A new bacterial species? Well, new to us, as it was never ‘seen’ or described by humans before.
For me, there is a very personal story attached to this new species. It started in 2017. I moved to central Portugal together with a friend. A place where time moves at a slower pace. We moved to a garden that was filled with olive, citrus, fig, plum and apple trees as well as lavender, rosemary and much more. Our goal was to create a food producing garden that needed little input. With input, I mean, mechanical input such as tilling, mowing and leaf blowing, and chemical input such as fertilizers and pesticides. Reducing input also entails sacrificing some output, harvest. But overall, this management should lead to a more sustainable ecosystem. This idea also lies at the basis of many agriculture movements you might have heard of, such as agroforestry and permaculture. Although it is debatable whether these low-input agricultural systems are a solution for our global food production, many ideas from low-input systems can be of great value for intensive agriculture. Searching for these sustainable solutions was an important inspiration for starting my PhD.
Now, when does this tiny new bacterium come into the picture? After I started my PhD at the Lebeerlab, I planned on returning to Portugal for a change of scenery while writing a review on biocontrol in the phyllosphere . To make things a bit more official, Prof. Sarah Lebeer said with a smile “OK, if you bring some phyllosphere samples with you to isolate bacteria from”. And so I returned with a bag full of icepack-chilled tubes filled with leaves. Airport security looked at the bag, made a little joke about the danger of cold leaves, and let me pass. Arriving late at Brussels airport, I rushed back to the lab and started processing the samples. The next days, colleague Leen Van Ham continued culturing the bacteria that had grown on the agar plates. The isolates were identified by sequencing a marker gene, the 16S rRNA gene, and comparing it to a database. I was thrilled because many isolates were lactic acid bacteria, uncommon and understudied inhabitants of plant leaves. However, I was still unaware of the real identity of some these isolates. The database comparison had shown a good match to already known species and didn’t reveal any novelty.
A few months later, my colleague Tom Eilers had news. He had been looking into the full genomes of these isolates and said that some matched only for 88% with their closest relatives. While it is known that bacteria from the same species have at least 93% identical DNA in their shared genomic regions. A similarity of 88% meant that the isolates in our freezer belonged to an unknown species!
So how is this possible, given that the 16S gene had not seemed so novel? It appears that in some cases, the 16S rRNA gene mutates very slowly, making relatively distant bacteria seem closely related. Alternatively, the gene may have been very recently exchanged between the new species and species whose 16S sequences are in the reference database. Using the entire genome avoids these pitfalls of single-gene analysis and allowed us to conclusively identify the isolates as a new bacterial species. On a side note, for mammals this “species threshold” is much higher. Did you know that we share 98.8% of our DNA with chimpanzees?
Next, we conducted a series of experiments to characterize the new species and to distinguish it from its closest relatives. You can read all about it in this manuscript . Some interesting observations were that the new species produces catalase, an enzyme protecting it against oxidative stress. It is able to consume typical plant-associated sugars, arabinose and sucrose. And the bacterium is yellow, as a result of the production of carotenoids, a pigment that protects the cells against UV stress. You could say these carotenoids act like sunscreen, quite useful when you are residing on a leaf during summer in Portugal 😎.
All these observations make us think that this species might be well equipped to survive on leaf surfaces, and that it could be used for applications in agriculture. Maybe one day, this bacterium, discovered thanks to our efforts in creating a sustainable forest garden, will contribute in solutions for crop production on a larger scale?
- Legein M, Smets W, Vandenheuvel D, Eilers T, Muyshondt B, et al. Modes of Action of Microbial Biocontrol in the Phyllosphere. Frontiers in Microbiology 2020;11:1619.
- Legein M, Wittouck S, Lebeer S. Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa). Int J Syst Evol Microbiol 2022;72:005193.
- Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020;70:2782–2858.