In my last post, I highlighted the great job that Wayne Reeve has been doing in getting rhizobial genomes sequenced and published. I listed 18 papers that he has published since the start of 2013 – each describing a genome. This is a very impressive effort! There may have been an incentive for this quick-fire rate of publication: the reports were all in a journal called Standards in Genomic Sciences (Impact Factor 2.0), which has recently been taken over by BMC, who are now imposing a hefty publication charge of £865 (about US$1450 or €1050) for each genome announcement.
SIGS is an unusual journal, specialising in bacterial and archaeal genome announcements in a short format that meets the Minimum Information about a Genome Sequence (MIGS) specification. Providing important information in a standard format is very sensible, though all the articles seem also to include a photo of the organism. I can see the attraction of this if the genome belongs to an endangered orchid or a cuddly mammal, but the genomes are all bacterial, and there is limited interest in a succession of pictures of grey sausages.
When the first bacterial genomes were sequenced, each one was a prodigious effort that merited a high profile publication. The first rhizobial genome was announced with characteristic Japanese understatement (Kaneko et al. 2000), but the second managed to garner a paper in Science and three papers in PNAS (see Downie and Young 2001). These days, bacterial genome sequences come off the production lines so fast that many never get a publication at all, and most of the rest only merit a relatively brief announcement. Besides SIGS, many bacterial genome announcements have appeared in Journal of Bacteriology, but the publishers, the American Society for Microbiology, have recently started a special journal called Genome Announcements (no impact factor yet). These announcements are limited to 500 words, and cost the authors US$500 (€360, £300), which works out at a dollar a word. ASM members get a reduced rate of US$330.
Of course, many people would like to write more than 500 words about their favourite genome, and if there is substantial biological interest that can be developed into a full paper, there are many journals that might publish it. An Open Access example would be BMC Genomics (IF 4.4). Publishing there will cost you a substantial £1325/$2215/€1600, though.
If you want to write more than 500 words, and Open Access appeals to you (it does increase visibility and citations, and many funders now require it), then I can offer you a less expensive alternative. I happen to be the editor of a relatively new journal called Genes, and we are keen to publish more bacterial genomes. We have already published the genome of the type strain of Bradyrhizobium japonicum (Kaneko et al. 2011), as well as several other bacterial genomes. We have recently been added to PubMed and PMC, so readers will be able to click straight through from GenBank entries to the linked articles. We do not have an Impact Factor yet, but we are aiming to get one. The cost of publication is a modest 500 Swiss Francs (about £340/$565/€410), and your article can be as long as you like (within reason!). I look forward to seeing your genome manuscripts!
Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S., … & Tabata, S. (2000). Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Research, 7(6), 331-338.
Downie, J. A., & Young, J. P. W. (2001). Genome sequencing: the ABC of symbiosis. Nature, 412(6847), 597-598.
Kaneko, T., Maita, H., Hirakawa, H., Uchiike, N., Minamisawa, K., Watanabe, A., & Sato, S. (2011). Complete genome sequence of the soybean symbiont Bradyrhizobium japonicum strain USDA6T. Genes, 2(4), 763-787.
The past year has seen a bonanza for rhizobial genome sequences. Here is a list of the the papers that I am aware of that were published in 2013 or 2014. Apart from the first two, they represent some of the fruits of the genome sequencing that Wayne Reeve persuaded the Joint Genome Institute to carry out. I know that many rhizobium researchers around the world provided strains and DNA for this effort, and there are many more genome sequences in the pipeline but not yet published. Some of these can already be accessed on the JGI web site or in the NCBI database. These genome sequences represent a great resource for rhizobium researchers. They will suggest new experiments – but even those who are not in a position to carry out lab work have the opportunity to use this free information to gain new insights through careful analysis in silico.
Crook, M. B., Mitra, S., Ané, J. M., Sadowsky, M. J., & Gyaneshwar, P. (2013). Complete genome sequence of the Sesbania symbiont and rice growth-promoting endophyte Rhizobium sp. strain IRBG74. Genome announcements, 1(6), e00934-13.
[This is a rhizobium that is actually an Agrobacterium. Yes, I know that some taxonomists would like us to expand Rhizobium to include Agrobacterium, which is presumably why the authors call this Rhizobium, but do not worry – Agrobacterium will be back soon! This strain is definitely in the genus Agrobacterium (Cummings et al. 2009).]
Martínez-Abarca, F., Martínez-Rodríguez, L., López-Contreras, J. A., Jiménez-Zurdo, J. I., & Toro, N. (2013). Complete genome sequence of the alfalfa symbiont Sinorhizobium/Ensifer meliloti strain GR4. Genome announcements, 1(1), e00174-12.
Willems, A., Tian, R., Brau, L., Goodwin, L., Han, J., Liolios, K., … & Reeve, W. G. (2013). Genome sequence of Burkholderia mimosarum strain LMG 23256 T; a Mimosa pigra microsymbiont from Anso, Taiwan. Standards in Genomic Sciences, 9(3).
Reeve, W. G., Tian, R., Brau, L., Goodwin, L., Munk, C., Detter, C., … & Willems, A. (2013). Genome sequence of Ensifer arboris strain LMG 14919 T; a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. Standards in Genomic Sciences, 9(3).
Reeve, W. G., Watkin, E., Tian, R., Bräu, L., O’Hara, G., Goodwin, L., … & Reeve, W. (2013). Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia. Standards in Genomic Sciences, 9(3).
Terpolilli, J., Hill, Y., Tian, R., Howieson, J., Bräu, L., Goodwin, L., … & Reeve, W. (2013). Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17. Standards in Genomic Sciences, 9(2).
Reeve, W. G., Ardley, J., Tian, R., De Meyer, S., Terpolilli, J., Melino, V., … & Kyrpides, N. C. (2013). Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557 T. Standards in Genomic Sciences, 9(3).
Terpolilli, J., Tian, R., Yates, R., Howieson, J., Poole, P., Munk, C., … & Reeve, W. (2013). Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum. Standards in Genomic Sciences, 9(3).
Reeve, W. G., Garau, G., Hill, Y., Tian, R., Howieson, J., Bräu, L., … & Reeve, W. (2013). Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos. Standards in Genomic Sciences, 9(2).
Reeve, W. G., Terpolilli, J., Melino, V., Ardley, J., Tian, R., De Meyer, S., … & Kyrpides, N. C. (2013). Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii srain WSM597. Standards in Genomic Sciences, 9(2).
Reeve, W., Nandasena, K., Yates, R., Tiwari, R., O’Hara, G., Ninawi, M., … & Howieson, J. (2013). Complete genome sequence of Mesorhizobium australicum type strain (WSM2073 T). Standards in Genomic Sciences, 9(2).
Reeve, W. G., Ballard, R., Howieson, J., Drew, E., Tian, R., Bräu, L., … & Kyrpides, N. (2013). Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece. Standards in Genomic Sciences, 9(3).
Reeve, W. G., Nandasena, K., Yates, R., Tiwari, R., O’Hara, G., Ninawi, M., … & Howieson, J. (2013). Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075 T. Standards in Genomic Sciences, 9(2).
Nanadasena, K., Yates, R., Tiwari, R., O’Hara, G., Howieson, J., Ninawi, M., … & Reeve, W. (2013). Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271 T). Standards in Genomic Sciences, 9(3).
Reeve, W. G., Drew, E., Ballard, R., Melino, V., Tian, R., De Meyer, S., … & Kyrpides, N. (2013). Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565. Standards in Genomic Sciences, 9(2).
Reeve, W. G., Terpolilli, J., Melino, V., Ardley, J., Tian, R., De Meyer, S., … & Kyrpides, N. C. (2013). Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417. Standards in Genomic Sciences, 9(2).
Tak, N., Gehlot, H. S., Kaushik, M., Choudhary, S., Tiwari, R., Tian, R., … & Reeve, W. (2013). Genome sequence of Ensifer sp. TW10; a “Tephrosia wallichii” (Biyani) microsymbiont native to the Indian Thar Desert. Standards in Genomic Sciences, 9(2).
Reeve, W. G., De Meyer, S., Terpolilli, J., Melino, V., Ardley, J., Tian, R., … & Kyrpides, N. C. (2013). Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471. Standards in Genomic Sciences, 9(2).
Reeve, W. G., De Meyere, S., Terpolilli, J., Melino, V., Ardley, J., Rui, T., … & Kyrpides, N. (2013). Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005 T. Standards in Genomic Sciences, 9(2).
Reeve, W. G., Ballard, R., Drew, E., Tian, R., Bräu, L., Goodwin, L., … & Kyrpides, N. (2014). Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128. Standards in Genomic Sciences, 9(3).
Happy New Year!
2013 has gone, and this blog seems to have missed most of it. To make amends, here are a few rather randomly chosen papers from the past year. You may have missed some of them. For all I know, you may have written some of them. They are not the most important papers of the year, but they are in the general area of rhizobial diversity and evolution. There are dozens of others I could equally well have chosen – maybe I will add some more over the next few days. If you have any suggestions, feel free to add them as comments on this post.
Friesen, M. L., & Heath, K. D. (2013). One hundred years of solitude: integrating single‐strain inoculations with community perspectives in the legume–rhizobium symbiosis. New Phytologist 198, 7-9.
Maren Friesen and Katy Heath respond to criticisms by Toby Kiers et al.
Ling, J., Zheng, H., Katzianer, D. S., Wang, H., Zhong, Z., & Zhu, J. (2013). Applying Reversible Mutations of Nodulation and Nitrogen-Fixation Genes to Study Social Cheating in Rhizobium etli-Legume Interaction. PloS one, 8(7), e70138.
An experimental contribution to the discussion of cheating in the rhizobium-legume symbiosis.
Takahara, M., Magori, S., Soyano, T., Okamoto, S., Yoshida, C., Yano, K., … & Kawaguchi, M. (2013). TOO MUCH LOVE, a Novel Kelch Repeat-Containing F-box Protein, Functions in the Long-Distance Regulation of the Legume–Rhizobium Symbiosis. Plant and Cell Physiology, 54(4), 433-447.
The name is irresistible, isn’t it? The work actually concerns regulation of nodulation by the plant, which is clearly part of the cheating/sanctioning story.
Sánchez-Cañizares, C., & Palacios, J. (2013). Construction of a marker system for the evaluation of competitiveness for legume nodulation in Rhizobium strains. Journal of microbiological methods, 92(3), 246-249.
A technique for marking strains with gusA or celB, which could be useful for investigating genes that affect competitiveness.
Vanderlinde, E. M., Hynes, M. F., & Yost, C. K. (2013). Homoserine catabolism by Rhizobium leguminosarum bv. viciae 3841 requires a plasmid‐borne gene cluster that also affects competitiveness for nodulation. Environmental Microbiology. DOI: 10.1111/1462-2920.12196
Many R. leguminosarum symbiovar viciae strains can utilise homoserine, which is present in pea root exudate. Genes for homoserine utilisation are identified and characterised.
Rashid, M., Gonzalez, J., Young, J. P. W., & Wink, M. (2013). Rhizobium leguminosarum is the symbiont of lentils in the Middle East and Europe but not in Bangladesh. FEMS Microbiology Ecology. DOI: 10.1111/1574-6941.12190
I am an author on this one, but the real work was done by Harun-or Rashid. He showed that lentils in Turkey, Syria and Germany were nodulated by “ordinary” R. leguminosarum sv. viciae, but the situation is very different in Bangladesh, where several new species are involved.
Nangul, A., Moot, D. J., Brown, D., & Ridgway, H. J. (2013). Nodule occupancy by Rhizobium leguminosarum strain WSM1325 following inoculation of four annual Trifolium species in Canterbury, New Zealand. New Zealand Journal of Agricultural Research, 56(3), 215-223.
A New Zealand group applied commercial inoculant of R. leguminosarum WSM1325 to four clover species in the field. They did not recover any WSM1325 from nodules – hardly surprising, since they showed that most of the live cells in the inoculant were contaminants. They did, however, recover dozens of different R. leguminosarum genotypes from these New Zealand soils (where clovers are not native), and found that one clover species had a distinctly different strain preference from the others.
Saïdi, S., Ramírez-Bahena, M. H., Santillana, N., Zúñiga, D., Álvarez-Martínez, E., Peix, A., … & Velázquez, E. (2013). Rhizobium laguerreae sp. nov. nodulates Vicia faba in several continents. International journal of systematic and evolutionary microbiology, doi: 10.1099/ijs.0.052191-0
A new species in the R. leguminosarum species complex, named after the late Gisèle Laguerre (see my post).
Andres, J., Arsène-Ploetze, F., Barbe, V., Brochier-Armanet, C., Cleiss-Arnold, J., Coppée, J. Y., … & Bertin, P. N. (2013). Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium Rhizobium sp. NT-26. Genome biology and evolution, 5(5), 934-953.
This is probably an Agrobacterium rather than a Rhizobium, but even with a complete genome sequence its exact phylogenetic position was ambiguous – which sheds an interesting light on the unreliability of “phylogenetic markers” in the face of widespread recombination. It does not seem to have Nod or Ti genes.
Maren Friesen is recruiting a postdoc for a new project. It is not exactly on rhizobia, but I am sure that experience with rhizobia would come in handy for this. Here is the message she has just circulated.
Nitrogen is one of the most limiting nutrients in terrestrial ecosystems. A new joint project between the Friesen lab at Michigan State University and the Rutherford & Buck labs at Imperial College London seeks to isolate and characterize microbes with novel biological nitrogen-fixation capabilities. A talented and collaborative individual is sought to join the Friesen lab as a postdoc to contribute to this project. Desired skills include microbiology, biochemistry, and genetics/genomics (there will be no plant work in the current phase of this project). The position will be located at MSU in East Lansing, MI, with opportunities to participate in field collections and collaborative stays in London. The successful candidate will be encouraged to develop independent lines of research and will benefit from an egalitarian and highly interactive lab environment. Start date is as soon as possible. Please send CV and ~1-page statement of research interests to firstname.lastname@example.org.
I have written before about the Centre for Genomic Sciences (CCG) in Cuernavaca, part of the National Autonomous University of Mexico (UNAM). Its scientists have played an important role in the development of rhizobium research for the past 30 years. Originally dedicated to nitrogen fixation research, the remit has been broadened to genomic sciences, but there is still a lot of interest in rhizobia. I have a lot of friends there, and they are doing good work.
Now, CCG is advertising five tenure-track positions:
- Bacterial or Plant Synthetic Biology.
- Bacterial or Plant Systems Biology.
- Bioinformatics applied to Bacterial or Plant models.
- Population or Evolutionary Genomics in Bacteria.
- Plant Functional Genomics (may include epigenetics, bacteria-plant interactions, signalling).
If you are interested, you will find details at http://www.ccg.unam.mx/en/positions/available
The closing date is 15 May.
The concept of a symbiovar is key to understanding the diversity of rhizobia. The genes that determine symbiotic host range are part of the accessory genome that can transfer between strains and between species. The consequence is that different bacterial species (usually closely related) may carry almost identical symbiosis genes and have the same host range, while strains that are in the same species may carry quite different symbiosis genes and have distinct host ranges. Jarvis et al. (1980) were the first to recognise this situation by proposing that clover symbionts formed a biovar of Rhizobium leguminosarum. With remarkable insight for the time, they speculated:
“It seems likely that specific plasmids confer plant specificity on basically similar strains of bacteria and thus provide an alternative mechanism for the acquisition of plant specificity which does not require evolutionary specialization and consequent genetic divergence.
Carl Jordan, writing in Bergey’s Manual (1984), formalised the description of three biovars of R. leguminosarum (bv. viciae, bv. trifolii, bv. phaseoli). Much later, the more specific term “symbiovar” was proposed by Rogel et al. (2011), who documented numerous examples (see my early post about symbiovars).
The species R. pisi was separated from R. leguminosarum because its core gene sequences are sufficiently different to merit species status. The symbiosis genes of its type strain are, however, almost the same as those of the R. leguminosarum type strain. Marek-Kozaczuk et al. (2013) have now described a symbiont isolated from red clover that is R. pisi according to its core gene phylogeny, but has symbiosis genes much the same as those of R. leguminosarum symbiovar trifolii strains. This strain K3.22 is, rather obviously, R. pisi sv. trifolii. This is totally unsurprising – R. leguminosarum and R. pisi are closely related species, and if they can share plasmids carrying sv. viciae symbiosis genes, there is no reason to think they would not also share sv. trifolii genes.
So far, no surprises. No surprise, either, that R. pisi sv. K3.22 nodulates and fixes nitrogen on the clovers Trifolium pratense and T. repens but not vetches, while the type strain R. pisi sv. viciae DSM 30132 is effective on the vetch Vicia villosa, but not on clovers. That is how the same biovars behave in R. leguminosarum. The most unexpected statement in this new paper, however, is that “both strains nodulated pea (P. sativum cv. Iłówiecki) and the Spanish bean cultivar (P. vulgaris cv. Slenderette).” Now, the bean Phaseolus vulgaris is well known as a promiscuous host that often lets the “wrong” rhizobia form nodules, but these nodules fix no nitrogen. That a sv. trifolii strain should form nodules on pea is quite unexpected, though. My first thought was that this was another case of occasional, ineffective nodules, but later the authors state that “K3.22 efficiently nodulated red clover, pea and some bean cultivars”, so it seems that this R. pisi sv. trifolii is truly something new – a clover symbiont that is also effective on a host that is normally only nodulated effectively by sv. viciae. This is certainly the most interesting observation in the whole paper but, frustratingly, those two quotes are the only times this is mentioned, and no data are presented to support this novel claim. We can only hope that work is under way to understand how this strain can form an efffective symbiosis with pea, and more information will be published soon.
R. pisi has gained a new symbiovar, but more interestingly, it seems that sv. trifolii has gained a new host.
Jarvis BDW, Dick AG, Greenwood RM (1980) Deoxyribonucleic acid homology among strains of Rhizobium trifolii and related species. International Journal of Systematic Bacteriology 30, 42-52. http://dx.doi.org/10.1099/00207713-30-1-42
Jordan DC (1984). Family III. Rhizobiaceae. In Bergey’s Manual of Systematic Bacteriology, vol. I, pp. 234–242. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams and Wilkins Co.
Rogel MA., Ormeño-Orrillo E, Martinez Romero E (2011) Symbiovars in rhizobia reflect bacterial adaptation to legumes. Systematic and applied microbiology, 34(2), 96-104. http://dx.doi.org/10.1016/j.syapm.2010.11.015
Marek-Kozaczuka M et al. (2013) Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster. Syst Appl Microbiol http://dx.doi.org/10.1016/j.syapm.2013.01.005
I did not set out to write a blog about gladiators, but it seems that the sword-bearers just won’t go away. Back in January, I wrote about a study that showed that deployment of a Type 6 Secretion System rendered the bearer more susceptible to a retaliatory attack by the T6SS of other cells. A new paper from Marek Basler and colleagues takes this story further (Basler et al. 2013), and is accompanied by a great video introduced by the head of the lab, John Mekalanos. In an amazing sequence of scenes with a cast of thousands, you can watch the swords of the rival armies flashing as the battlefield becomes littered with the bodies of the vanquished foe. The Pseudomonas aeruginosa cells kill Vibrio cells that unsheath their T6SS, but leave unarmed cells alone.
Does this have any relevance to rhizobia? I remind you that an early report of a phenomenon that turned out to involve a T6SS was in Rhizobium leguminosarum (Roest et al. 1997; Bladergroen et al. 2003). I mentioned this in a post last year. A strain with a functional imp locus was unable to nodulate Pisum sativum or Vicia hirsuta, although it formed normal nodules on V. sativa. A mutation in imp (the T6SS) allowed nodulation of all these hosts. These rhizobia had no other bacteria to fight, but there are now many studies showing that T6SS can be used to penetrate eukaryotic host cells (Records 2011), so I imagine that an interaction with legume cells is at the root (sorry!) of this phenomenon. Host specificity is an interesting and incompletely understood aspect of the rhizobium-legume interaction, and it seems that T6SS might be one piece in the jigsaw. I would be surprised, though, if T6SS did not sometimes also play a role in competitive interactions between rhizobia in the rhizosphere.
Basler M, Ho Brian T, Mekalanos John J (2013) Tit-for-Tat: Type VI Secretion System Counterattack during Bacterial Cell-Cell Interactions. Cell 152, 884-894.
Bladergroen, M. R., Badelt, K., and Spaink, H. P. (2003) Infection-blocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion. Mol. Plant-Microbe Interact. 16:53-64
Records, A. R. (2011). The type VI secretion system: a multipurpose delivery system with a phage-like machinery. Molecular Plant-Microbe Interactions, 24, 751-757.
Roest, H. P., Mulders, I. H. M., Spaink, H. P., Wijffelman, C. A., and Lugtenberg, B. J. J. (1997) A Rhizobium leguminosarum biovar trifolii locus not localized on the sym plasmid hinders effective nodulation on plants of the pea cross-inoculation group. Mol. Plant-Microbe Interact. 10:938-941.