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rhizobium

writing about bacteria and their genomes
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I plan to make my Wordpress blog on rhizobium available through Scoop.it

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Chang Fu Tian's comment, February 5, 2013 7:33 AM
Hi Peter,Glad to be able to access your blog on rhizobium!
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Population genomics of Rhizobium leguminosarum – 3

Population genomics of Rhizobium leguminosarum – 3 | rhizobium blog | Scoop.it
Here are some more thoughts on issues raised by our new paper:
Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X.
Peter Young's insight:

Here are some more thoughts on issues raised by our new paper:

Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. 2015 Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol. 5: 140133.

rsob.royalsocietypublishing.org/content/5/1/140133

 

First, I should note that our paper has been covered in an article in the online newspaper, The Speaker.

Phenotype: the problem with polyphasic taxonomy

Ganesh Lad grew our 72 strains on Biolog plates to test their ability to grow on each of 95 substrates.  He found that almost every strain had a unique pattern, just as we had found with gene content.  As a geneticist, I naturally believe that such phenotypes are determined by genes.  We were able to prove that connection for one substrate, gamma-hydroxybutyrate, but it was not easy to map phenotypes to genes more generally.  There were no patterns of substrate utilisation that were characteristic of particular genospecies – by contrast, there were some accessory genes that were found only in one of the genospecies, so there might be some genospecies-specific phenotypes, but they were not among the “easy” ones that we looked at.

Many of these “easy” phenotypes are the ones that taxonomists conventionally report when describing a new species.  When we looked up the species description for Rhizobium leguminosarum, we found a long list of substrates that this species can, or cannot grow on.  However, when we cross-checked this list against our data for the same substrates, we found that the majority of these assertions were actually wrong – they were disobeyed by some of our strains, even though we have good evidence that they do belong to this species, as normally defined.  It seems clear that the tables of differences between species in substrate utilisation, beloved of taxonomists, are largely a fiction based on an inadequate sampling of the variation within species.  Fifty years ago, phenotypes were all that bacteriologists had to go on when trying to classify bacteria, but nobody should rely on these metabolic phenotypes to identify bacteria these days, when DNA sequence is so much easier and more conclusive.  Ernesto Ormeño-Orrillo and Esperanza Martínez-Romero (2013) have already made a similar point, and I agree with them.

Now that we know so much more about bacterial genomes, thanks to thousands of genome sequences, we can propose a bacterial classification that reflects the reality of core and accessory genomes.  The sequences of core genes provide a robust phylogeny that allows stable species to be defined and recognised, even if strains differ in phenotype.  On the other hand, the possession of important phenotypes, conferred by clusters of accessory genes, should play no part in defining species, but can be recognised as “biovars”.  These phenotypes include pathogenesis, metabolic traits, or – in the special case of rhizobia – symbiotic capabilities.  They are the “apps” that bacteria download from the microbial internet, and they determine most of the “interesting” things that bacteria do.

Ormeño-Orrillo E, Martínez-Romero E. 2013 Phenotypic tests in Rhizobium species description: an opinion and (a sympatric speciation) hypothesis.  Syst. Appl. Microbiol. 36, 145 – 147. (doi:10.1016/j.syapm.2012.11.009)
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Population genomics of Rhizobium leguminosarum

Population genomics of Rhizobium leguminosarum | rhizobium blog | Scoop.it
I am following up my last post with some slightly more technical comments about our new paper.  Firstly, here is the full reference, and a link that I hope will work better: Kumar N, Lad G, Giuntin...
Peter Young's insight:

I am following up my last post with some slightly more technical comments about our new paper.  Firstly, here is the full reference, and a link that I hope will work better:

Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. 2015 Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol. 5: 140133.

rsob.royalsocietypublishing.org/content/5/1/140133

For those interested in Rhizobium, the first point is that, although we only looked in one square metre, we found five genetic clusters within our R. leguminosarum population that were sufficiently distinct in sequence that each could be described as a new species.  Furthermore, these genospecies, and a small number of others, can also be identified in locations around the world.  All of these fall within R. leguminosarum as presently defined, and are definitely more similar to each other than to related species such as R. pisi, R. fabae, R. phaseoli or R. etli.  On the other hand, the recently described R. laguerreae seems much closer, though it is not possible to match it with any one of these genospecies on the basis of the very limited sequence information that is currently available for it.  At the moment, our five genospecies have no distinguishing phenotypic features, so traditional taxonomists are unlikely to let us describe them as formal species.  I wouldn’t want to, anyway – it would just create unnecessary complications for people who wanted to use R. leguminosarum to do some real science.

Another interesting point is that a large part of the extrachromosomal genome seems to have little mobility between the genospecies.  This is not just true of the two chromids (chromosome-like plasmids) that are homologous to pRL12 and pRL11, but also of the genes that occur on the smaller pRL10 and pRL9.  Incidentally, a search for the repABC genes reveals that all 72 isolates have replicons equivalent to pRL12 and pRL11, and nearly all have one like pRL10.  The other replicons of strain 3841 are relatively rare in our population, though all of them are found.  Much more frequent is the replicon of the pR132503 plasmid of strain WSM 1325.  This information on plasmids is not in the paper – it comes from an extensive analysis in the PhD thesis of Nayoung Kim, who has now returned to a bioinformatics job in Korea.

A study of 72 genome sequences is bound to reveal a lot of things, and there are plenty more points I would like to draw to your attention, but I will save them for future posts.

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European Nitrogen Fixation Conference – deadline today!

European Nitrogen Fixation Conference – deadline today! | rhizobium blog | Scoop.it
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...
Peter Young's insight:

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 MeetingWorkshop on the Genomics of N-Fixing OrganismsDream Hotel, Gran Tacande, Tenerife7 September 2014

Organiser: Peter Young (York, UK)

 

08.30 – 09.00              Registration for Workshop09.00 – 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!

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Announcing rhizobial genomes

Announcing rhizobial genomes | rhizobium blog | Scoop.it
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.
Peter Young's insight:

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.

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Some 2013 papers

Some 2013 papers | rhizobium blog | Scoop.it
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.  F...
Peter Young's insight:

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.

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Faculty positions in genomics

Faculty positions in genomics | rhizobium blog | Scoop.it
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...
Peter Young's insight:

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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From Rhizobium to Sinorhizobium, from Sinorhizobium to Ensifer?

From Rhizobium to Sinorhizobium, from Sinorhizobium to Ensifer? | rhizobium blog | Scoop.it
There are many publications on the bacteria that most people know as Sinorhizobium meliloti, S.
Peter Young's insight:

There are many publications on the bacteria that most people know as Sinorhizobium meliloti, S. fredii, and related species.  The name of their genus has changed over the years, and I used Web of Science to track the changing use of the different names in the titles of published articles.

Some key dates are:

1926: the species Rhizobium meliloti proposed.

1982: the genus Ensifer proposed for some nonsymbiotic bacteria.

1984: the species Rhizobium fredii proposed.

1988: the genus Sinorhizobium proposed for R. fredii

1994: the genus Sinorhizobium relaunched to include R. meliloti

2003: the proposed amalgamation of Sinorhizobium with Ensifer (under the rules of precedence, the combined genus should be Ensifer)

Here are the figures for the number of publications each year that used each of these names.  Some papers gave two alternatives, one in parentheses.  I leave the interpretation of these data as an exercise for the reader.  I will probably discuss them in later posts, however.

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Scoop it!

Scoop it! | rhizobium blog | Scoop.it
Since this time last year, my rhizobium blog has had 1687 views from Japan, 1340 views from Canada (thanks, Ivan!
Peter Young's insight:

This was first posted 5 February 2013

 

Since this time last year, my rhizobium blog has had 1687 views from Japan, 1340 views from Canada (thanks, Ivan!) … and zero views from China.  Since Chinese researchers are among the most active in the area of rhizobial diversity, this is disappointing.  Are my views too contentious to be allowed in the People’s Republic?  Actually, I have discovered that the whole wordpress.com web site is invisible to the Chinese – and also, apparently, to the Iranians.  There are thriving rhizobium research communities in both those countries, and I would not like to exclude them from the conversation, so I am experimenting with another way to reach them.  I have copied the most recent posts from this blog to http://www.scoop.it/t/rhizobium-blog .  Scoop.it is a site for posting links to other pages on the web, with comments.  I have copied the entire text of the posts into a comment, so it should be visible to visitors to Scoop.it.

I learned about Scoop.it by finding the excellent Rhizobium Research resource that is maintained by Ivan Oresnik at http://www.scoop.it/t/rhizobium-catabollism Here, he provides copious links to recent papers on rhizobia and the legume symbiosis that have caught his attention.  No doubt it serves as a compulsory reading list for his own students, and it is also a valuable resource for the rest of us.  I recommend it.

By the way, I know very few Japanese rhizobium researchers, so if you are in Japan and have looked at this blog 1687 times (or even just once), please add a comment to tell us who you are and what you are interested in.

 

Peter

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IvanOresnik's comment, February 8, 2013 11:24 AM
I freely admit that I have checked your blog regularly after finding it. I very excitedly sent the link to just about everyone I knew-I think that might have something to do with the number of Canadian page views. It is a topic I like reading about.
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Another gamma paper-from Peter Young's Rhizobium blog | Rhizobium Research

Another gamma paper-from Peter Young's Rhizobium blog | Rhizobium Research | rhizobium blog | Scoop.it
In my last post, I referred to a paper about gammaproteobacteria that were not rhizobia. Here is another one (Huang et al. 2012).
Peter Young's insight:

This was first posted 27 January 2013

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Peter Young's comment, February 5, 2013 9:18 AM
In my last post, I referred to a paper about gammaproteobacteria that were not rhizobia. Here is another one (Huang et al. 2012). The difference is that these authors try to persuade us that their gammaproteobacterium is a rhizobium. I am not convinced.

It is not that I don’t believe that gamma-rhizobia can exist. Indeed, I argued in an earlier post that they probably do. The discovery of beta-rhizobia in 2001 opened our eyes to the possibility of legume symbionts that were not alphaproteobacteria, and after more than a decade of further research, we now know a fair amount about beta-rhizobia in the genera Burkholderia and Cupriavidus (Gyaneshwar et al. 2011).

Huang et al. start from an unusual perspective on our current knowledge of the taxonomic diversity of rhizobia. They introduce their paper like this:

Currently 56 species, 11 genera symbiotic nitrogen-fixing bacteria have been identified, including not only traditional rhizobia that belong to genera Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium and Agrobacterium, but also some symbiotic nitrogen-fixing bacteria that have previously been categorized as non-symbiotic: some species in Phyllobacterium, Ochrobacterum, and Methylobacterium can all grow symbiotically with legumes and fix nitrogen [2–6].

In their Discussion section, their list is even more restricted:

Currently there are six genera of bacteria that can nodulate legumes, including Rhizobium, Sinorhizobium, Allorhizobium, Mesorhizobium, Bradyrhizobium, and Azorhizobium [24].

At the end of this post, I have listed the references that Huang et al. used to support these statements. You will notice that references [2-4] are all descriptions of beta-rhizobia. Reference [24] was published in 2004, so should have covered beta-rhizobia, but it is, unfortunately, only available in China.

It is clear that Huang et al. cannot have been unaware of the existence of beta-rhizobia, so it is a mystery why they chose to air-brush them out of the picture. We must focus, though, on their claim to have discovered the first gamma-rhizobium, which is not dependent on their interpretation of history.

The paper describes a bacterial strain, D5, isolated from nodules of Acacia confusa in Guangxi, south China. Inoculation with D5 resulted in N-fixing nodules on several Acacia species, but not on soybean. However, the nodules were formed 90 days after inoculation, which is very late. PCR based on a culture of D5 yielded a 16S rRNA gene sequence that is indisputably from a species of Pseudomonas, although it has no exact match in GenBank. PCR also yielded partial sequences of nodA and nifH genes, and these were similar to those previously reported from some Bradyrhizobium strains.

For nodA, the top three hits are strains from Uraria in Australia, Phaseolus in the USA, and Abrus in Senegal. Not much clue there about host specificity, therefore. The only common link is that all three were from different studies authored by Tomasz Stępkowski, but I think that just reflects Tomasz’s expertise in exotic bradyrhizobia. The nodA sequence from D5 has a frameshift caused by two extra bases about 30 bases from the start. This would make the gene nonfunctional, of course, but it might just be a sequencing error.

The nifH sequence from D5 has a 33-base deletion and a frameshift when compared to other nifH sequences, but the alignable bases are 100% identical to those of Bradyrhizobium sp. SEMIA 695 from Neonotonia (a relative of soybean), and similar to those of many other bradyrhizobia.

How can we interpret these results? Clearly, the predominant organism in the D5 culture was a Pseudomonas, but there was something in there that had bradyrhizobial nod and nif genes and probably formed the nodules on Acacia. Pseudomonads grow rapidly and bradyrhizobia very slowly, so it would be easy for a few Bradyrhizobium cells to remain undetected in a Pseudomonas culture. The plant would then select these few cells, though nodulation might be delayed because the effective inoculum was very dilute. Unfortunately, Huang et al. did not address Koch’s fourth postulate, which is that the organism that can be isolated at the end of the infection should be the same as the one that was introduced. It remains possible that the nodules they saw were filled only with bradyrhizobia. Even if there were pseudomonads in the nodules, though, it would not prove that those pseudomonads caused the formation of the nodule. The claim for nodulating pseudomonads that Huang et al. make is essentially the same as that of Benhizia et al. (2004)*. That claim was later retracted by Muresu et al. (2008), who documented extensive colonisation of nodules by non-nodulating gammaproteobacteria.

Most of us who isolate bacteria from wild nodules know that there are frequently “contaminants”, i.e. bacteria that are not capable of inducing nodule formation but grow within nodules that are induced by other bacteria (the actual rhizobia). Sometimes these free-loaders are the most abundant bacteria in cultures from the nodule, and it can be hard to separate them from the true rhizobia even when taking what appear to be single colonies from plates. How can we address this problem? Fortunately, there is a simple strategy that can help. Most bacteria can mutate spontaneously to a high level of resistance to the antibiotic streptomycin, though the frequency is normally less than one in a million cells. Plating a culture on streptomycin allows only these rare mutants to grow and form colonies. Since it is unlikely that two different bacteria will mutate at the same spot on the plate, the colonies that appear are likely to be pure. I would predict that, if one plated the D5 culture on streptomycin and waited patiently for ten days, one would see small bradyrhizobial colonies in places where they had not been overgrown by the pseudomonad.

I still believe that there are gammaproteobacteria that can nodulate legumes, and we will find them one day. That day has not yet arrived, though.

* Lionel Moulin mentioned this work in a comment on my earlier post.

References

Huang, B., Lv, C., Zhao, Y., and Huang, R. A novel strain D5 isolated from Acacia confusa. PLoS ONE 7: e49236. http://dx.doi.org/10.1371/journal.pone.0049236

Gyaneshwar, P., Hirsch, A.M., Moulin, L., Chen, W.-M., Elliott, G.N., Bontemps, C. et al. (2011) Legume-nodulating betaproteobacteria: diversity, host range and future prospects. Molecular Plant-Microbe Interactions. http://dx.doi.org/10.1094/mpmi-06-11-0172

Benhizia, Y., Benhizia, H., Benguedouar, A., Muresu, R., Giacomini, A., and Squartini, A. (2004) Gamma proteobacteria can nodulate legumes of the genus Hedysarum. Systematic and Applied Microbiology 27: 462-468. http://dx.doi.org/http://dx.doi.org/10.1078/0723202041438527

Muresu, R., Polone, E., Sulas, L., Baldan, B., Tondello, A., Delogu, G. et al. (2008) Coexistence of predominantly nonculturable rhizobia with diverse, endophytic bacterial taxa within nodules of wild legumes. FEMS Microbiology Ecology 63: 383-400. http://dx.doi.org/10.1111/j.1574-6941.2007.00424.x

Selected references from the paper by Huang et al.

2. Moulin L, Munive A, Dreyfus B, Boivin-Masson C (2001) Nodulation of legumes by members of the beta-subclass of proteobacteria. Nature, 411: 948–950.

3. Chen WM, Laevens S, Lee TM, Coenye T, DeVos P, et al. (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int. J. Syst. Evol. Microbiol. 51(5): 1729–1735.

4. Vandamme P, Goris J, Chen WM, de Vos P, Willems A (2002) Burkholder-iatuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. Syst. Applied Microbiology, 25(4): 507–512.

5. Zurdo-Pineiro JL, Rivas R, Trujillo ME, Vizcaino N, Carrasco JA, et al. (2007) Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol, 57(4): 784–788.

6. Mantelin S, Saux MF, Zakhia F, Béna G, Bonneau S, et al. (2006) Emended description of the genus Phyllobacterium and description of fournovel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium legum inum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int J Syst Evo Microbiol, 56(4): 827– 839.

24. Chen WX, Wang ET, Chen WF (2004) The relationship between the symbiotic promiscuity of rhizobia and legumes and their geographical environments. Scientia Agricultura Sinca, 37(1): 81,86.
Praveen Rahi's comment, February 9, 2013 12:20 PM
Dear Prof. Young, If we look at the gel picture of (Figure 2. PCR results of 16S rRNA of strain D5), there are two bands there. So there you may be right about contamination in the culture. I have observed that, generally the PCR product of alphaproteobacteria is approx. 1435 bp and nearly 1500 bp for gammaproteobacteria.
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Subcommittee of what?

Subcommittee of what? | rhizobium blog | Scoop.it
In my last post, I referred to the website of the ICSP Subcommittee on the Taxonomy of Rhizobium and Agrobacterium.  You may be wondering what this is a subcommittee of.  The International Committee on Systematics of Prokaryotes (ICSP) is “the body...
Peter Young's insight:

This was first posted 20 August 2012

 

In my last post, I referred to the website of the ICSP Subcommittee on the Taxonomy of Rhizobium and Agrobacterium.  You may be wondering what this is a subcommittee of.  The International Committee on Systematics of Prokaryotes (ICSP) is “the body that oversees the nomenclature of prokaryotes, determines the rules by which prokaryotes are named and whose Judicial Commission issues Opinions concerning taxonomic matters, revisions to the Bacteriological Code, etc.”, according to its own website.  This lists 28 subcommittees, each covering a genus or a group of related genera.  Of course there are far more bacterial genera than this, so only certain well-studied groups are covered.  Actually, 12 of these subcommittees seem to be defunct, as no list of members or further information is provided, and 3 more appear to be moribund, as their last recorded meeting was in 2002 or 2003.  Overall, the coverage of bacterial taxa could be described as “patchy”.

What do the subcommittees do?  Well, they have meetings: most of them meet every three years at the International Microbiology Congresses, though the meetings may also be held at more specialised conferences.  They discuss recent developments in the systematics of their bacteria, and they may publish recommended minimal standards for the description of new taxa.  Actually, their powers to decide anything are very limited, since the ICSP controls the Bacteriological Code, which sets out the rules for the valid publication of bacterial taxa.  Subcommittees try to keep track of the validly published names within their remit, but in fact the definitive list for all bacteria is maintained on behalf of the ICSP by Dr Jean Euzéby.  He does a superb job of keeping track of all the relevant publications, and his list of species is always up to date and linked to the relevant literature.  His website should be the first place you look if you want to check the valid description of a bacterial species.  It does not tell you which name to use, but it tells you which names are available to use, and their history.

The Agrobacterium and Rhizobium Subcommittee is the only one to have its own website. There, you will find a list of the species in those two genera, but also a list of legume root-nodule symbionts that belong to other genera.  This might appear to be an unjustified extension of the subcommittee’s remit, but it illustrates a general problem in bacterial systematics.  The taxonomy of bacteria was established in a bygone era, when it was innocently assumed that bacterial genera and species could be defined by listing a set of phenotypic properties.  Rhizobium was easy: all bacteria that fixed nitrogen in nodules on legume roots were Rhizobium, and vice versa.  Similarly, Agrobacterium was the genus for bacteria that induced crown galls or root proliferation by transferring DNA to the plant.

Of course, we can now appreciate that this was all hopelessly naïve.  The bacteria that induce legume root nodules are far too diverse to be accommodated in a single genus, and many of them fit best into genera that were first described for bacteria with quite different properties.  These days, we determine the taxonomy of bacteria using the similarity of DNA sequences: 16S rRNA genes, other core genes, or the approximation provided by DNA-DNA hybridisation (a tedious and unreliable technique that should have been abandoned years ago).  DNA provides objective phylogenetic information that can guide our taxonomic decisions.  Unfortunately, it leads to taxa that are not phenotypically homogeneous: not all isolates of Rhizobium make root nodules because making root nodules, like most important ecological characteristics of bacteria, is determined by mobile accessory genes, not by the core genome

This poses a dilemma for the Subcommittee.  Is it about rhizobia (root-nodule bacteria) or about Rhizobium (the formal genus)?  Is it based on an ecological niche or a taxonomic clade?  The traditional Subcommittees were set up to deal with taxonomic clades, so technically it should confine itself to “Rhizobium and Agrobacterium” as its name specifies, or perhaps broaden this to the Rhizobiaceae, whether they nodulate or not.  This would exclude Bradyrhizobium, let alone Burkholderia, and is not what most people would expect.  On the other hand, if its remit is all rhizobia and agrobacteria, defined by their plant interactions, what happens to strains that have lost the relevant plasmid and no longer have the defining phenotype?   Most biologists are more interested in the phenotype of their organisms than in the taxonomy.  We are increasingly realising that, among bacteria, taxonomy is not a good guide to phenotype.

Here are those website addresses:

Rhizobium and Agrobacterium:     http://edzna.ccg.unam.mx/rhizobial-taxonomy/

ISCP:      http://www.the-icsp.org

List of Prokaryotes:    http://www.bacterio.cict.fr/

 

Peter

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Aminobacter huakuii

Aminobacter huakuii | rhizobium blog | Scoop.it
The first complete rhizobial genome to be published was that of Aminobacter huakuii symbiovar loti strain MAFF303099.  “What?”, I hear you say, “I thought it was Mesorhizobium loti!”.
Peter Young's insight:

This was first posted 30 August 2012

 

The first complete rhizobial genome to be published was that of Aminobacter huakuii symbiovar loti strain MAFF303099.  “What?”, I hear you say, “I thought it was Mesorhizobium loti!”.

Well, for a start, core gene sequences of MAFF303099 are not close to those of the type strain of M. loti; they are closer to those of M. huakuii.  On the other hand, MAFF303099 nodulates Lotus (unlike the type strain of M. huakuii, which nodulates Astragalus), and its nodA gene is similar to those of M. loti strains that also nodulate Lotus (Turner et al. 2002).  Since strains that nodulate the same hosts and have closely related nodulation genes are said to belong to the same symbiovar (Rogel et al. 2011), MAFF303099 could be called M. huakuii symbiovar loti.

In 2003, Willems et al. proposed the amalgamation of the genera Sinorhizobium and Ensifer.  They suggested using Sinorhizobium as the name for the combined genus, but under the rules of precedent, Ensifer has to be used for the combined genus because this name was published earlier (Judicial Commission 2008).

In 2004, in a talk at the North American Rhizobium Conference in Bozeman, Montana, I pointed out that a similar situation existed for the genera Mesorhizobium and Aminobacter, since the 16S SSU sequence of A. aminovorans fell inside the clade of Mesorhizobium sequences (Sawada et al. 2003).  A combined genus would, under the rules of precedent, be called Aminobacter, so I suggested that MAFF303099 might become Aminobacter huakuii biovar loti.

I was half joking, and certainly not keen to see it become official, but it seems that we are now a step further down that road.  Maynaud et al. (2012) have described a new species of Aminobacter that nodulates Anthyllis.  They say it represents “the first occurrence of legume symbionts in the genus Aminobacter“.  Their core gene phylogenies certainly show the symbiotic strains to be close to Aminobacter species, but they do not show a convincing separation between Aminobacter and Mesorhizobium.  I feel it is only a matter of time before some taxonomist spots the opportunity for a quick publication and proposes the amalgamation of the genera.

Remember, you read it here first!

 

Peter

 

Judicial Commission of the International Committee on Systematics of Prokaryotes (2008) The genus name Sinorhizobium Chen et al. 1988 is a later synonym of Ensifer Casida 1982 and is not conserved over the latter genus name, and the species name ‘Sinorhizobium adhaerens‘ is not validly published. Opinion 84. International Journal of Systematic and Evolutionary Microbiology 58: 1973. http://dx.doi.org/10.1099/ijs.0.2008/005991-0

Maynaud, G., Willems, A., Soussou, S., Vidal, C., Mauré, L., Moulin, L. et al. Molecular and phenotypic characterization of strains nodulating Anthyllis vulneraria in mine tailings, and proposal of Aminobacter anthyllidis sp. nov., the first definition of Aminobacter as legume-nodulating bacteria. Systematic and Applied Microbiology 35: 65-72. http://dx.doi.org/10.1016/j.syapm.2011.11.002

Rogel, M.A., Ormeño-Orrillo, E., and Martinez Romero, E. (2011) Symbiovars in rhizobia reflect bacterial adaptation to legumes. Systematic and Applied Microbiology 34: 96-104. http://dx.doi.org/10.1016/j.syapm.2010.11.015

Sawada, H., Kuykendall, L.D., and Young, J.M. (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. The Journal of General and Applied Microbiology 49: 155-179. http://dx.doi.org/10.2323/jgam.49.155

Turner, S.L., Zhang, X.X., Li, F.D., and Young, J.P.W. (2002) What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti. Microbiology 148: 3330-3331.

Willems, A., Fernandez-Lopez, M., Muñoz-Adelantado, E., Goris, J., De Vos, P., Martinez-Romero, E. et al. (2003) Description of new Ensifer strains from nodules and proposal to transfer Ensifer adhaerens Casida 1982 to Sinorhizobium as Sinorhizobium adhaerens comb. nov. Request for an Opinion. International Journal of Systematic and Evolutionary Microbiology 53: 1207-1217. http://dx.doi.org/10.1099/ijs.0.02264-0

 

 

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How bacteria are like smartphones

How bacteria are like smartphones | rhizobium blog | Scoop.it
Here is one final post about our recent paper on rhizobium population genomics (1).
Peter Young's insight:

Here is one final post about our recent paper on rhizobium population genomics (1). For me, it marks an important milestone in my long investigation into the diversity of Rhizobium leguminosarum, which began thirty years ago with the publication of my very first paper on rhizobial diversity (2). Curiously, that paper raised some of the issues that are still being addressed today, as it showed that isolates of symbiovars viciae and trifolii shared a number of distinct chromosomal genotypes. Of course, the tools available at the time allowed only a very blurred picture – it is wonderful to return to the story with the clarity of genome sequencing. If you wonder what I have been doing in the intervening thirty years, you will find a complete list of my publications on Google Scholar (http://scholar.google.co.uk/citations?hl=en&user=ordDMX0AAAAJ&view_op=list_works&sortby=pubdate).   (I recommend that everyone gets a Google Scholar profile – it is such a useful way to keep track of your publications – and those of others.)

Back in 1985, publishing a paper involved massive sheaves of typescript, with glossy photos and hand-inked drawings for the figures. Months after acceptance, your article would arrive in the library in a paper issue of the journal. In the weeks and months after that, you would send out paper reprints in response to requests on postcards and airmail letters (those from India always smelt of curry). Finally, after a year or two, people would start to cite your paper in their own work.

Now, the pace of publication has accelerated, like al aspects of life, as a result of the internet. Our latest paper was accepted a week before Christmas and the final version was published online just two weeks into the new year.   One great thing about online publication is almost instant gratification, because you can immediately see how much interest a publication is generating. The “Info & Metrics” tab on the article’s web page tells me that, since publication on 14 January, our article’s abstract has been viewed 552 times, the full text 1160 times, and the PDF has been downloaded 192 times. Not bad for less than two weeks. I hope all those readers are going to cite our paper!

The article also scores 19 in Altmetrics. This is not something I was really familiar with, but it is based on interest in social media. The article has been blogged once (not including this blog), tweeted by 15 people, and featured on 1 Facebook page. So, thank you to all the rhizobium fans who have tweeted us to stardom! Apparently, an Altmetric of 19 already puts the article in the top 5% of all articles.

Of course, attention on social media does not measure scientific quality, but this did alert me to a couple of interesting web pages. SciGuru (http://www.sciguru.org/newsitem/18225/how-bacteria-are-smartphones) provides short commentaries on interesting recent papers covering all aspects of science. They headlined with “How bacteria are like smartphones”, picking up on an analogy that I used in the press release that I wrote for our university (http://www.york.ac.uk/biology/news-event/news/understandingthepersonalitiesofbacteria/). A Facebook community called Microbiology also featured us on 15 January (https://www.facebook.com/Microbiology.LabRootsPage). One more news item that did not make it into Altmetrics was in an online newspaper called The Speaker (http://thespeaker.co/bacterial-cells-unique-despite-identical-core-genome-due-accessory-packages/).

I don’t usually think of writing a press release when I publish a paper, but in this case I thought the work could be of wider interest, and I was also worried that Open Biology is a relatively new journal, and not yet widely associated with microbiology, so people might miss it. The wider attention came largely through two popular analogies – the idea that bacteria are all indviduals with “personalities”, and that they achieve this by acting like smartphones. Each phone comes out of the factory with standard hardware and operating system (core genome), but gains a unique combination of capabilities through apps (accessory genes) downloaded through the internet (by horizontal gene transfer).

A gimmick, perhaps, but rhizobia do not get enough attention from the rest of the world, so sometimes we rhizobiologists need to wave our arms a bit.

 

Kumar, N., Lad, G., Giuntini, E., Kaye, M. E., Udomwong, P., Shamsani, N. J., Young, J. P. W. & Bailly, X. (2015). Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biology, 5(1), 140133.

http://rsob.royalsocietypublishing.org/content/5/1/140133

 

Young, J. P. W. (1985). Rhizobium population genetics: enzyme polymorphism in isolates from peas, clover, beans and lucerne grown at the same site. Journal of General Microbiology, 131, 2399-2408.

http://mic.sgmjournals.org/content/131/9/2399.short

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Sohini Guha's curator insight, April 20, 2015 2:39 PM

an excellent concept....

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Population genomics of Rhizobium leguminosarum - 2

Population genomics of Rhizobium leguminosarum - 2 | rhizobium blog | Scoop.it
I am continuing my commentary on some of the issues raised by our new paper: Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. 2015 Bacterial genospecies that are n...
Peter Young's insight:

I am continuing my commentary on some of the issues raised by our new paper:

Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. 2015 Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol. 5: 140133.

rsob.royalsocietypublishing.org/content/5/1/140133

Gene content and gene transfer

The 72 strains that we sequenced are all unique.  A small part of their individuality stems from allelic variation in core genes.  Although core genes do not appear to recombine between genospecies very often, they certainly experience a lot of recombination within the genospecies.  Nitin Kumar demonstrated that by showing that most core genes have phylogenies that are significantly different from the consensus, and by using the ClonalFrame software to quantify the effect of recombination on core genes.

A more important part of the individuality of strains is conferred by the accessory genome: almost every strain had a unique set of genes, differing from its nearest relative by at least one cluster of five or more adjacent genes.  All these strains were collected from one square metre, and sometimes even from separate nodules on the same plant.  This implies that the gain and loss of accessory genes occurs very often.  A nodule is most often founded by a single rhizobial lineage.  When the nodule senesces and releases its bacteria, we assume that they are still more or less clonal (has anybody tested that?).  By the time they form nodules of their own, though, these bacteria are likely to have shed some of their genes, or gained new ones from a donor, so that they have clearly diverged from each other.

A reference genome like that of 3841 is of limited use when exploring the accessory gene pool of a population.  Nitin looked at all the contigs that could be assembled from the 72 genomes but had no similarity to sequences in 3841.  He found 13,252 putative complete genes in addition to those that were in 3841 – more than twice the typical total number of genes in any strain!  When considering the whole population, the accessory genome is much larger than the core genome. A few years ago, the concept of a species “pangenome” was popular. This comprised all the core and accessory genes found in a bacterial species.  As long as only a few strains were sequenced, this was manageable, but as more and more genomes became available, the number of accessory genes in most species just seemed to grow without limit – an “open pangenome”.  Every new genome contributed new genes, just as we are seeing in R. leguminosarum.  A species seems to sample very widely from the pool of genes available to bacteria in general.  The species pangenome concept does not seem very useful if it just means “all the genes there are in bacteria”.

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Understanding the personalities of bacteria

Understanding the personalities of bacteria | rhizobium blog | Scoop.it
Today sees the publication of a paper that I regard as a landmark in my decades-long study of Rhizobium leguminosarum.  The paper ‘Bacterial genospecies that are not ecologically coherent: populati...
Peter Young's insight:

Today sees the publication of a paper that I regard as a landmark in my decades-long study of Rhizobium leguminosarum.  The paper ‘Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum’ Open Biol. 5: 140133 is published in the Royal Society’s journal Open Biology rsob.royalsocietypublishing.org and descibes a population genomics study that changes our perception of the species.  It also illustrates a changing view of bacterial diversity in general, and that is what I have emphasised in the press release that our university is issuing, which I have copied below.  Readers of this blog will be more interested in the detailed picture of a rhizobium population that it reveals.  The paper is Open Access, so you can read it here:

rsob.royalsocietypublishing.org/content/5/1/140133

Understanding the personalities of bacteria

Bacteria are as individual as people, according to new research by Professor Peter Young and his team in the Department of Biology at the University of York. Bacteria are essential to health, agriculture and the environment, and new research tools are starting to shed more light on them.

The York team dug up a square metre of roadside verge on the University campus in search of a bacterium called Rhizobium leguminosarum. The name means “root dweller of the legumes”, and these bacteria are natural fertilizer factories that extract nitrogen from the air and make it available to peas, beans, clover and their wild relatives.

In the laboratory, the team extracted the bacteria from the plant roots and established 72 separate strains. They determined the DNA sequence of the genome of each strain. Their research, published today in Open Biology, shows that each of those 72 strains is unique –each has different genes and is capable of growing on different food sources.

People are unique because each of us inherits half our genes from our mother and half from our father, but bacteria reproduce by binary fission, making two identical daughters. What bacteria are good at, though, is passing packages of genes from one cell to another. It is this process of horizontal gene transfer that made every rhizobium unique.

“We can think of the bacterial genome as having two parts,” says Professor Young. “The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world.

“Bacteria are like smartphones. Each phone comes out of the factory with standard hardware and operating system (core genome), but gains a unique combination of capabilities through apps (accessory genes) downloaded through the internet (by horizontal gene transfer).”

We increasingly recognise the vital roles played by bacterial communities, such as those in our gut or on the roots of plants. Many researchers have used variation in a standard core gene to draw up lists of the species in a community, but the new research shows that a list of names is not sufficient.

“There may be 300 people called Baker in your city, but you can’t assume that there are 300 people baking bread,” explains Professor Young.

It is possible, with more sequencing effort, to look at all the genes in a bacterial community – an approach called “metagenomics” – but to understand how they are functioning we also need to know which genes occur together in the same bacterium. This new study helps us to understand the way in which bacterial genomes are assembled.

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Meeting on the Genomics of Nitrogen-Fixing Organisms

Meeting on the Genomics of Nitrogen-Fixing Organisms | rhizobium blog | Scoop.it
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.
Peter Young's insight:

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.

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Rhizobial genomes galore

Rhizobial genomes galore | rhizobium blog | Scoop.it
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.
Peter Young's insight:

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).

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Postdoc position in nitrogen fixation

Postdoc position in nitrogen fixation | rhizobium blog | Scoop.it
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 ...
Peter Young's insight:

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.

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Rhizobium pisi gains a symbiovar

Rhizobium pisi gains a symbiovar | rhizobium blog | Scoop.it
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...
Peter Young's insight:

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

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T6SS sword fighting - the battle video

T6SS sword fighting - the battle video | rhizobium blog | Scoop.it
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...
Peter Young's insight:

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.

Video: http://www.youtube.com/watch?v=aQIU5CvsIjw&noredirect=1

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Writing interestingly « rhizobium

Writing interestingly « rhizobium | rhizobium blog | Scoop.it
Try not to write “Interestingly, …”. Some authors pepper their bland academic prose with such words in an attempt to spice it up: “interestingly”, notably”, “surprisingly”, “strikingly”, “remarkably”, “importantly”.
Peter Young's insight:

This was first posted 2 February 2013

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Peter Young's comment, February 5, 2013 4:52 AM
Try not to write “Interestingly, …”.

Some authors pepper their bland academic prose with such words in an attempt to spice it up: “interestingly”, notably”, “surprisingly”, “strikingly”, “remarkably”, “importantly”. I have even seen “astonishingly” and “noteworthily”.

What do these words mean? Essentially, the authors are saying to the reader “We know we have just bored you senseless with a page and a half of utterly trivial and inconclusive details, but pay attention because finally we are about to say something that is worth reading!”.

Here is a sentence taken, more or less verbatim, from a manuscript I once read.

Interestingly, the results of a Shimodaira and Hasegawa (S-H) test (Shimodaira and Hasegawa, 1999) comparing the topologies of the 16S and nodD phylogenies showed that the nodD phylogeny was significantly (P<0.01) different from the 16S phylogeny.

This sentence is lifeless, and adorning it with “interestingly” is merely painting lipstick on a corpse. What was the cause of death? The first obstacle that readers face is an impenetrable thicket of Japanese polysyllabicism (Fullupia japonica). Having hacked their way to the centre of the sentence, readers find a complex and repetitive statement that needs some careful deconstruction.

Can we bring this sentence back to life? Here are three strategies.

Start a sentence with the most important part, unless you have a good reason to do differently.
Get the technical details out of the sentence altogether. Scientific papers have a Methods section, which nobody expects to be fun to read. This is the place to dump the important but cumbersome details.
Write as simply and briefly as you can.

How about this:

The nodD and 16S phylogenies are significantly incongruent (P<0.01, S-H test, see Methods).

Even the busiest readers will have time to read and understand that, and they can decide for themselves whether it is interesting*. Let us assume that the authors have used the Introduction to prepare readers to expect congruence in this particular situation, so they are shocked and interested to read about the incongruence.

There is just one more issue, and that is to make sure the readers actually read our interesting sentence. What about the page and a half of tedious stuff they had to skim through first? Why not just delete it? What! I know you spent weeks running your data through complex software and many hours transcribing the output into the manuscript, but if the results do not tell a compelling and convincing story, why inflict them on the reader? As with a sentence, it is best to start with the most important message. Continue for as long as you have interesting things to say. Then stop.

Try not to write “Interestingly, …”.

Try to write interestingly.





* Actually, at first sight it does not seem very interesting. Dozens of studies over decades have found that nodulation genes do not have the same phylogeny as core genes, presumably as a result of gene transfer. We first demonstrated the mismatch in a Rhizobium leguminosarum population (Young & Wexler 1988). These days, it is more surprising if symbiosis genes do have a similar phylogeny to core genes, as observed for Burkholderia in Brazil (Bontemps et al, 2010).

Young, J.P.W., and Wexler, M. (1988) Sym plasmid and chromosomal genotypes are correlated in field populations of Rhizobium leguminosarum. Journal of General Microbiology 134: 2731-2739. http://dx.doi.org/10.1099/00221287-134-10-2731

Bontemps, C., Elliott, G.N., Simon, M.F., dos Reis Júnior, F.B., Gross, E., Lawton, R.C. et al. (2010) Burkholderia species are ancient symbionts of legumes. Molecular Ecology 19: 44-52. http://dx.doi.org/10.1111/j.1365-294X.2009.04458.x
Chang Fu Tian's comment, February 5, 2013 7:41 AM
This is very educative for authors from non-English speaking country. Thanks.
Peter Young's comment, February 5, 2013 9:04 AM
Thanks, Chang Fu! I think that the principles of effective writing apply in any language, not just in English. I don't mean that you should NEVER write "interestingly", of course - just that you should think carefully before using it.
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Return of the Sword-Bearer « rhizobium

Return of the Sword-Bearer « rhizobium | rhizobium blog | Scoop.it
Last year I wrote about a very obscure bacterium called Ensifer. Its name means “the sword-bearer” because it has a rod with which it appears to stab and kill other bacterial cells. I suggested that this was a Type VI Secretion ...
Peter Young's insight:

This was first posted 19 January 2013

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Peter Young's comment, February 5, 2013 9:17 AM
Last year I wrote about a very obscure bacterium called Ensifer. Its name means “the sword-bearer” because it has a rod with which it appears to stab and kill other bacterial cells. I suggested that this was a Type VI Secretion System (T6SS – Hello Marek!). I still think that is what it is, although Marek Basler expressed doubts, and he is an expert.

The other day, I came across another paper about T6SS. The bacteria involved were Pseudomonas aeruginosa and Salmonella enterica (both gammaproteobacteria), and Burkholderia thailandensis (a betaproteobacterium). None of them were rhizobia, so I would not ordinarily mention it here, but I was struck by the title: ” Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword”.

So, the sword-bearer returns. As far as I can tell, the authors were not literally thinking of the physical structure as a sword. They observed that the deployment of the T6SS made the bearer more susceptible to attack by the T6SS of other cells, and described this as a “double-edged sword” in a purely abstract metaphor meaning a weapon that can also injure the holder. I like to think, though, that Ensifer had seeped into their subconscious.



LeRoux, M., De Leon, J.A., Kuwada, N.J., Russell, A.B., Pinto-Santini, D., Hood, R.D. et al. Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword. Proceedings of the National Academy of Sciences 109: 19804-19809. http://dx.doi.org/10.1073/pnas.1213963109
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Gisèle Laguerre « rhizobium

Gisèle Laguerre « rhizobium | rhizobium blog | Scoop.it
Gisèle Laguerre died last night. She was just 55 years old but had been ill for some months. She was such a good colleague and friend over many years, and made important contributions to rhizobial science.
Peter Young's insight:

This was first posted 16 January 2013

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Peter Young's comment, February 5, 2013 9:18 AM
Gisèle Laguerre died last night. She was just 55 years old but had been ill for some months. She was such a good colleague and friend over many years, and made important contributions to rhizobial science.

I first met Gisèle more than 20 years ago, when she worked with Noëlle Amarger at INRA in Dijon. We shared an interest in the genetic diversity of Rhizobium leguminosarum at a time when studies of bacterial population genetics were rare. This is not the time for a comprehensive review of her work, but here are a few of her early contributions to our knowledge of rhizobia. It was an exciting time of discovery, and I remember many discussions with Gisèle while this work was in progress. She demonstrated that plasmid profiles could be highly variable and made them into a useful tool for characterising strains (1), enabling her to demonstrate that genetic transfer had occurred (2). In a technically difficult study that has seldom been followed up, she and her student isolated R. leguminosarum directly from soil and demonstrated that many strains did not carry nodulation genes (3-5). She characterised the symbionts of Phaseolus vulgaris in European soils and demonstrated that they were not all R. leguminosarum (6-8). She developed PCR-based methods for characterising strain diversity (9-10). She found a strain of R. leguminosarum that appeared to have the nodulation genes carried in the chromosome (11). She demonstrated variation in host compatibility within R. leguminosarum biovar viciae (12). Those are just a few of her earlier papers, mostly on R. leguminosarum – she continued to publish important work on this species, on other rhizobia, and on other bacteria.

Gisèle has left us far too early, but we still have the wealth of knowledge about rhizobia that she brought us.



(1) Laguerre, G., Mazurier, S.I., and Amarger, N. (1992) Plasmid profiles and restriction fragment length polymorphism of Rhizobium leguminosarum bv viciae in field populations. FEMS Microbiology Ecology 101: 17-26. http://dx.doi.org/10.1016/0378-1097(92)90693-I

(2) Laguerre, G., Geniaux, E., Mazurier, S.I., Casartelli, R.R., and Amarger, N. (1993) Conformity and diversity among field isolates of Rhizobium leguminosarum bv. viciae, bv. trifolii, and bv. phaseoli revealed by DNA hybridization using chromosome and plasmid probes. Canadian Journal of Microbiology 39: 412-419.

(3) Laguerre, G., Bardin, M., and Amarger, N. (1993) Isolation from soil of symbiotic and nonsymbiotic Rhizobium leguminosarum by DNA hybridization. Canadian Journal of Microbiology 39: 1142-1149.

(4) Louvrier, P., Laguerre, G., and Amarger, N. (1995) Semiselective medium for isolation of Rhizobium leguminosarum from soils. Soil Biology & Biochemistry 27: 919-924.

(5) Louvrier, P., Laguerre, G., and Amarger, N. (1996) Distribution of symbiotic genotypes in Rhizobium leguminosarum biovar viciae populations isolated directly from soils. Applied and Environmental Microbiology 62: 4202-4205.

(6) Geniaux, E., Laguerre, G., and Amarger, N. (1993) Comparison of geographically distant populations of rhizobium isolated from root nodules of Phaseolus vulgaris. Molecular Ecology 2: 295-302. http://dx.doi.org/10.1111/j.1365-294X.1993.tb00022.x

(7) Amarger, N., Bours, M., Revoy, F., Allard, M.R., and Laguerre, G. (1994) Rhizobium tropici nodulates field-grown Phaseolus vulgaris in France. Plant and Soil 161: 147-156.

(8) Amarger, N., Macheret, V., and Laguerre, G. (1997) Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. International Journal of Systematic Bacteriology 47: 996-1006.

(9) Laguerre, G., Allard, M.R., Revoy, F., and Amarger, N. (1994) Rapid identification of rhizobia by Restriction Fragment Length Polymorphism analysis of PCR-amplified 16S ribosomal-RNA genes. Applied and Environmental Microbiology 60: 56-63.

(10) Laguerre, G., Mavingui, P., Allard, M.R., Charnay, M.P., Louvrier, P., Mazurier, S.I. et al. (1996) Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: Application to Rhizobium leguminosarum and its different biovars. Applied and Environmental Microbiology 62: 2029-2036.

(11) Mazurier, S.I., and Laguerre, G. (1997) Unusual localization of nod and nif genes in Rhizobium leguminosarum bv. viciae. Canadian Journal of Microbiology 43: 399-402.

(12) Laguerre, G., Louvrier, P., Allard, M.R., and Amarger, N. (2003) Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes. Applied and Environmental Microbiology 69: 2276-2283.
Praveen Rahi's comment, February 9, 2013 10:49 AM
RIP Gisèle Laguerre.