ topic we have Tracy Palmer generally produces such good biocontrol agents. FRS from the University of Newcastle, and for our ‘Microbial The next two papers concern bacteria of the genus Vibrio, evolution’ topic we have Mike Brockhurst from the Univer- both the classical pathogenic species V. cholerae and the sity of Liverpool, while Steve Diggle from Georgia Tech will gastrointestinal pathogen V. vulnificus [3, 4]. In the first paper lead the ‘Microbial interactions and communities’ topic and from Nabendu Chatterjee’s group at the National Institute of Martin Welch, University of Cambridge, will co- lead the Cholera and Enteric Diseases, Kolkata, India [3], the authors large ‘Microbial physiology, biochemistry and metabolism’ further characterize the V. cholerae transcription factor CytR, topic. I am delighted to bring these new faces into our senior which is already known from the work of Brian Hammer’s team to bring the journal to its 75th anniversary and beyond. (@briankhammer) group at Georgia Tech, USA, to regulate Also, three of the topic areas relate to areas of research where competence, some type VI secretion systems and chitinase the Microbiology Society has identified clear roles for our gene expression [5]. In this work the authors find that a cytR subject in delivering solutions to global problems by linking mutant has an additional defect in growth on porcine mucin them to the United Nations Sustainable Development Goals as the sole source of carbon, which is also correlated with (UN SDGs). We have mapped the ‘circular economy’ to our observed reductions in motility and mucin penetration. Some ‘Biotechnology and synthetic biology’ topic, ‘soil health’ to our of the known chitinases are thought to be secreted enzymes ‘Plant microbiology and soil health’ topic and ‘antimicrobial involved in the breakdown of small N- acetylglucosamine Received 21 December 2020; Published 23 December 2020 Author affiliations: 1Department of Biology, University of York, York, YO10 5YW, UK. *Correspondence: Gavin H. Thomas, gavin. thomas@ york. ac. uk Abbreviations: 3D- SIM, 3D structured illumination microscopy; STED, stimulated emission depletion. 001019 © 2020 The Authors This is an open- access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution. 1107 Thomas, Microbiology 2020;166:1107–1109 Table 1. New topic areas for Microbiology as the positive inside rule described by Gunnar in 1986 [8], which then agreed with the structure published a few years New topic area later [9]. Daniel then comes along and builds on the strength Antimicrobials and AMR (UN SDG 'AMR') of these computational models to use a single C- terminal Biotechnology and synthetic biology (UN SDG 'circular economy') GFP tag fused separately to all of the 601 Escherichia coli inner membrane proteins and determine a complete inner Cell and developmental microbiology membrane protein topology map! [10]. This kind of blew my Microbial cell surfaces mind and I remember spending a lot of time reading and annotating these data for EchoBASE [11] as the first genome- Microbial evolution wide experimental study of protein structure. Anyway, I Microbial interactions and communities digress. The paper in this issue from Bill Söderström (@Bill- Microbial physiology, biochemistry and metabolism Soderstrom) and Alessandro Ruda, with colleagues from the Daley group, describes a new fluorescently labelledd - alanine Microbial virulence and pathogenesis for labelling peptidoglycan, which has improved function- Plant microbiology and soil health (UN SDG 'Soil health') ality for use in the most recent iterations of microscopy that Regulation, sensing and signalling can be applied to small bacterial cells [12]. The new label uses OreganGreen488 as the fluorophore, which has higher resistance to photobleaching and is more photo-stable than (GlcNAc) containing oligosaccharides released from mucin other commonly used fluorophores. This is important for [6], so this could also explain part of this phenotype. They also new super-resolution methods such as 3D structured illu- find the mutant is less able to adhere to intestinal epithelia mination microscopy (3D- SIM) and stimulated emission and has a colonization defect in a suckling mouse model. depletion (STED), which are now being applied to bacteria These additional functions, alongside its established func- cells [13]. They demonstrate that their new label is efficiently tions, demonstrate that CytR is an important regulator of incorporated into peptidoglycan, first in a range of Gram- V. cholerae pathogenesis. The second Vibrio paper focuses positive bacteria, and compare this to a similar fluorescein- on the foodborne pathogen V. vulnificus, a nasty bug with based label, where the new label is able to resolve at much a high fatality rate in the USA. The study by Laura Cutugno higher resolution. Using a pulse of their new label followed (@LauraCutugno) from the group of Aoife Boyd, with Conor by another of a different colour, they observe labelling of new O’Byrne (@cpobyrne) at the University of Galway, Ireland, peptidoglycan at the division site and then this moving away looked at the responses of the well-studied clinical strain as the cell grows. As the new molecule, OGDA, is ~500 Da, it CMCP6 when this is selected for rifampicin resistance [4]. cannot label E. coli very efficiently as it needs to get into the This is known to occur clinically, although fortunately these cell to be built into the peptidoglycan precursor molecule, bacteria are still sensitive to most antibiotics, and from although they did see good labelling in the biotechnologically isolating independent genetic lines with this phenotype, relevant Gram- negative bacterium Zymomonas mobilis. This which results in mutations in rpoB, they were able to show a is an exciting new development and no doubt Söderström wide range of pleiotropic phenotypes, which varied consider- will be using this in his new laboratory at the ithree institute ably with the nature of the allele of rpoB, with only reduced (@ithreeinst)
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