Genetic diversity and structure of a recent fish invasion: Tench ( Tinca tinca) in eastern North America

Thaïs A. Bernos, Sunčica Avlijaš, Jaclyn Hill, Olivier Morissette, Anthony Ricciardi, Nicholas E. Mandrak, Kenneth M. Jeffries

Evol Appl 2022 Dec 20;16(1):173-188. doi: 10.1111/eva.13520

PMID: 36699124

Abstract

Introduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such phenomena limits the success of introduced populations. Using 1900 SNPs obtained from restriction-site-associated DNA sequencing, we evaluated hypotheses related to the invasion history and connectivity of an invasive population of Tench (Tinca tinca), a Eurasian freshwater fish that has been expanding geographically in eastern North America for three decades. Consistent with the reported history of a single introduction event, our findings suggest that multiple introductions from distinct genetic sources are unlikely as Tench had a small effective population size (~114 [95% CI = 106-123] individuals), no strong population subdivision across time and space, and evidence of a recent genetic bottleneck. The large genetic neighbourhood size (220 km) and weak within-population genetic substructure suggested high connectivity across the invaded range, despite the relatively large area occupied. There was some evidence for a small decay in genetic diversity as the species expanded northward, but not southward, into new habitats. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed-and possibly local-scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study indicates that introduced populations can thrive and exhibit relatively high levels of genetic diversity despite severe bottlenecks (<1.5% of the ancestral effective population size) and suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.

Epidemiology of Clonal Pseudomonas aeruginosa Infection in a Canadian Cystic Fibrosis Population

Middleton MA, Layeghifard M, Klingel M, Stanojevic S, Yau YCW, Zlosnik JEA, Coriati A, Ratjen FA, Tullis ED, Stephenson A, Wilcox P, Freitag A, Chilvers M, McKinney M, Lavoie A, Wang PW, Guttman DS, Waters VJ

Ann Am Thorac Soc 2018 Jun;

PMID: 29911888

Abstract

RATIONALE: The extent of the genetic relatedness among Pseudomonas aeruginosa isolates and its impact on clinical outcomes in the cystic fibrosis (CF) population is poorly understood.

OBJECTIVES: The objectives of this study were to determine the prevalence of clonal P. aeruginosa infection in Canada and to associate P. aeruginosa genotypes with clinical outcomes.

METHODS: This was an observational study of adult and pediatric CF patients across Canada. Isolates were typed using multi-locus sequence typing (MLST). A clone was defined as sharing >6 of 7 alleles. Genotyping results were associated with clinical outcomes including forced expiratory volume in 1 second (FEV1), body mass index (BMI), rate of pulmonary exacerbation, and death/transplant.

RESULTS: 1,537 P. aeruginosa isolates were genotyped to 403 unique sequence types (STs) in 402 individuals with CF. Although 39% of STs were shared, most were shared only among a small number of subjects and the majority (79%) of the genetic diversity in P. aeruginosa isolates was observed between patients. There were no significant differences in clinical outcomes according to genotype. However, patients with a dynamic, changing ST infection pattern had both a steeper decline in FEV1 (-2.9% predicted change/yr, 95% CI -3.8, -1.9 compared to 0.4, 95% CI -0.3, 1.0) (p<0.001) and BMI (-1.0 percentile change/yr, 95% CI -1.6, -0.3 compared to -0.1, 95% CI -0.7, 0.5) (p=0.047) than those with a stable infection with the same ST.

CONCLUSIONS: There was no widespread sharing of dominant clones in our CF population, and the majority of the genetic diversity in P. aeruginosa was observed between patients. Changing genotypes over time within an individual was associated with worse clinical outcomes.

Diversification of Pseudomonas aeruginosa within the CF lung

Clark ST, Guttman DS, Hwang DM

FEMS Microbiol. Lett. 2018 Feb;

PMID: 29401362

Abstract

The evolution and diversification of bacterial pathogens within human hosts represent potential barriers to the diagnosis and treatment of life-threatening infections. Tremendous genetic and phenotypic diversity is characteristic of host adaptation in strains of Pseudomonas aeruginosa that infect the airways of individuals with chronic lung diseases and prove to be extremely difficult to eradicate. In this MiniReview, we examine recent advances in understanding within-host diversity and antimicrobial resistance in P. aeruginosa populations from the lower airways of individuals with the fatal genetic disease cystic fibrosis and the potential impacts that this diversity may have on detecting and interpreting antimicrobial susceptibility within these populations.

An extracellular network of Arabidopsis leucine-rich repeat receptor kinases

Smakowska-Luzan E, Mott GA, Parys K, Stegmann M, Howton TC, Layeghifard M, Neuhold J, Lehner A, Kong J, Grünwald K, Weinberger N, Satbhai SB, Mayer D, Busch W, Madalinski M, Stolt-Bergner P, Provart NJ, Mukhtar MS, Zipfel C, Desveaux D, Guttman DS, Belkhadir Y

Nature 2018 01;553(7688):342-346

PMID: 29320478

Abstract

The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs), which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance. Although the principles that govern LRR-RK signalling activation are emerging, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay, and produced an LRR-based cell surface interaction network (CSI) that consists of 567 interactions. To demonstrate the power of CSI for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSI operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.

Association of host genome with intestinal microbial composition

Turpin W, Espin-Garcia O, Xu W, Silverberg MS, Kevans D, Smith MI, Guttman DS, Griffiths A, Panaccione R, Otley A, Xu L, Shestopaloff K, Moreno-Hagelsieb G; GEM Project Research Consortium, Paterson AD, Croitoru K.

Nat Genet. 2016 Nov;48(11):1413-1417.

PMID: 27694960

Abstract

Intestinal microbiota is known to be important in health and disease. Its composition is influenced by both environmental and host factors. Few large-scale studies have evaluated the association between host genetic variation and the composition of microbiota. We recruited a cohort of 1,561 healthy individuals, of whom 270 belong in 123 families, and found that almost one-third of fecal bacterial taxa were heritable. In addition, we identified 58 SNPs associated with the relative abundance of 33 taxa in 1,098 discovery subjects. Among these, four loci were replicated in a second cohort of 463 subjects: rs62171178 (nearest gene UBR3) associated with Rikenellaceae, rs1394174 (CNTN6) associated with Faecalibacterium, rs59846192 (DMRTB1) associated with Lachnospira, and rs28473221 (SALL3) associated with Eubacterium. After correction for multiple testing, 6 of the 58 associations remained significant, one of which replicated. These results identify associations between specific genetic variants and the gut microbiome.

Multiple Calmodulin-Binding Sites Regulate Arabidopsis CNGC12

DeFalco TA, Marshall CB, Munro K, Kang HG, Moeder W, Ikura M, Snedden WA, Yoshioka K

Plant Cell 2016 Jul;28(7):1738-51

PMID: 27335451

Abstract

Ca(2+) signaling is critical to plant immunity; however, the channels involved are poorly characterized. Cyclic nucleotide-gated channels (CNGCs) are nonspecific, Ca(2+)-permeable cation channels. Plant CNGCs are hypothesized to be negatively regulated by the Ca(2+) sensor calmodulin (CaM), and previous work has focused on a C-terminal CaM-binding domain (CaMBD) overlapping with the cyclic nucleotide binding domain of plant CNGCs. However, we show that the Arabidopsis thaliana isoform CNGC12 possesses multiple CaMBDs at cytosolic N and C termini, which is reminiscent of animal CNGCs and unlike any plant channel studied to date. Biophysical characterizations of these sites suggest that apoCaM interacts with a conserved isoleucine-glutamine (IQ) motif in the C terminus of the channel, while Ca(2+)/CaM binds additional N- and C-terminal motifs with different affinities. Expression of CNGC12 with a nonfunctional N-terminal CaMBD constitutively induced programmed cell death, providing in planta evidence of allosteric CNGC regulation by CaM. Furthermore, we determined that CaM binding to the IQ motif was required for channel function, indicating that CaM can both positively and negatively regulate CNGC12. These data indicate a complex mode of plant CNGC regulation by CaM, in contrast to the previously proposed competitive ligand model, and suggest exciting parallels between plant and animal channels.

Impacts on gut microbiota during the first year of life

Azad MB, Konya T, Persaud RR, Guttman DS, Chari RS, Field CJ, Sears MR, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA, Kozyrskyj AL,

BJOG 2016 May;123(6):983-993

PMID: 26412384

Abstract

OBJECTIVE: Dysbiosis of the infant gut microbiota may have long-term health consequences. This study aimed to determine the impact of maternal intrapartum antibiotic prophylaxis (IAP) on infant gut microbiota, and to explore whether breastfeeding modifies these effects.

DESIGN: Prospective pregnancy cohort of Canadian infants born in 2010-2012: the Canadian Healthy Infant Longitudinal Development (CHILD) Study.

SETTING: General community.

SAMPLE: Representative sub-sample of 198 healthy term infants from the CHILD Study.

METHODS: Maternal IAP exposures and birth method were documented from hospital records and breastfeeding was reported by mothers. Infant gut microbiota was characterised by Illumina 16S rRNA sequencing of faecal samples at 3 and 12 months.

MAIN OUTCOME MEASURES: Infant gut microbiota profiles.

RESULTS: In this cohort, 21% of mothers received IAP for Group B Streptococcus prophylaxis or pre-labour rupture of membranes; another 23% received IAP for elective or emergency caesarean section (CS). Infant gut microbiota community structures at 3 months differed significantly with all IAP exposures, and differences persisted to 12 months for infants delivered by emergency CS. Taxon-specific composition also differed, with the genera Bacteroides and Parabacteroides under-represented, and Enterococcus and Clostridium over-represented at 3 months following maternal IAP. Microbiota differences were especially evident following IAP with emergency CS, with some changes (increased Clostridiales and decreased Bacteroidaceae) persisting to 12 months, particularly among non-breastfed infants.

CONCLUSIONS: Intrapartum antibiotics in caesarean and vaginal delivery are associated with infant gut microbiota dysbiosis, and breastfeeding modifies some of these effects. Further research is warranted to explore the health consequences of these associations.

TWEETABLE ABSTRACT: Maternal #antibiotics during childbirth alter the infant gut #microbiome.