Seeking the genetic basis of phenotypic differences among bacterial species

1998 ◽  
pp. 221-235
Author(s):  
Howard Ochman ◽  
Eduardo A. Groisman
Keyword(s):  
Genetic Basis ◽  
Bacterial Species ◽  
Phenotypic Differences

scholarly journals Influence of Tomato Genotype on Growth of Inoculated and Indigenous Bacteria in the Spermosphere

2001 ◽  
Vol 67 (2) ◽  
pp. 514-520 ◽  
Author(s):  
Holly M. Simon ◽  
Kevin P. Smith ◽  
Jeremy A. Dodsworth ◽  
Bobbi Guenthner ◽  
Jo Handelsman ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Biological Control Agent ◽  
Bacterial Species ◽  
Control Agent ◽  
Growth Patterns ◽  
Host Genotype ◽  
Host Effect ◽  
Tomato Genotype ◽  
Total Bacteria ◽  
Soil Changes

ABSTRACT We previously demonstrated a genetic basis in tomato for support of the growth of a biological control agent, Bacillus cereusUW85, in the spermosphere after seed inoculation (K. P. Smith, J. Handelsman, and R. M. Goodman, Proc. Natl. Acad. Sci. USA 96:4786–4790, 1999). Here we report results of studies examining the host effect on the support of growth of Bacillus andPseudomonas strains, both inoculated on seeds and recruited from soil, using selected inbred tomato lines from the recombinant inbred line (RIL) population used in our previous study. Two tomato lines, one previously found to support high and the other low growth ofB. cereus UW85 in the spermosphere, had similar effects on growth of each of a diverse, worldwide collection of 24 B. cereus strains that were inoculated on seeds and planted in sterilized vermiculite. In contrast, among RILs that differed for support of B. cereus UW85 growth in the spermosphere, we found no difference for support of growth of the biocontrol strainsPseudomonas fluorescens 2-79 or Pseudomonas aureofaciens AB254. Thus, while the host effect on growth extended to all strains of B. cereus examined, it was not exerted on other bacterial species tested. When seeds were inoculated with a marked mutant of B. cereus UW85 and planted in soil, RIL-dependent high and low support of bacterial growth was observed that was similar to results from experiments conducted in sterilized vermiculite. When uninoculated seeds from two of these RILs were planted in soil, changes in population levels of indigenousBacillus and fluorescent Pseudomonas bacteria differed, as measured over time by culturing and direct microscopy, from growth patterns observed in the inoculation experiments. Neither RIL supported detectable levels of growth of indigenousBacillus soil bacteria, while the line that supported growth of inoculated B. cereus UW85 supported higher growth of indigenous fluorescent pseudomonads and total bacteria. The vermiculite system used in these experiments was predictive for growth of B. cereus UW85 inoculated on seeds and grown in soil, but the patterns of growth of inoculated strains—bothBacillus and Pseudomonas spp.—did not reflect host genotype effects on indigenous microflora recruited from soil to the spermosphere.

scholarly journals Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 467 ◽  
Author(s):  
Ninghan Yang ◽  
Andrew Farrell ◽  
Wendy Niedelman ◽  
Mariane Melo ◽  
Diana Lu ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Genetic Basis ◽  
Type I ◽  
Phenotypic Differences

scholarly journals Genetic architecture of male courtship behavior differences in the parasitoid wasp genus Nasonia (Hymenoptera; Pteromalidae)

2019 ◽  
Author(s):  
J Gadau ◽  
C. Pietsch ◽  
S. Gerritsma ◽  
S. Ferber ◽  
L. van de Zande ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Mapping Population ◽  
Courtship Behavior ◽  
Parasitoid Wasp ◽  
Phenotypic Variance ◽  
Male Courtship ◽  
Phenotypic Differences ◽  
A Genome ◽  
Male Courtship Behavior

AbstractVery little is known about the genetic basis of behavioral variation in courtship behavior, which can contribute to speciation by prezygotic isolation of closely related species. Here, we analyze the genetic basis and architecture of species differences in the male courtship behavior of two closely related parasitoid wasps Nasonia vitripennis and N. longicornis. Both species occur microsympatrically in parts of their ranges and have been found in the same host pupae. Despite strong postzygotic isolation mechanisms between these two Nasonia species, viable hybrid females can be produced in the laboratory if both species are cured of their Wolbachia endosymbionts. We used haploid F2 hybrid males derived from virgin F1 hybrid females of two independent mapping populations to study the genetic architecture of five quantitative and two qualitative components of their courtship behavior. A total of 14 independent Quantitative Trait Loci (QTL) were found in the first mapping population (320 males), which explained 4-25% of the observed phenotypic variance. Ten of these QTL were confirmed by a second independent mapping population (112 males) and no additional ones were found. A genome-wide scan for two-loci interactions revealed many unique but mostly additive interactions explaining an additional proportion of the observed phenotypic variance. Courtship QTL were found on all five chromosomes and four loci were associated with more than one QTL, indicating either possible pleiotropic effects of individual QTL or individual loci contributing to multiple courtship components. Our results indicate that these two evolutionary young species have rapidly evolved multiple significant phenotypic differences in their courtship behavior that have a polygenic and highly interactive genetic architecture. Based on the location of the QTL and the published Nasonia genome sequence we were able to identify a series of candidate genes for further study.

scholarly journals Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci

mSystems ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Irina M. Velsko ◽  
Brinta Chakraborty ◽  
Marcelle M. Nascimento ◽  
Robert A. Burne ◽  
Vincent P. Richards
Keyword(s):  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Bacterial Species ◽  
Arginine Deiminase ◽  
Poor Correlation ◽  
Oral Streptococci ◽  
Single Strain ◽  
Content Type ◽  
A Genome ◽  
Probiotic Strains

ABSTRACTHealth-associated oralStreptococcusspecies are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oralStreptococcusisolates and examined the genetic basis of variability in ADS and antagonistic activities. A total of 113 isolates were included and represented 10 species:Streptococcus australis, A12-like,S. cristatus,S. gordonii,S. intermedius,S. mitis,S. oralisincludingS. oralissubsp.dentisani,S. parasanguinis,S. salivarius, andS. sanguinis. Mean ADS activity and antagonism onStreptococcus mutansUA159 were measured for each isolate, and each isolate was whole genome shotgun sequenced on an Illumina MiSeq. Phylogenies were built of genes known to be involved in ADS activity and antagonism. Several approaches to correlate the pan-genome with phenotypes were performed. Phylogenies of genes previously identified in ADS activity and antagonism grouped isolates by species, but not by phenotype. A genome-wide association study (GWAS) identified additional genes potentially involved in ADS activity or antagonism across all the isolates we sequenced as well as within several species. Phenotypic heterogeneity in oral streptococci is not necessarily reflected by genotype and is not species specific. Probiotic strains must be carefully selected based on characterization of each strain and not based on inclusion within a certain species.IMPORTANCERepresentative type strains are commonly used to characterize bacterial species, yet species are phenotypically and genotypically heterogeneous. Conclusions about strain physiology and activity based on a single strain therefore may be inappropriate and misleading. When selecting strains for probiotic use, the assumption that all strains within a species share the same desired probiotic characteristics may result in selection of a strain that lacks the desired traits, and therefore makes a minimally effective or ineffective probiotic. Health-associated oral streptococci are promising candidates for anticaries probiotics, but strains need to be carefully selected based on observed phenotypes. We characterized the genotypes and anticaries phenotypes of strains from 10 species of oral streptococci and demonstrate poor correlation between genotype and phenotype across all species.

scholarly journals The Genetic Basis of Laboratory Adaptation in Caulobacter crescentus

2010 ◽  
Vol 192 (14) ◽  
pp. 3678-3688 ◽  
Author(s):  
Melissa E. Marks ◽  
Cyd Marie Castro-Rojas ◽  
Clotilde Teiling ◽  
Lei Du ◽  
Vinayak Kapatral ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Caulobacter Crescentus ◽  
Polymorphic Locus ◽  
Molecular Genetic ◽  
Growth And Survival ◽  
Phenotypic Differences ◽  
History Of ◽  
Genetic Mechanisms ◽  
Stationary Phase Survival ◽  
History Of Culture

ABSTRACT The dimorphic bacterium Caulobacter crescentus has evolved marked phenotypic changes during its 50-year history of culture in the laboratory environment, providing an excellent system for the study of natural selection and phenotypic microevolution in prokaryotes. Combining whole-genome sequencing with classical molecular genetic tools, we have comprehensively mapped a set of polymorphisms underlying multiple derived phenotypes, several of which arose independently in separate strain lineages. The genetic basis of phenotypic differences in growth rate, mucoidy, adhesion, sedimentation, phage susceptibility, and stationary-phase survival between C. crescentus strain CB15 and its derivative NA1000 is determined by coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. This study evidences multiple genetic mechanisms of bacterial evolution as driven by selection for growth and survival in a new selective environment and identifies a common polymorphic locus, zwf, between lab-adapted C. crescentus and clinical isolates of Pseudomonas aeruginosa that have adapted to a human host during chronic infection.

scholarly journals Comparative Analysis of Two Emerging Rice Seed Bacterial Pathogens

2014 ◽  
Vol 104 (5) ◽  
pp. 436-444 ◽  
Author(s):  
P. A. Fory ◽  
L. Triplett ◽  
C. Ballen ◽  
J. F. Abello ◽  
J. Duitama ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Central American ◽  
Yield Reduction ◽  
Genotypic Differences ◽  
Rice Seed ◽  
Secretion Systems ◽  
Burkholderia Glumae ◽  
Phenotypic Differences ◽  
Genes Encoding ◽  
Inoculation Assay

Seed sterility and grain discoloration limit rice production in Colombia and several Central American countries. In samples of discolored rice seed grown in Colombian fields, the species Burkholderia glumae and B. gladioli were isolated, and field isolates were compared phenotypically. An artificial inoculation assay was used to determine that, although both bacterial species cause symptoms on rice grains, B. glumae is a more aggressive pathogen, causing yield reduction and higher levels of grain sterility. To identify putative virulence genes differing between B. glumae and B. gladioli, four previously sequenced genomes of Asian and U.S. strains of the two pathogens were compared with each other and with two draft genomes of Colombian B. glumae and B. gladioli isolates generated for this study. Whereas previously characterized Burkholderia virulence factors are highly conserved between the two species, B. glumae and B. gladioli strains are predicted to encode distinct groups of genes encoding type VI secretion systems, transcriptional regulators, and membrane-sensing proteins. This study shows that both B. glumae and B. gladioli can threaten grain quality, although only one species affects yield. Furthermore, genotypic differences between the two strains are identified that could contribute to disease phenotypic differences.

scholarly journals Craniofacial shape transition across the house mouse hybrid zone: implications for the genetic architecture and evolution of between-species differences

2016 ◽  
Author(s):  
Luisa F. Pallares ◽  
Leslie M. Turner ◽  
Diethard Tautz
Keyword(s):  
House Mouse ◽  
Hybrid Zone ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Species Differences ◽  
Food Sources ◽  
Species Variation ◽  
Shape Transition ◽  
Phenotypic Differences ◽  
Quantitative Changes

AbstractCraniofacial shape differences between taxa have often being linked to environmental adaptation, e.g. to new food sources, or have been studied in the context of domestication. Evidence for the genetic basis of such phenotypic differences to date suggests that within- as well as between-species variation has an oligogenic basis, i.e. few loci of large effect explain most of the variation. In mice, it has been shown that within-population craniofacial variation has a highly polygenic basis, but there are no data regarding the genetic basis of between-species differences. Here, we address this question using a phenotype-focused approach. Using 3D geometric morphometrics, we phenotyped a panel of mice derived from a natural hybrid zone between M. m. domesticus and M. m. musculus, and quantify the transition of craniofacial shape along the hybridization gradient. We find a continuous shape transition along the hybridization gradient, and unaltered developmental stability associated with hybridization. This suggests that the morphospace between the two subspecies is continuous despite reproductive isolation and strong barriers to gene flow. We show that quantitative changes in genome composition generate quantitative changes in craniofacial shape; this supports a highly polygenic basis for between-species craniofacial differences in the house mouse. We discuss our findings in the context of oligogenic versus polygenic models of the genetic architecture of morphological traits.

scholarly journals Shallow evolutionary divergence between two Andean hummingbirds: Speciation with gene flow?

2018 ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M. Cuervo ◽  
F. Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Basis ◽  
Flow Model ◽  
Evolutionary Divergence ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Divergence With Gene Flow ◽  
Neutral Markers

AbstractEcological speciation can proceed despite genetic interchange when selection counteracts homogeneizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, two parapatric Andean hummigbirds with marked plumage divergence. We sequenced neutral markers (mtDNA and nuclear ultra conserved elements) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Glogers’ rule that darker forms occur in more humid environments, and compared ecomorphological variables to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was very low and coalescent estimates of migration were consistent with divergence with gene flow. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in ecomorphology. Although we reject adaptation to variation in humidity as the cause of divergence, we hypothesize that speciation likely occurred in the face of gene flow, driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

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