2011: a rhizobial travelogue
As 2011 is ending, I am looking back on a year when I made a lot of scientific trips outside the UK. I met up with many old and new friends, and learned a huge amount during my travels. Altogether, I made eight journeys, of which four were rhizobium-related. Here is a brief tour of the places I visited and the interesting work that people are doing there.
In February I visited Bielefeld in Germany at the invitation of Alf Pühler and Stefan Weidner. After the European N-Fixation Conference last year, I contacted various people to sound out the possibility of establishing a collaborative web-based information resource for researchers interested in rhizobial genomes and post-genomic data. In Bielefeld, they certainly have the infrastructure to handle something like this – over the past decade, they have established extensive hardware and bioinformatic rsources for handling bacterial genome projects. Whether we can find funding for a community resource is another matter. In Bielefeld, they work on many different bacteria, but there are still some rhizobia among their current projects. In 2011, they have published genome data for four different species.
Every genome sequence is just a snapshot of one individual at one moment, so it is always important to have more than one genome available if we want to understand a bacterial species. For a long time, the genome of Sinorhizobium meliloti has been represented by strain Rm1021, but soon we will have quite a few genomes of this species. The Bielefeld group has contributed strain SM11, which has a chromosome and equivalents of pSymA and pSymB, but also two smaller plasmids that were sequenced and published some time ago.
Schneiker-Bekel, S., Wibberg, D., Bekel, T., Blom, J., Linke, B., Neuweger, H. et al. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. J Biotechnol 155: 20-33. DOI: 10.1016/j.jbiotec.2010.12.018
Sinorhizobium fredii is a fast-growing symbiont of soybeans. There will also be several genomes of S. fredii strains within the next year or so. It will be interesting to compare these with the genome of Sinorhizobium sp. NGR234, which is a broad-host-range symbiovar rather than a soybean symbiont, but which NCBI is now calling S. fredii. It is certainly closely related, but it will be good to have some “real” S. fredii for comparison. The Bielefeld group have announced a draft assembly of strain HH103.
Margaret, I., Becker, A., Blom, J., Bonilla, I., Goesmann, A., Göttfert, M. et al. Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. J Biotechnol 155: 11-19. DOI: 10.1016/j.jbiotec.2011.03.016
Alfalfa is usually a very specific host, nodulated by Sinorhizobium meliloti and S. medicae, but occasionally other symbionts have been found, such as Or191 (originally from Oregon) and related strains, that may fix poorly on alfalfa but also nodulate Phaseolus. The exact identity of these strains was rather mysterious, but they seemed to be Rhizobium rather than Sinorhizobium. A first look at genomic data from one of them has confirmed this, though it does not tell us much more than that so far. The paper provides a useful review of our knowledge of these strains, though.
Torres Tejerizo, G., Del Papa, M.F., Draghi, W., Lozano, M., Giusti, M.d.l.Á., Martini, C. et al. First genomic analysis of the broad-host-range Rhizobium sp. LPU83 strain, a member of the low-genetic diversity Oregon-like Rhizobium sp. group. J Biotechnol 155: 3-10. DOI: 10.1016/j.jbiotec.2011.01.011
There is an unusual story behind the last Bielefeld paper that I will highlight. The Bielefeld group wanted a special retirement gift for their beloved Professor Alf Pühler, so they decided to sequence the bacterium that he worked on for his own first project forty years ago. He developed the molecular genetics of a bacterium called Rhizobium lupini. Of course, that was back in the days when all rhizobia were Rhizobium; in fact, lupin symbionts are usually Bradyrhizobium, but we do not know exactly what that R. lupini was. Perhaps we never will know, because it proved impossible to track down a culture, so the strain that was sequenced was a different one that was also described as R. lupini. This turned out to belong to Agrobacterium genomic species G1, but functionally it is neither an agrobacterium (no Ti plasmid for tumour induction) nor a rhizobium (no nodulation genes). Like strain C58 (genomic species G8), it has a linear chromid – it will be interesting to see whether this is also true for other Agrobacterium genomic species.
Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B. et al. Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. J Biotechnol 155: 50-62. DOI: 10.1016/j.jbiotec.2011.01.010
In April, I was in Thailand visiting three PhD students who had all spent time in my lab in York. None were studying rhizobia – two worked on mycorrhizal fungi and one on bacteria in bee guts. A paper on the bee bacteria has recently resulted from this – it is the first study that looked at juveniles as well as adults. Many of the bacteria found in adult guts in Thailand have been reported previously from insect guts elsewhere, which suggests that there is a consistent gut community. However, the microbiome of larval and pupal guts is quite different from that of adults in the same hive, which raises some questions about the factors that lead to the development of the gut community.
Disayathanoowat, T., Young, J.P.W., Helgason, T., and Chantawannakul, P. (2011) T-RFLP analysis of bacterial communities in the midguts of Apis mellifera and Apis cerana honey bees in Thailand. FEMS Microbiology Ecology: doi: 10.1111/j.1574-6941.2011.01216.x
In the first week of May, I was in Finland for a course organised by Kristina Lindström and for discussions with her and her student Janina Österman, who has also visited us in York previously. They are sequencing representative genomes of the two biovars of Rhizobium galegae, which will be interesting because of their different host specificities for effective nitrogen fixation, and also because the phylogenetic place of this species is not very well defined – it is perhaps more of an Agrobacterium than a Rhizobium. Kristina’s group have not got the R. galegae genomes ready yet, but they have an new paper on genetic diversity in the host plants. This includes symbiosis-related genes, which is good because if we aim to understand specificity then we need to consider the relevant genetic differences in both the bacterial and the plant partner.
Österman, J., Chizhevskaja, E.P., Andronov, E.E., Fewer, D.P., Terefework, Z., Roumiantseva, M.L. et al. Galega orientalis is more diverse than Galega officinalis in Caucasus—whole-genome AFLP analysis and phylogenetics of symbiosis-related genes. Molecular Ecology 20: 4808-4821. DOI: 10.1111/j.1365-294X.2011.05291.x
I returned home from Finland just long enough to replace the clothes in my bag with lighter ones and head off again, this time to Italy. Paola Bonfante’s group in Turin have contributed greatly to our understanding of the arbuscular mycorrhizal (AM) symbiosis. They do not work on rhizobia, but it is important for rhizobium researchers to know about the AM symbiosis because the molecular signalling between rhizobia and legumes appears to have evolved from the much older AM fungal symbiosis.
This first paper is a review by Paola of recent advances in our knowledge of this signalling.
Bonfante, P., and Requena, N. (2011) Dating in the dark: how roots respond to fungal signals to establish arbuscular mycorrhizal symbiosis. Current Opinion in Plant Biology 14: 451-457. DOI: 10.1016/j.pbi.2011.03.014
The second paper describes calcium spiking in root cells in response to AM fungi. Of course, this is also an important part of the response to rhizobial nod factors.
Chabaud, M., Genre, A., Sieberer, B.J., Faccio, A., Fournier, J., Novero, M. et al. (2011) Arbuscular mycorrhizal hyphopodia and germinated spore exudates trigger Ca2+ spiking in the legume and nonlegume root epidermis. New Phytologist 189: 347-355. DOI: 10.1111/j.1469-8137.2010.03464.x
Finally, a bacterial genome paper. Not a rhizobium, but a bacterium that lives permanently in the cytoplasm of an AM fungus – a symbiont within a symbiont. It is a Burkholderia, and hence related to the beta-rhizobial symbionts of Mimosa. As an obligate symbiont, its genes have evolved rapidly, and the authors suggest that it should have its own genus. They call it Candidatus Glomeribacter gigasporarum. “Candidatus” is used to indicate a bacterial species that has not yet been cultured, so is not entitled to a normal species name. If anyone succeeds in establishing a culture, it will then become Glomeribacter gigasporarum. It is not entirely clear what it does inside the fungus, but the authors draw some conclusions about its metabolism based on the genome data.
Ghignone, S., Salvioli, A., Anca, I., Lumini, E., Ortu, G., Petiti, L. et al. (2011) The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. ISME Journal 6: 136-145. DOI: 10.1038/ismej.2011.110
After a couple of months back home, I was off to Italy again, this time to visit Marco Bazzicalupo in Florence. His group does state-of-the-art bacterial genomics in the most unlikely surroundings: an eighteenth-century natural history museum where you can see a stuffed pet hippopotamus, apparently. The crumbling building, backing onto the Boboli Gardens, is certainly more appropriate for stuffed beasts than for molecular biology, but Marco has an excellent team.
This year, they published two more Sinorhizobium meliloti genomes.
Galardini, M., Mengoni, A., Brilli, M., Pini, F., Fioravanti, A., Lucas, S. et al. (2011) Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomics 12: 235. DOI: 10.1186/1471-2164-12-235
They also took advantage of the growing number of available rhizobial genomes to look for features of rhizobia and, more widely, of plant-associated bacteria.
Pini, F., Galardini, M., Bazzicalupo, M., and Mengoni, A. (2011) Plant-bacteria association and symbiosis: are there common genomic traits in Alphaproteobacteria? Genes 2: 1017-1032. DOI: 10.3390/genes2041017
In August I went to a conference that was, for me, rather strange: the European Conference on Artificial Life. This was a conference primarily for computer scientists who use evolutionary ideas to create interesting computer software. It is the only conference I have been to that had an artist-in-residence and a musician-in-residence. I have been participating in an interdisciplinary project on evolutionary computation; if you are interested, you can read one of the papers that we contributed to the conference at http://plazzmid.org/papers/11ECALemb.pdf . I say “we”, but my role has been largely to keep the biological aspects reasonably close to reality while the computer scientists gallop off into the misty distance.
In October, it was France again – this time, the delightful little Breton port of Roscoff for a Jacques Monod Conference on “Integrative Ecological Genomics”. Apart from my own talk, there was nothing on rhizobia, but a lot of fascinating data about other bacteria, especially some huge metagenomic data sets from marine microbes. The other dominant theme was viruses, and this reminded me that the study of rhizobial phages is a very neglected field. Phages can impose strong selective pressures on bacteria, and can be important agents of horizontal gene transfer. It is really shameful that we know so little about the phages that live with our favourite bacteria. Is anyone out there studying phages of rhizobia?
In November, I went to Mexico. This was my final trip of 2011, but you already know about that from my previous post, so I do not need to say any more here.
It just remains to wish all my readers a very
Happy New Year!