Ecology

Positive correlation between biosynthetic gene cluster (BGC) and phylogenetic distance in the genus Bacillus
BGCs are responsible for the synthesis of secondary metabolites involved in microbial interference competition. To investigate the relationship between BGC and phylogenetic distance within the genus Bacillus, we collected 4268 available Bacillus genomes covering 139 species from the NCBI database (Supplementary Data 1). Phylogenetic analysis based on the sequences of 120 ubiquitous single-copy proteins27 showed that the 139 species could be generally clustered into four clades (Fig. 1 and Supplementary Data 2; the phylogenetic tree including all the detailed species information is shown in Supplementary Fig. 1), including a subtilis clade that includes species from diverse niches and can be further divided into the subtilis and pumilus subclades, a cereus clade that contains typical pathogenic species (B. cereus, B. anthracis, B. thuringiensis, etc.), a megaterium clade, and a circulans clade.Fig. 1: Phylogram of the tested Bacillus genomes.The maximum likelihood (ML) phylogram of 4268 Bacillus genomes was based on the sequences of 120 ubiquitous single-copy proteins27. The phylogenetic tree shows that Bacillus species can be generally clustered into the subtilis (light green circle; further includes subtilis (dark green) and pumilus (blue) subclades as shown in the branches), cereus (red), megaterium (yellow), and circulans (gray) clades. For detailed information of the species, please refer to the phylogenetic tree in Supplementary Fig. 1.Full size imagePrediction using the bioinformatic tool antiSMASH15 detected 49,671 putative BGCs in the 4268 genomes, corresponding to an average of 11.6 BGCs per genome (Supplementary Data 3). The subtilis clade had the most BGCs, 13.1 BGCs per genome (Fig. 2a); the subtilis subclade especially accommodates a high abundance of BGCs as 13.6 per genome (Supplementary Fig. 2a), which corresponds to their adaptation in diverse competitive habitats such as plant rhizosphere. The cereus and megaterium clades possessed moderate number of BGCs as 11.7 and 7.4 per genome, respectively; while the circulans clade only had 4.3 BGCs/genome (Fig. 2a and Supplementary Table 1), suggesting a distinct physiological feature and niche adaptation strategy. The two most abundant BGC classes were nonribosomal peptide-synthetase (NRPS) and RiPPs, which had an abundance of 3.7 and 3.1 per genome on average, respectively (Supplementary Fig. 2b and Supplementary Table 1). Interestingly, subtilis clade accommodated significantly higher abundance of BGCs in another polyketide synthase (PKSother; 2.0 per genome vs. 0.0–1.1 per genome) and PKS-NRPS Hybrids (0.7 vs. 0.0–0.2) classes, as compared with the three other clades (Supplementary Table 1); while cereus clade had more BGCs in RiPPs than other clades on average (Supplementary Table 1). Overall, the profile of BGC products and classification was generally consistent with the phylogenetic tree (Supplementary Fig. 3).Fig. 2: Biosynthetic gene cluster (BGC) distribution is correlated with phylogeny in the genus Bacillus.a The numbers of BGCs in the 4268 Bacillus genomes from different clades as defined by antiSMASH15. In the violin plot, the centre line represents the median, violin edges show the 25th and 75th percentiles, and whiskers extend to 1.5× the interquartile range. b Hierarchal clustering among the 545 representative Bacillus genomes based on the abundance of the different biosynthesis gene cluster families (GCFs). Each column represents a GCF, which was classified through BiG-SCAPE by calculating the Jaccard index (JI), adjacency index (AI), and domain sequence similarity (DSS) of each BGC28; the color bar on the top of the heatmap represents the BGC class of each GCF, where PKS includes classes of PKSother and PKSI, PKS-NRPS means PKS-NRPS Hybrids, Others includes classes of saccharides, terpene, and others. Each row represents a Bacillus genome, and the abundance of each GCF in different genomes is shown in the heatmap. The left tree was constructed based on the distribution pattern of GCFs, which showes a similar pattern to the phylogram in Fig. 1. c The correlation between the BGC and phylogenetic distance of the 545 representative Bacillus genomes (P  More

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CAREER Q&A
22 February 2022

Marching in the streets for climate-crisis action

Conservationist Charlie Gardner explains why he joined Scientists for Extinction Rebellion and its civil-disobedience protests.

Christine Ro

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Christine Ro

Christine Ro is a freelance journalist based in Buenos Aires.

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Charlie Gardner speaks at an Extinction Rebellion protest.Credit: Louise Jasper Photography

Conservationist, consultant and activist Charlie Gardner is a lecturer in conservation biology at the Durrell Institute of Conservation and Ecology at the University of Kent in Canterbury, UK. He regularly participates in protests with Scientists for Extinction Rebellion, an offshoot of a broader movement that uses nonviolent civil disobedience to push for action on the climate and biodiversity crises. He has also advised on legislation such as the UK Climate and Ecological Emergency Bill, which seeks to curb UK greenhouse-gas emissions and biodiversity loss, and is currently making its way through Parliament. What drove you to activism? Teaching. Five or six years ago, I was standing in front of a lecture theatre, full of young people who are going to suffer the consequences of climate change much more than I am. I couldn’t stand that I wasn’t doing everything I could. When Extinction Rebellion (XR) was launched in the United Kingdom in October 2018, it felt like the answer. As conservationists, we silently wish that members of the general public cared more about the destruction of nature. Now they are taking to the streets and I have this moral obligation to be there in support.How have you been working with Scientists for XR?In October 2019, a group of scientists came together to create Scientists for XR, which has carried out many actions. These include pasting scientific papers to the walls of the London headquarters of News Corp in 2021 in protest against inadequate climate-change coverage in the company’s newspapers. The group has different functions. One is to provide scientific support for the wider XR movement, so that it remains founded on solid scientific ground. And a second is to advocate. Scientists vocally supporting XR sends a powerful message. Society trusts scientists. A third function is direct action. Scientists for XR groups have been involved in a number of XR events, such as marches and roadblocks. For example, at the 2021 opening of a London Science Museum exhibition sponsored by oil and gas company Shell, some scientists locked themselves to parts of the exhibition in protest against the sponsorship, while our scientist group set up a table outside to demonstrate principles of atmospheric cooling to engage with the public. Events such as this serve to highlight the issue of science museums accepting sponsorship from fossil-fuel companies.How can scientists dip their toes into this type of work?What the public sees of these direct actions is the tip of the iceberg. For every person out on the streets, there are 20 more behind the scenes involved in other tasks: organizing, producing press releases, baking cakes for marchers. Whatever you enjoy doing and have skills in, there is a role for you. Taking part does not have to involve engaging in civil disobedience yourself, or putting yourself in a risky position. One of the most important jobs at a protest is for people to stand at the edges, engaging the public in conversations. That’s a role that scientists can perform fantastically.How have your advocacy and activism benefited you?There’s this crazy notion that scientists shouldn’t speak out because it will damage their reputations. But activism has had the opposite effect on my career. My research is based on conservation in Madagascar; it’s fairly niche. I previously had no global reputation. Since becoming a vocal scientist-activist, my reputation and my visibility as a scientist have soared. Also, activism is great for my mental health. Knowing I’m doing what I can is important to me. There are simply the best people in these movements, and there’s a sense of community. Does being a vocal activist diminish your scientific credibility?Popular perception holds that scientists must be neutral purveyors of information and not speak up about what that information means. Somehow, if we do so, it could damage our credibility.But when scientists take personal risks and make personal sacrifices, that communicates the urgency of the situation in an important way. If scientists are saying that it’s time for action, but not acting themselves, that undermines their own arguments. How do you balance your academic responsibilities with advocacy?For five years, I worked half-time at the University of Kent. I did this deliberately, to allow me the freedom to engage in other activities, including conservation consultancy, activism and writing popular non-fiction. I left that post last year, partly to focus on activism and writing, and partly out of frustration with the precarity of academic life.There are things that enable me to be less single-minded in the pursuit of my career: I come from a position of relative privilege; I’m not interested in accumulating money; and I don’t have children. So I think academia has been a good fit for me, but only because it doesn’t fill my life.

doi: https://doi.org/10.1038/d41586-022-00518-4This interview has been edited for length and clarity.

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