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Shaping bacterial symbiosis with legumes by experimental evolution

Shaping bacterial symbiosis with legumes by experimental evolution | Learning, researching and sharing | Scoop.it

Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta-in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.

 

Marchetti M, Jauneau A, Capela D, Remigi P, Gris C, Batut J, Masson-Boivin C. (2014). Mol Plant Microbe Interact.(9):956-64.


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Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction | Learning, researching and sharing | Scoop.it

Many bacteria carry two or more chromosome-like replicons. This occurs in pathogens such as Vibrio cholerea and Brucella abortis as well as in many N2-fixing plant symbionts including all isolates of the alfalfa root-nodule bacteria Sinorhizobium meliloti. Understanding the evolution and role of this multipartite genome organization will provide significant insight into these important organisms; yet this knowledge remains incomplete, in part, because technical challenges of large-scale genome manipulations have limited experimental analyses. The distinct evolutionary histories and characteristics of the three replicons that constitute the S. meliloti genome (the chromosome (3.65 Mb), pSymA megaplasmid (1.35 Mb), and pSymB chromid (1.68 Mb)) makes this a good model to examine this topic. We transferred essential genes from pSymB into the chromosome, and constructed strains that lack pSymB as well as both pSymA and pSymB. This is the largest reduction (45.4%, 3.04 megabases, 2866 genes) of a prokaryotic genome to date and the first removal of an essential chromid. Strikingly, strains lacking pSymA and pSymB (ΔpSymAB) lost the ability to utilize 55 of 74 carbon sources and various sources of nitrogen, phosphorous and sulfur, yet the ΔpSymAB strain grew well in minimal salts media and in sterile soil. This suggests that the core chromosome is sufficient for growth in a bulk soil environment and that the pSymA and pSymB replicons carry genes with more specialized functions such as growth in the rhizosphere and interaction with the plant. These experimental data support a generalized evolutionary model, in which non-chromosomal replicons primarily carry genes with more specialized functions. These large secondary replicons increase the organism's niche range, which offsets their metabolic burden on the cell (e.g. pSymA). Subsequent co-evolution with the chromosome then leads to the formation of a chromid through the acquisition of functions core to all niches (e.g. pSymB).

 

George C. diCenzo, Allyson M. MacLean, Branislava Milunovic, G. Brian Golding, and Turlough M. Finan (2014).  PLoS Genet 10(10): e1004742.


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Molecular Genetics of Nodulation Control in Legumes

Professor Peter M. Gresshoff QAAFI Science Seminar -- 27 May 2014 http://www.uq.edu.au/agriculture/petergresshoff Most legume plants, such as soybean, are capable of nodulation, that is developmen...
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Legume nodulation

Legume nodulation | Learning, researching and sharing | Scoop.it

For reasons that are unclear, no eukaryotic enzymes can break the triple bond of N2. The reduction of N2 to NH3 (nitrogen fixation) is limited to prokaryotes and is catalysed by nitrogenase. Since most of the nitrogen entering the biosphere (around 100 million metric tonnes of N2 per annum) does so through nitrogenase activity (lightning contributes about 10%), those plants that associate with nitrogen-fixing bacteria have a significant selective advantage under conditions of limiting nitrogen

 

J. Allan Downie (2014). Current Biology Volume 24, Issue 5, 3 March 2014, Pages R184–R19

 


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Evolutionary history and genetic parallelism affect correlated responses to evolution - Gac - 2013 - Molecular Ecology - Wiley Online Library

Evolutionary history and genetic parallelism affect correlated responses to evolution - Gac - 2013 - Molecular Ecology - Wiley Online Library | Learning, researching and sharing | Scoop.it

We investigated the relationship between genomic and phenotypic evolution among replicate populations of Escherichia coli evolved for 1000 generations in four different environments. By resequencing evolved genomes, we identified parallel changes in genes encoding transcription regulators within and between environments. Depending on both the environment and the altered gene, genetic parallelism at the gene level involved mutations that affected identical codons, protein domains or were widely distributed across the gene. Evolved clones were characterized by parallel phenotypic changes in their respective evolution environments but also in the three alternative environments. Phenotypic parallelism was high for clones that evolved in the same environment, even in the absence of genetic parallelism. By contrast, clones that evolved in different environments revealed a higher parallelism in correlated responses when they shared mutated genes. Altogether, this work shows that after an environmental change or the colonization of a new habitat, similar ecological performance might be expected from individuals that share mutated genes or that experienced similar past selective pressures.

 Le Gac, M., Cooper, T.F., Cruveiller, S., Médigue, C., and Schneider, D. (2013). Evolutionary history and genetic parallelism affect correlated responses to evolution. Mol. Ecol. 22, 3292–3303.


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Population genetics and substitution models of adaptive evolution

Population genetics and substitution models of adaptive evolution | Learning, researching and sharing | Scoop.it
Population genetics and substitution models of adaptive evolution Mario dos Reis (Submitted on 26 Nov 2013) The ratio of non-synonymous to synonymous substitutions ω(=dN/dS) has been widely used as...

Via Mel Melendrez-Vallard
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Mapping the Epigenetic Basis of Complex Traits

Mapping the Epigenetic Basis of Complex Traits | Learning, researching and sharing | Scoop.it

Quantifying the impact of heritable epigenetic variation on complex traits is an emerging challenge in population genetics. Here, we analyze a population of isogenic Arabidopsis lines that segregate experimentally induced DNA methylation changes at hundreds of regions across the genome. We demonstrate that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait loci (QTLepi), accounting for 60 to 90% of the heritability for two complex traits, flowering time and primary root length. These QTLepi are reproducible and can be subjected to artificial selection. Many of the experimentally induced DMRs are also variable in natural populations of this species and may thus provide an epigenetic basis for Darwinian evolution independently of DNA sequence changes.


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Nature's microbiome: introduction - Molecular Ecology Special Issue

Nature's microbiome: introduction - Molecular Ecology Special Issue | Learning, researching and sharing | Scoop.it

In this special issue of Molecular Ecology, we present 28 articles incorporating molecular and bioinformatics tools to dissect the intimate and prolonged associations that define symbioses. We have organized these studies into three sections, focused on (i) the composition of symbiotic communities and how this varies across hosts, tissues and development, and in response to environmental change (‘The Dynamic Microbiome’); (ii) the roles that microbes play for their hosts and the underlying mechanisms behind these functions (‘Microbiome Function’); and (iii) the nature and mechanisms of interactions between hosts and symbionts and between the co-inhabiting symbionts themselves (‘The Interactive Microbiome’). These articles highlight the state-of-the-art in microbiome research, with novel discoveries for well-developed models and for other budding systems beyond the human realm.


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From Rhizobium to Sinorhizobium, from Sinorhizobium to Ensifer?

From Rhizobium to Sinorhizobium, from Sinorhizobium to Ensifer? | Learning, researching and sharing | Scoop.it
There are many publications on the bacteria that most people know as Sinorhizobium meliloti, S.

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Peter Young's curator insight, April 18, 2013 7:11 AM

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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Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software | Learning, researching and sharing | Scoop.it
Ying Cao's insight:

I found the useful resources on the MBE.

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Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis

Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis | Learning, researching and sharing | Scoop.it

The stabilization of host–symbiont mutualism against the emergence of parasitic individuals is pivotal to the evolution of cooperation. One of the most famous symbioses occurs between legumes and their colonizing rhizobia, in which rhizobia extract nutrients (or benefits) from legume plants while supplying them with nitrogen resources produced by nitrogen fixation (or costs). Natural environments, however, are widely populated by ineffective rhizobia that extract benefits without paying costs and thus proliferate more efficiently than nitrogen-fixing cooperators. How and why this mutualism becomes stabilized and evolutionarily persists has been extensively discussed. To better understand the evolutionary dynamics of this symbiosis system, we construct a simple model based on the continuous snowdrift game with multiple interacting players. We investigate the model using adaptive dynamics and numerical simulations. We find that symbiotic evolution depends on the cost–benefit balance, and that cheaters widely emerge when the cost and benefit are similar in strength. In this scenario, the persistence of the symbiotic system is compatible with the presence of cheaters. This result suggests that the symbiotic relationship is robust to the emergence of cheaters, and may explain the prevalence of cheating rhizobia in nature. In addition, various stabilizing mechanisms, such as partner fidelity feedback, partner choice, and host sanction, can reinforce the symbiotic relationship by affecting the fitness of symbionts in various ways. This result suggests that the symbiotic relationship is cooperatively stabilized by various mechanisms. In addition, mixed nodule populations are thought to encourage cheater emergence, but our model predicts that, in certain situations, cheaters can disappear from such populations. These findings provide a theoretical basis of the evolutionary dynamics of legume–rhizobia symbioses, which is extendable to other single-host, multiple-colonizer systems


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Jean-Michel Ané's curator insight, September 22, 2014 10:56 PM

Wow... very nice modeling paper!

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Biology Project Video - Nitrogen Fixing Bacteria

Video of my experiment involving the amount of nitrogen-fixing bacteria in different locations. The song I used in this video is "Beethoven's 5 Secrets", whi...
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Isolating rhizobia from root nodules

A short video of how rhizobia are isolated from root nodules under laboratory conditions.
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Synonymous and Nonsynonymous Polymorphisms versus Divergences in Bacterial Genomes

Synonymous and Nonsynonymous Polymorphisms versus Divergences in Bacterial Genomes | Learning, researching and sharing | Scoop.it

Comparison of the ratio of nonsynonymous to synonymous polymorphisms within species with the ratio of nonsynonymous to synonymous substitutions between species has been widely used as a supposed indicator of positive Darwinian selection, with the ratio of these 2 ratios being designated as a neutrality index (NI). Comparison of genome-wide polymorphism within 12 species of bacteria with divergence from an outgroup species showed substantial differences in NI among taxa. A low level of nonsynonymous polymorphism at a locus was the best predictor of NI < 1, rather than a high level of nonsynonymous substitution between species. Moreover, genes with NI < 1 showed a strong tendency toward the occurrence of rare nonsynonymous polymorphisms, as expected under the action of ongoing purifying selection. Thus, our results are more consistent with the hypothesis that a high relative rate of between-species nonsynonymous substitution reflects mainly the action of purifying selection within species to eliminate slightly deleterious mutations rather than positive selection between species. This conclusion is consistent with previous results highlighting an important role of slightly deleterious variants in bacterial evolution and suggests caution in the use of the McDonald–Kreitman test and related statistics as tests of positive selection.


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Random drift and phenotypic evolution

Random drift and phenotypic evolution | Learning, researching and sharing | Scoop.it
This week we have a guest post from Markku Karhunen. Markku’s research at the University of Helsinki included the development and implementation of a number of very interesting and useful population genetics methods.

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Tackling soil diversity with the assembly of large, complex metagenomes

Tackling soil diversity with the assembly of large, complex metagenomes | Learning, researching and sharing | Scoop.it

The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.


Via Stéphane Hacquard, Jean-Michel Ané, Francis Martin
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A Tale of Two Data Sets: New DNA Analysis Strategy Helps Researchers Cut through the Dirt

A Tale of Two Data Sets: New DNA Analysis Strategy Helps Researchers Cut through the Dirt | Learning, researching and sharing | Scoop.it

For soil microbiology, it is the best of times. While no one has undertaken an accurate census, a spoonful of soil holds hundreds of billions of microbial cells, encompassing thousands of species. “It’s one of the most diverse microbial habitats on Earth, yet we know surprisingly little about the identities and functions of the microbes inhabiting soil,” said Jim Tiedje, Distinguished Professor at the Center for Microbial Ecology at Michigan State University. Tiedje, along with MSU colleagues and collaborators from the U.S. Department of Energy Joint Genome Institute (DOE JGI) and Lawrence Berkeley National Laboratory (Berkeley Lab), have published the largest soil DNA sequencing effort to date in the March 10, 2014, issue of Proceedings of the National Academy of Sciences (PNAS). What has emerged in this first of the studies to come from this project is a simple, elegant solution to sifting through the deluge of information gleaned, as well as a sobering reality check on just how hard a challenge these environments will be. Read more ...


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Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum Group Ia strains as Bradyrhizobium diazoefficiens sp. nov.

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Rhizobium pisi gains a symbiovar

Rhizobium pisi gains a symbiovar | Learning, researching and sharing | 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...

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Peter Young's curator insight, April 19, 2013 5:21 AM

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