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European Nitrogen Fixation Conference – deadline today!

The 11th European Nitrogen Fixation Conference will be held on September 7 to 10, 2014 at Tenerife, Canary Islands, Spain.  I would like to remind you that today is the deadline for early registration: the price goes up tomorrow.  Today is also the deadline for offering an oral presentation.

There is already a great line-up of invited speakers for the conference – check the web site – but the full programme is not yet decided because the organisers will be choosing more speakers from the abstracts that have been offered.  This is your opportunity for 15 minutes of fame, so get your abstract in today!

As usual, I am organising a satellite workshop on the genomics of N-fixers, and this will take place on Sunday 7 September before the main meeting opens.  The workshop consists entirely of offered talks, and I have had plenty of offers, so the programme is already full and I can share it with you here and now.

 

Satellite Meeting

Workshop on the Genomics of N-Fixing Organisms

Dream Hotel, Gran Tacande, Tenerife

7 September 2014

Organiser: Peter Young (York, UK)

 

08.30 – 09.00              Registration for Workshop

09.00 – 10.40       Session 1

 

09.00 – 09.20

Anton Hartmann (Munich, Germany): Genomic comparison of Azospirillum brasilense with the opportunistic human pathogens Roseomonas fauriae and Roseomonas genomospecies 6

09.20 – 09.40

David Durán (Madrid, Spain): Comparative Genome Analysis of Bradyrhizobium valentinum sp. nov. LmjM3T Isolated from Lupinus mariae-josephae and related Bradyrhizobium strains.

09.40 – 10.00

Kristina Lindström (Helsinki, Finland): Neorhizobium galegae: ten genomes to describe the two symbiovars

10.00 – 10.20

George diCenzo (Hamilton, Canada): Genomic analysis of the pSymA megaplasmid and pSymB chromid of Sinorhizobium meliloti

10.20 – 10.40

Jelena Chuklina (Moscow, Russia): Transcription Start Site and Promoter Map of Bradyrhizobium japonicum USDA 110

 

10.40 – 11.10             Coffee


11.10 – 12.50       Session 2

 

11.10 – 11.30

Xavier Perret (Geneva, Switzerland): Transcriptome analyses of Sinorhizobium fredii strain NGR234 and associated hosts

11.30 – 11.50

Dagmar Krysciak (Hamburg, Germany): RNA-seq analysis of Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant

11.50 – 12.10

Changfu Tian (Beijing, China): Host adaptation of Sinorhizobium sp. NGR234 as revealed by RNA-seq and reverse genetics

12.10 – 12.30

Ana Alexandre (Évora, Portugal): Global transcriptional analysis of Mesorhizobium loti MAFF303099 shows a reduced general stress response

12.30 – 12.50

Sharon Long (Stanford, CA, USA): Bioinformatic and experimental analyses of Sinorhizobium meliloti gene expression.

12.50 – 13.50            Lunch

 

13.50 – 15.30      Session 3

 

13.50 – 14.10

José Vinardell (Sevilla, Spain): Analyses of the Sinorhizobium fredii HH103 genome and of its secretome in the presence and absence of genistein

14 .10 – 14.30

Marina Roumiantseva (St Petersburg, Russia): Genomic islands in bacteria: with particular focus on Sinorhizobium meliloti

14.30 – 14.50

Beatriz Jorrín (Madrid, Spain): Genomic Structure of a Soil Rhizobium leguminosarum bv. viciae Population

14.50 – 15.10

Alessio Mengoni (Florence, Italy): Evolution of regulatory networks in Sinorhizobium meliloti is species- and replicon-specific

15.10 – 15.30

Michael Hynes (Calgary, Canada): Genomics of rhizobial phages

15.30                         End of workshop

 

I hope you agree that this programme looks really exciting, so don’t forget to register for the Genomics Workshop at the same time as you register for the main ENFC.  I look forward to seeing you in Tenerife!

Meeting on the Genomics of Nitrogen-Fixing Organisms

No doubt many of you are planning to attend the 11th European Nitrogen Fixation Conference, which will be held in Tenerife on 7-10 September 2014. This is one of the major international conferences for rhizobium researchers, attended by people from around the world, not just Europe. I am, once again, organising  a satellite meeting on “Genomics of Nitrogen-Fixing Organisms” on Sunday 7 September before the main conference begins. Similar workshop meetings at previous conferences have been very popular.

The workshop covers the analysis of genomes of N-fixing bacteria or archaea, as well as post-genomic studies such as transcriptomics and proteomics.  The format is a series of short offered talks, probably 15 minutes plus 5 minutes for questions.  There has been a flood of new genomes since the last workshop in 2012, so there should be plenty to talk about. I would welcome analyses that compared multiple genomes, as well as detailed studies of individual strains.

If you, or one of your colleagues, would like to give a talk at the workshop, please let me have a title and a very brief abstract (<100 words) by email to peter.young@york.ac.uk. This does not have to be your final abstract – just a few words so that I can check that your contribution is relevant and can decide where to place it in the programme.  I will accommodate as many speakers as possible, but may have to be selective if we get too many offers. To have the best chance, please apply as soon as possible. The deadline is 15 May, but don’t wait till then as we may fill the programme sooner. You do not need to register before contacting me.

If you know of any other labs who are working on the genomics of N-fixers and may be interested, please let me know. Note that this workshop is restricted to the genomics of the N-fixing organisms themselves, not their symbiotic partners, and I also want to avoid any overlap with the talks already scheduled for the main meeting. However, our workshop could be a good place for postdocs or students to present more detailed aspects of the work than will be possible in the more formal setting.  This can include material presented as posters in the main conference – but if your contribution is  selected for oral presentation in the main sessions, we will take it out of the workshop to avoid duplication.

The workshop will be held in the morning and afternoon of Sunday 7 September, before the opening of the main conference.  There will be an additional registration charge for the genomics workshop (€50, €25 for students), which will include the cost of lunch and coffee breaks, so please make sure that you sign up for this when you register for the main conference. This charge is payable by everyone who attends, including the speakers.

I do hope that you will be able to join us for a busy and lively day.

Announcing rhizobial genomes

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.

Rhizobial genomes galore

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).

 

 

Some 2013 papers

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.

http://onlinelibrary.wiley.com/doi/10.1111/nph.12173/full

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.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0070138

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.

http://pcp.oxfordjournals.org/content/54/4/433.short

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.

http://www.sciencedirect.com/science/article/pii/S0167701213000031

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

http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12196/abstract

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

http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12190/full

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.

http://www.tandfonline.com/doi/abs/10.1080/00288233.2013.815637#.UsSH1o1Rcgw

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

http://ijs.sgmjournals.org/content/early/2013/09/25/ijs.0.052191-0.short

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.

http://gbe.oxfordjournals.org/content/5/5/934.full

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.

Postdoc position in nitrogen fixation

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 mfriesen@msu.edu.

Faculty positions in genomics

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.

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